Starting phenix.real_space_refine on Fri Mar 14 02:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx3_38744/03_2025/8xx3_38744.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx3_38744/03_2025/8xx3_38744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx3_38744/03_2025/8xx3_38744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx3_38744/03_2025/8xx3_38744.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx3_38744/03_2025/8xx3_38744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx3_38744/03_2025/8xx3_38744.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 66 5.16 5 C 6014 2.51 5 N 1638 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9488 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 336 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 452 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2207 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 5.49, per 1000 atoms: 0.58 Number of scatterers: 9488 At special positions: 0 Unit cell: (88.1875, 121.388, 152.512, 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 66 16.00 O 1770 8.00 N 1638 7.00 C 6014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.26 Conformation dependent library (CDL) restraints added in 1.2 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 35.7% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 56 through 69 removed outlier: 3.915A pdb=" N GLN E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.005A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 116 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.735A pdb=" N GLN R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.583A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.560A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.788A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 304 through 315 removed outlier: 4.389A pdb=" N CYS R 308 " --> pdb=" O ILE R 304 " (cutoff:3.500A) Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 removed outlier: 3.596A pdb=" N ARG R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.787A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.113A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.706A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.609A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.014A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.809A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.137A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.401A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.963A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.600A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.567A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.721A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.511A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1323 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: 2.52 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3070 1.34 - 1.46: 2062 1.46 - 1.58: 4451 1.58 - 1.70: 0 1.70 - 1.83: 91 Bond restraints: 9674 Sorted by residual: bond pdb=" N GLY E 17 " pdb=" CA GLY E 17 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N GLN D 60 " pdb=" CA GLN D 60 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.59e+00 bond pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.66e+00 bond pdb=" CA ALA R 273 " pdb=" CB ALA R 273 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.69e-02 3.50e+03 3.95e+00 bond pdb=" N THR R 279 " pdb=" CA THR R 279 " ideal model delta sigma weight residual 1.455 1.480 -0.024 1.25e-02 6.40e+03 3.82e+00 ... (remaining 9669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 12934 1.69 - 3.38: 167 3.38 - 5.07: 36 5.07 - 6.76: 2 6.76 - 8.45: 3 Bond angle restraints: 13142 Sorted by residual: angle pdb=" N VAL D 59 " pdb=" CA VAL D 59 " pdb=" C VAL D 59 " ideal model delta sigma weight residual 110.23 103.06 7.17 1.04e+00 9.25e-01 4.75e+01 angle pdb=" N LYS D 65 " pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 112.23 103.78 8.45 1.26e+00 6.30e-01 4.50e+01 angle pdb=" N LEU R 272 " pdb=" CA LEU R 272 " pdb=" C LEU R 272 " ideal model delta sigma weight residual 111.03 105.46 5.57 1.11e+00 8.12e-01 2.52e+01 angle pdb=" C THR B 87 " pdb=" N ASN B 88 " pdb=" CA ASN B 88 " ideal model delta sigma weight residual 122.67 115.36 7.31 1.73e+00 3.34e-01 1.79e+01 angle pdb=" N THR R 279 " pdb=" CA THR R 279 " pdb=" C THR R 279 " ideal model delta sigma weight residual 112.93 108.20 4.73 1.12e+00 7.97e-01 1.78e+01 ... (remaining 13137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5270 17.31 - 34.62: 425 34.62 - 51.92: 57 51.92 - 69.23: 10 69.23 - 86.54: 5 Dihedral angle restraints: 5767 sinusoidal: 2132 harmonic: 3635 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS R 39 " pdb=" SG CYS R 39 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 62.55 30.45 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1357 0.063 - 0.126: 163 0.126 - 0.188: 8 0.188 - 0.251: 1 0.251 - 0.314: 3 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ILE D 66 " pdb=" N ILE D 66 " pdb=" C ILE D 66 " pdb=" CB ILE D 66 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA VAL D 59 " pdb=" N VAL D 59 " pdb=" C VAL D 59 " pdb=" CB VAL D 59 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1529 not shown) Planarity restraints: 1675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO G 55 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 236 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 310 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO R 311 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 311 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 311 " 0.019 5.00e-02 4.00e+02 ... (remaining 1672 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1496 2.76 - 3.30: 8999 3.30 - 3.83: 15238 3.83 - 4.37: 17651 4.37 - 4.90: 31675 Nonbonded interactions: 75059 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.258 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.262 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" O PRO A 294 " model vdw 2.316 3.040 ... (remaining 75054 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: 0.600 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.003 0.044 9674 Z= 0.182 Angle : 0.530 8.448 13142 Z= 0.331 Chirality : 0.044 0.314 1532 Planarity : 0.003 0.040 1675 Dihedral : 12.555 86.538 3396 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1237 helix: 1.88 (0.27), residues: 405 sheet: 0.04 (0.28), residues: 341 loop : -0.38 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS R 242 PHE 0.014 0.001 PHE B 234 TYR 0.016 0.001 TYR S 178 ARG 0.004 0.000 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 27 ASN cc_start: 0.7650 (t0) cc_final: 0.6811 (p0) REVERT: D 56 SER cc_start: 0.8160 (t) cc_final: 0.7892 (p) REVERT: R 41 PRO cc_start: 0.7351 (Cg_endo) cc_final: 0.6927 (Cg_exo) REVERT: R 89 ASN cc_start: 0.8547 (m-40) cc_final: 0.8149 (m110) REVERT: R 145 TYR cc_start: 0.8507 (t80) cc_final: 0.8178 (t80) REVERT: R 203 ASN cc_start: 0.6818 (t0) cc_final: 0.6309 (m-40) REVERT: A 231 TYR cc_start: 0.7313 (m-10) cc_final: 0.6926 (m-80) REVERT: A 298 GLU cc_start: 0.8210 (mp0) cc_final: 0.7864 (pp20) REVERT: A 334 VAL cc_start: 0.8950 (t) cc_final: 0.8614 (t) REVERT: B 211 TRP cc_start: 0.6826 (m-10) cc_final: 0.6496 (m-10) REVERT: B 325 MET cc_start: 0.7604 (tpp) cc_final: 0.7188 (tpp) REVERT: G 19 LEU cc_start: 0.9284 (mt) cc_final: 0.9079 (mt) REVERT: G 30 VAL cc_start: 0.8792 (m) cc_final: 0.8587 (p) REVERT: S 151 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7939 (mttp) REVERT: S 208 GLU cc_start: 0.8363 (tt0) cc_final: 0.6760 (pt0) REVERT: S 211 ASP cc_start: 0.5966 (m-30) cc_final: 0.5700 (m-30) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.2605 time to fit residues: 113.9243 Evaluate side-chains 187 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN D 34 HIS R 89 ASN R 319 GLN A 256 ASN B 6 GLN B 35 ASN B 75 GLN B 88 ASN B 156 GLN B 176 GLN B 220 GLN G 18 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.110569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086436 restraints weight = 22614.505| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.28 r_work: 0.3157 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 9674 Z= 0.281 Angle : 0.639 14.093 13142 Z= 0.340 Chirality : 0.044 0.217 1532 Planarity : 0.004 0.038 1675 Dihedral : 4.068 28.805 1345 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.71 % Allowed : 11.42 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.90 (0.24), residues: 1237 helix: 2.19 (0.26), residues: 417 sheet: -0.00 (0.27), residues: 345 loop : -0.29 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 207 HIS 0.005 0.001 HIS B 142 PHE 0.013 0.002 PHE S 165 TYR 0.025 0.002 TYR S 178 ARG 0.004 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.7996 (t) cc_final: 0.7621 (p) REVERT: R 245 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7647 (mp10) REVERT: A 21 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8508 (mttm) REVERT: A 243 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8508 (ttm-80) REVERT: S 82 GLN cc_start: 0.8241 (tp40) cc_final: 0.8032 (tp40) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 0.2644 time to fit residues: 71.9724 Evaluate side-chains 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS R 150 HIS ** R 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN S 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.106967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082501 restraints weight = 22489.771| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.23 r_work: 0.3053 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9674 Z= 0.378 Angle : 0.678 15.392 13142 Z= 0.361 Chirality : 0.046 0.236 1532 Planarity : 0.004 0.044 1675 Dihedral : 4.476 31.298 1345 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.41 % Allowed : 14.43 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.64 (0.24), residues: 1237 helix: 2.12 (0.25), residues: 410 sheet: -0.14 (0.27), residues: 344 loop : -0.57 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.005 0.001 HIS B 142 PHE 0.017 0.002 PHE S 165 TYR 0.027 0.002 TYR S 178 ARG 0.005 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8083 (t) cc_final: 0.7619 (p) REVERT: R 145 TYR cc_start: 0.8738 (t80) cc_final: 0.8464 (t80) REVERT: R 198 GLU cc_start: 0.8633 (mp0) cc_final: 0.8375 (mm-30) REVERT: A 21 LYS cc_start: 0.9043 (tmtt) cc_final: 0.8450 (mttm) REVERT: B 215 GLU cc_start: 0.8871 (mp0) cc_final: 0.8544 (mp0) REVERT: B 258 ASP cc_start: 0.7734 (t0) cc_final: 0.7219 (t0) REVERT: G 13 ARG cc_start: 0.8728 (mtt-85) cc_final: 0.8485 (mtt-85) REVERT: S 89 GLU cc_start: 0.8109 (pp20) cc_final: 0.7786 (pp20) outliers start: 34 outliers final: 25 residues processed: 199 average time/residue: 0.3010 time to fit residues: 80.5687 Evaluate side-chains 186 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS R 89 ASN ** R 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN ** G 18 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 = 0.3707 r_free = 0.3707 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081800 restraints weight = 22492.914| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.81 r_work: 0.3112 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9674 Z= 0.241 Angle : 0.614 16.681 13142 Z= 0.326 Chirality : 0.044 0.210 1532 Planarity : 0.004 0.037 1675 Dihedral : 4.258 27.532 1345 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.81 % Allowed : 16.53 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.64 (0.24), residues: 1237 helix: 2.20 (0.25), residues: 411 sheet: -0.09 (0.27), residues: 344 loop : -0.70 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 59 TYR 0.021 0.001 TYR S 178 ARG 0.005 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8313 (t) cc_final: 0.7947 (p) REVERT: R 145 TYR cc_start: 0.8708 (t80) cc_final: 0.8394 (t80) REVERT: A 21 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8465 (mttm) REVERT: A 318 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: B 258 ASP cc_start: 0.7737 (t0) cc_final: 0.7277 (t0) outliers start: 28 outliers final: 18 residues processed: 201 average time/residue: 0.2339 time to fit residues: 63.3686 Evaluate side-chains 181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 34 HIS G 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.105857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079468 restraints weight = 22327.001| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.80 r_work: 0.3066 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9674 Z= 0.388 Angle : 0.704 18.059 13142 Z= 0.371 Chirality : 0.046 0.228 1532 Planarity : 0.004 0.039 1675 Dihedral : 4.559 24.103 1345 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.81 % Allowed : 17.54 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.46 (0.24), residues: 1237 helix: 2.05 (0.25), residues: 412 sheet: -0.14 (0.27), residues: 344 loop : -0.85 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.005 0.001 HIS B 311 PHE 0.012 0.002 PHE S 165 TYR 0.026 0.002 TYR B 105 ARG 0.006 0.001 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8375 (t) cc_final: 0.8019 (p) REVERT: R 145 TYR cc_start: 0.8789 (t80) cc_final: 0.8520 (t80) REVERT: A 55 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6717 (mt) REVERT: A 318 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: B 258 ASP cc_start: 0.7887 (t0) cc_final: 0.7679 (t0) REVERT: B 322 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: S 91 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8803 (p) outliers start: 38 outliers final: 22 residues processed: 189 average time/residue: 0.2400 time to fit residues: 61.5268 Evaluate side-chains 184 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN D 34 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084010 restraints weight = 22294.079| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.87 r_work: 0.3135 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9674 Z= 0.172 Angle : 0.624 18.379 13142 Z= 0.327 Chirality : 0.044 0.222 1532 Planarity : 0.003 0.037 1675 Dihedral : 4.175 21.161 1345 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.61 % Allowed : 18.94 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.66 (0.24), residues: 1237 helix: 2.26 (0.26), residues: 411 sheet: -0.03 (0.27), residues: 331 loop : -0.76 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.003 0.000 HIS S 35 PHE 0.010 0.001 PHE R 59 TYR 0.017 0.001 TYR S 178 ARG 0.004 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8345 (t) cc_final: 0.7990 (p) REVERT: R 145 TYR cc_start: 0.8702 (t80) cc_final: 0.8330 (t80) REVERT: A 318 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: B 10 GLU cc_start: 0.9015 (pm20) cc_final: 0.8732 (pm20) REVERT: B 12 GLU cc_start: 0.8763 (mp0) cc_final: 0.8538 (mp0) REVERT: B 215 GLU cc_start: 0.8666 (mp0) cc_final: 0.8359 (mp0) REVERT: G 21 MET cc_start: 0.8253 (tpp) cc_final: 0.7936 (tpp) outliers start: 26 outliers final: 17 residues processed: 187 average time/residue: 0.2653 time to fit residues: 67.8196 Evaluate side-chains 179 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 0.0370 chunk 114 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082360 restraints weight = 22547.595| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.85 r_work: 0.3110 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9674 Z= 0.219 Angle : 0.629 12.602 13142 Z= 0.328 Chirality : 0.044 0.335 1532 Planarity : 0.003 0.036 1675 Dihedral : 4.181 18.279 1345 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.91 % Allowed : 19.44 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.62 (0.24), residues: 1237 helix: 2.16 (0.25), residues: 412 sheet: 0.02 (0.27), residues: 329 loop : -0.77 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.009 0.001 PHE R 59 TYR 0.021 0.001 TYR S 178 ARG 0.006 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 SER cc_start: 0.8396 (t) cc_final: 0.8058 (p) REVERT: R 113 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8516 (pt) REVERT: R 145 TYR cc_start: 0.8735 (t80) cc_final: 0.8342 (t80) REVERT: A 318 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: G 21 MET cc_start: 0.8203 (tpp) cc_final: 0.7918 (tpp) outliers start: 29 outliers final: 20 residues processed: 184 average time/residue: 0.2336 time to fit residues: 58.0219 Evaluate side-chains 174 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2299 > 50: distance: 10 - 11: 10.088 distance: 11 - 12: 6.710 distance: 11 - 14: 6.139 distance: 12 - 13: 5.455 distance: 12 - 17: 3.187 distance: 14 - 15: 3.558 distance: 14 - 16: 12.239 distance: 17 - 18: 6.510 distance: 18 - 19: 6.079 distance: 18 - 21: 6.584 distance: 19 - 20: 7.543 distance: 19 - 23: 4.002 distance: 21 - 22: 5.961 distance: 23 - 24: 8.887 distance: 24 - 27: 15.813 distance: 25 - 26: 9.706 distance: 25 - 29: 7.724 distance: 27 - 28: 9.893 distance: 29 - 30: 10.469 distance: 30 - 31: 19.717 distance: 30 - 33: 13.995 distance: 31 - 32: 12.622 distance: 31 - 36: 8.450 distance: 33 - 34: 4.020 distance: 33 - 35: 28.076 distance: 36 - 37: 5.673 distance: 36 - 42: 15.247 distance: 37 - 38: 12.114 distance: 37 - 40: 8.274 distance: 38 - 39: 30.583 distance: 38 - 43: 4.046 distance: 40 - 41: 17.990 distance: 41 - 42: 8.387 distance: 43 - 44: 7.470 distance: 44 - 45: 7.545 distance: 44 - 47: 7.528 distance: 45 - 46: 27.414 distance: 45 - 50: 29.393 distance: 47 - 48: 11.014 distance: 47 - 49: 15.857 distance: 50 - 51: 6.835 distance: 51 - 52: 15.423 distance: 51 - 54: 13.408 distance: 52 - 53: 8.995 distance: 52 - 57: 5.324 distance: 54 - 55: 34.269 distance: 54 - 56: 18.258 distance: 57 - 58: 12.327 distance: 57 - 63: 7.352 distance: 58 - 59: 6.423 distance: 58 - 61: 6.032 distance: 59 - 60: 21.393 distance: 59 - 64: 14.660 distance: 61 - 62: 10.168 distance: 62 - 63: 4.890 distance: 64 - 65: 12.851 distance: 65 - 66: 11.394 distance: 66 - 67: 3.550 distance: 66 - 68: 10.779 distance: 68 - 69: 4.180 distance: 69 - 70: 18.311 distance: 69 - 72: 8.681 distance: 70 - 71: 12.625 distance: 70 - 77: 19.427 distance: 72 - 73: 11.625 distance: 73 - 74: 4.082 distance: 74 - 75: 10.662 distance: 74 - 76: 8.301