Starting phenix.real_space_refine on Fri Aug 22 18:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmd_60243/08_2025/8zmd_60243.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmd_60243/08_2025/8zmd_60243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zmd_60243/08_2025/8zmd_60243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmd_60243/08_2025/8zmd_60243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zmd_60243/08_2025/8zmd_60243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmd_60243/08_2025/8zmd_60243.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.021 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 46 5.16 5 C 4498 2.51 5 N 1179 2.21 5 O 1289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7012 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1804 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2486 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 82 Chain: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 321 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2401 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 1.90, per 1000 atoms: 0.27 Number of scatterers: 7012 At special positions: 0 Unit cell: (90.2, 101.2, 134.2, 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 46 16.00 O 1289 8.00 N 1179 7.00 C 4498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 226 " 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: 0.60 Conformation dependent library (CDL) restraints added in 400.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 44.9% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.519A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.560A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.618A pdb=" N LEU A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.759A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.577A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.507A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.869A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.917A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.739A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.616A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 76 through 102 removed outlier: 3.902A pdb=" N ILE R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 81 " --> pdb=" O PHE R 77 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 108 through 125 removed outlier: 3.720A pdb=" N ASN R 116 " --> pdb=" O ILE R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 137 removed outlier: 3.852A pdb=" N LYS R 131 " --> pdb=" O TRP R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 178 removed outlier: 3.810A pdb=" N ASN R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 203 Processing helix chain 'R' and resid 204 through 205 No H-bonds generated for 'chain 'R' and resid 204 through 205' Processing helix chain 'R' and resid 206 through 210 removed outlier: 3.538A pdb=" N LEU R 209 " --> pdb=" O THR R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 236 Processing helix chain 'R' and resid 237 through 250 removed outlier: 3.558A pdb=" N ASN R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 270 Processing helix chain 'R' and resid 278 through 317 removed outlier: 3.909A pdb=" N ARG R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 322 through 334 removed outlier: 3.570A pdb=" N TYR R 326 " --> pdb=" O VAL R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 340 Processing helix chain 'R' and resid 341 through 343 No H-bonds generated for 'chain 'R' and resid 341 through 343' Processing helix chain 'R' and resid 349 through 359 removed outlier: 3.592A pdb=" N ASP R 353 " --> pdb=" O HIS R 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.528A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.044A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.272A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.003A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.161A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.983A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.796A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 38 through 40 removed outlier: 6.050A pdb=" N LEU R 38 " --> pdb=" O LEU R 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'R' and resid 215 through 218 358 hydrogen bonds defined for protein. 1032 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: 1.05 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1279 1.32 - 1.45: 2016 1.45 - 1.58: 3800 1.58 - 1.71: 0 1.71 - 1.84: 66 Bond restraints: 7161 Sorted by residual: bond pdb=" C ILE B 58 " pdb=" O ILE B 58 " ideal model delta sigma weight residual 1.238 1.199 0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" C ALA B 60 " pdb=" O ALA B 60 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" CA ALA B 60 " pdb=" CB ALA B 60 " ideal model delta sigma weight residual 1.532 1.490 0.043 1.68e-02 3.54e+03 6.45e+00 bond pdb=" C TYR B 59 " pdb=" O TYR B 59 " ideal model delta sigma weight residual 1.235 1.204 0.032 1.31e-02 5.83e+03 5.85e+00 bond pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.16e-02 7.43e+03 3.50e+00 ... (remaining 7156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 9458 2.05 - 4.10: 262 4.10 - 6.15: 33 6.15 - 8.21: 5 8.21 - 10.26: 2 Bond angle restraints: 9760 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.06 116.99 -6.93 1.43e+00 4.89e-01 2.35e+01 angle pdb=" C GLN A 59 " pdb=" N MET A 60 " pdb=" CA MET A 60 " ideal model delta sigma weight residual 122.66 115.00 7.66 1.63e+00 3.76e-01 2.21e+01 angle pdb=" CA ALA B 60 " pdb=" C ALA B 60 " pdb=" O ALA B 60 " ideal model delta sigma weight residual 121.38 116.58 4.80 1.06e+00 8.90e-01 2.05e+01 angle pdb=" CA TYR B 59 " pdb=" C TYR B 59 " pdb=" O TYR B 59 " ideal model delta sigma weight residual 119.41 114.40 5.01 1.13e+00 7.83e-01 1.96e+01 angle pdb=" N VAL R 125 " pdb=" CA VAL R 125 " pdb=" CB VAL R 125 " ideal model delta sigma weight residual 112.39 107.52 4.87 1.17e+00 7.31e-01 1.73e+01 ... (remaining 9755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 3797 13.95 - 27.89: 287 27.89 - 41.84: 94 41.84 - 55.78: 21 55.78 - 69.73: 6 Dihedral angle restraints: 4205 sinusoidal: 1494 harmonic: 2711 Sorted by residual: dihedral pdb=" CB CYS R 148 " pdb=" SG CYS R 148 " pdb=" SG CYS R 226 " pdb=" CB CYS R 226 " ideal model delta sinusoidal sigma weight residual 93.00 132.71 -39.71 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 936 0.062 - 0.125: 196 0.125 - 0.187: 21 0.187 - 0.249: 0 0.249 - 0.311: 1 Chirality restraints: 1154 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL B 100 " pdb=" CA VAL B 100 " pdb=" CG1 VAL B 100 " pdb=" CG2 VAL B 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA MET A 60 " pdb=" N MET A 60 " pdb=" C MET A 60 " pdb=" CB MET A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1151 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO G 49 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.96e+00 pdb=" N PRO B 236 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 253 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO R 254 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO R 254 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 254 " 0.027 5.00e-02 4.00e+02 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 423 2.72 - 3.27: 6611 3.27 - 3.81: 10585 3.81 - 4.36: 11785 4.36 - 4.90: 21379 Nonbonded interactions: 50783 Sorted by model distance: nonbonded pdb=" NE2 GLN A 59 " pdb=" O SER A 366 " model vdw 2.181 3.120 nonbonded pdb=" OD1 ASP A 249 " pdb=" N SER A 250 " model vdw 2.199 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.227 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.235 3.040 ... (remaining 50778 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.007 0.052 7162 Z= 0.300 Angle : 0.822 10.256 9762 Z= 0.486 Chirality : 0.050 0.311 1154 Planarity : 0.005 0.067 1232 Dihedral : 12.138 69.730 2444 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.14 % Allowed : 0.28 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.27), residues: 915 helix: 0.91 (0.26), residues: 383 sheet: 0.34 (0.40), residues: 177 loop : -1.06 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.019 0.003 TYR A 37 PHE 0.026 0.003 PHE B 151 TRP 0.026 0.003 TRP B 82 HIS 0.006 0.002 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00668 ( 7161) covalent geometry : angle 0.81857 ( 9760) SS BOND : bond 0.00383 ( 1) SS BOND : angle 4.99470 ( 2) hydrogen bonds : bond 0.15532 ( 358) hydrogen bonds : angle 5.56147 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.263 Fit side-chains REVERT: A 34 LYS cc_start: 0.7783 (tttt) cc_final: 0.7432 (ttmm) REVERT: A 252 ASP cc_start: 0.7409 (t70) cc_final: 0.6931 (t70) REVERT: A 292 ASN cc_start: 0.8245 (t0) cc_final: 0.8014 (t0) REVERT: A 381 ASP cc_start: 0.8064 (t70) cc_final: 0.7598 (t70) REVERT: B 76 ASP cc_start: 0.7319 (m-30) cc_final: 0.6932 (m-30) REVERT: B 300 LEU cc_start: 0.8534 (mt) cc_final: 0.8266 (mp) REVERT: R 212 VAL cc_start: 0.8151 (t) cc_final: 0.7941 (t) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.0909 time to fit residues: 19.1494 Evaluate side-chains 150 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116261 restraints weight = 10391.610| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.63 r_work: 0.3345 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7162 Z= 0.173 Angle : 0.612 8.218 9762 Z= 0.331 Chirality : 0.045 0.182 1154 Planarity : 0.005 0.062 1232 Dihedral : 4.971 50.269 991 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.80 % Allowed : 6.22 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.28), residues: 915 helix: 1.42 (0.26), residues: 392 sheet: 0.22 (0.37), residues: 194 loop : -1.04 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 265 TYR 0.021 0.002 TYR R 296 PHE 0.018 0.002 PHE B 199 TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7161) covalent geometry : angle 0.61050 ( 9760) SS BOND : bond 0.00554 ( 1) SS BOND : angle 3.34401 ( 2) hydrogen bonds : bond 0.07568 ( 358) hydrogen bonds : angle 4.26263 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.261 Fit side-chains REVERT: A 34 LYS cc_start: 0.8012 (tttt) cc_final: 0.7710 (ttmm) REVERT: A 221 MET cc_start: 0.8457 (ttp) cc_final: 0.8196 (ttp) REVERT: A 252 ASP cc_start: 0.7684 (t70) cc_final: 0.7179 (t70) REVERT: A 381 ASP cc_start: 0.8340 (t70) cc_final: 0.7984 (t70) REVERT: B 76 ASP cc_start: 0.7546 (m-30) cc_final: 0.7308 (m-30) REVERT: B 300 LEU cc_start: 0.8602 (mt) cc_final: 0.8388 (mp) REVERT: R 112 ILE cc_start: 0.7549 (mm) cc_final: 0.7243 (tt) REVERT: R 295 MET cc_start: 0.8000 (mmt) cc_final: 0.7748 (mmm) outliers start: 13 outliers final: 10 residues processed: 153 average time/residue: 0.0866 time to fit residues: 17.0660 Evaluate side-chains 143 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117525 restraints weight = 10297.121| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.51 r_work: 0.3386 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7162 Z= 0.139 Angle : 0.549 6.251 9762 Z= 0.296 Chirality : 0.043 0.160 1154 Planarity : 0.004 0.060 1232 Dihedral : 4.304 23.078 989 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.66 % Allowed : 9.53 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.28), residues: 915 helix: 1.79 (0.27), residues: 391 sheet: 0.30 (0.38), residues: 196 loop : -0.95 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.016 0.001 TYR R 296 PHE 0.018 0.002 PHE R 77 TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7161) covalent geometry : angle 0.54760 ( 9760) SS BOND : bond 0.00528 ( 1) SS BOND : angle 3.18976 ( 2) hydrogen bonds : bond 0.06412 ( 358) hydrogen bonds : angle 3.96258 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.250 Fit side-chains REVERT: A 252 ASP cc_start: 0.7780 (t70) cc_final: 0.7287 (t70) REVERT: A 344 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 381 ASP cc_start: 0.8460 (t70) cc_final: 0.8125 (t70) REVERT: B 197 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7805 (tpp80) REVERT: B 300 LEU cc_start: 0.8678 (mt) cc_final: 0.8442 (mp) REVERT: R 112 ILE cc_start: 0.7482 (mm) cc_final: 0.7132 (tt) REVERT: R 155 PHE cc_start: 0.6791 (t80) cc_final: 0.6396 (t80) REVERT: R 295 MET cc_start: 0.7928 (mmt) cc_final: 0.7725 (mmm) outliers start: 12 outliers final: 9 residues processed: 151 average time/residue: 0.0875 time to fit residues: 16.9815 Evaluate side-chains 148 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 276 GLU Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 79 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117871 restraints weight = 10395.528| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.59 r_work: 0.3381 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7162 Z= 0.130 Angle : 0.530 6.714 9762 Z= 0.286 Chirality : 0.043 0.157 1154 Planarity : 0.004 0.059 1232 Dihedral : 4.146 22.767 989 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.62 % Allowed : 10.50 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.28), residues: 915 helix: 2.01 (0.27), residues: 391 sheet: 0.38 (0.38), residues: 196 loop : -0.99 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.014 0.001 TYR R 296 PHE 0.019 0.002 PHE R 77 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7161) covalent geometry : angle 0.52805 ( 9760) SS BOND : bond 0.00068 ( 1) SS BOND : angle 3.41282 ( 2) hydrogen bonds : bond 0.06104 ( 358) hydrogen bonds : angle 3.85114 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.267 Fit side-chains REVERT: A 252 ASP cc_start: 0.7734 (t70) cc_final: 0.7267 (t70) REVERT: A 344 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7398 (tm-30) REVERT: B 197 ARG cc_start: 0.8010 (tpp80) cc_final: 0.7802 (tpp80) REVERT: B 300 LEU cc_start: 0.8667 (mt) cc_final: 0.8439 (mp) REVERT: R 112 ILE cc_start: 0.7421 (mm) cc_final: 0.7197 (tt) REVERT: R 295 MET cc_start: 0.7973 (mmt) cc_final: 0.7767 (mmm) REVERT: R 307 LEU cc_start: 0.8279 (tp) cc_final: 0.7926 (tt) outliers start: 19 outliers final: 12 residues processed: 156 average time/residue: 0.0994 time to fit residues: 20.0149 Evaluate side-chains 153 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115723 restraints weight = 10365.583| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.63 r_work: 0.3334 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7162 Z= 0.177 Angle : 0.569 5.792 9762 Z= 0.308 Chirality : 0.044 0.151 1154 Planarity : 0.004 0.059 1232 Dihedral : 4.256 24.205 989 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.90 % Allowed : 12.57 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.28), residues: 915 helix: 1.96 (0.27), residues: 391 sheet: 0.31 (0.37), residues: 196 loop : -1.01 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.020 0.002 TYR R 296 PHE 0.020 0.002 PHE R 77 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7161) covalent geometry : angle 0.56709 ( 9760) SS BOND : bond 0.00301 ( 1) SS BOND : angle 2.90254 ( 2) hydrogen bonds : bond 0.07103 ( 358) hydrogen bonds : angle 3.99272 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.206 Fit side-chains REVERT: A 252 ASP cc_start: 0.7616 (t70) cc_final: 0.7188 (t70) REVERT: A 344 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7307 (mm-30) REVERT: B 197 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7625 (tpp80) REVERT: R 112 ILE cc_start: 0.7436 (mm) cc_final: 0.7212 (tt) REVERT: R 295 MET cc_start: 0.7921 (mmt) cc_final: 0.7678 (mmm) outliers start: 21 outliers final: 16 residues processed: 160 average time/residue: 0.0972 time to fit residues: 20.0619 Evaluate side-chains 162 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114565 restraints weight = 10480.878| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.60 r_work: 0.3363 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7162 Z= 0.167 Angle : 0.565 7.025 9762 Z= 0.305 Chirality : 0.044 0.156 1154 Planarity : 0.004 0.059 1232 Dihedral : 4.243 23.988 989 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.35 % Allowed : 12.85 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.28), residues: 915 helix: 2.00 (0.27), residues: 391 sheet: 0.32 (0.37), residues: 196 loop : -1.05 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.019 0.002 TYR R 296 PHE 0.017 0.002 PHE B 199 TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7161) covalent geometry : angle 0.56342 ( 9760) SS BOND : bond 0.00293 ( 1) SS BOND : angle 3.39966 ( 2) hydrogen bonds : bond 0.06911 ( 358) hydrogen bonds : angle 3.97865 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.306 Fit side-chains REVERT: A 252 ASP cc_start: 0.7750 (t70) cc_final: 0.7305 (t70) REVERT: A 344 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 197 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7806 (tpp80) REVERT: R 112 ILE cc_start: 0.7546 (mm) cc_final: 0.7332 (tt) REVERT: R 295 MET cc_start: 0.7949 (mmt) cc_final: 0.7706 (mmm) outliers start: 17 outliers final: 16 residues processed: 160 average time/residue: 0.0820 time to fit residues: 17.1801 Evaluate side-chains 161 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 276 GLU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 347 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8541 > 50: distance: 85 - 89: 5.642 distance: 90 - 91: 3.263 distance: 90 - 93: 3.518 distance: 91 - 92: 7.635 distance: 91 - 96: 15.610 distance: 93 - 95: 12.508 distance: 96 - 97: 14.551 distance: 97 - 98: 6.783 distance: 97 - 100: 24.198 distance: 98 - 99: 10.045 distance: 98 - 104: 14.176 distance: 100 - 101: 12.187 distance: 100 - 102: 23.243 distance: 101 - 103: 27.349 distance: 104 - 105: 8.428 distance: 105 - 106: 23.931 distance: 105 - 108: 10.348 distance: 106 - 107: 32.173 distance: 106 - 110: 8.550 distance: 108 - 109: 18.563 distance: 110 - 111: 6.744 distance: 111 - 112: 4.529 distance: 111 - 114: 7.162 distance: 112 - 113: 13.381 distance: 112 - 117: 5.331 distance: 113 - 216: 14.089 distance: 114 - 115: 15.507 distance: 114 - 116: 14.605 distance: 117 - 118: 4.838 distance: 118 - 119: 13.367 distance: 118 - 121: 9.449 distance: 119 - 120: 5.819 distance: 119 - 125: 12.144 distance: 121 - 122: 8.494 distance: 121 - 123: 17.490 distance: 122 - 124: 19.380 distance: 125 - 126: 6.870 distance: 125 - 219: 20.834 distance: 126 - 127: 9.358 distance: 126 - 129: 5.894 distance: 127 - 128: 20.542 distance: 127 - 133: 16.461 distance: 128 - 229: 15.079 distance: 129 - 130: 7.948 distance: 130 - 131: 10.216 distance: 130 - 132: 13.395 distance: 133 - 134: 15.366 distance: 134 - 135: 19.852 distance: 134 - 137: 19.914 distance: 135 - 136: 14.431 distance: 135 - 144: 25.685 distance: 137 - 138: 11.467 distance: 138 - 139: 23.492 distance: 138 - 140: 16.146 distance: 139 - 141: 9.004 distance: 140 - 142: 14.370 distance: 141 - 143: 5.576 distance: 142 - 143: 22.088 distance: 144 - 145: 10.590 distance: 144 - 232: 6.791 distance: 145 - 146: 6.974 distance: 145 - 148: 21.286 distance: 146 - 147: 12.238 distance: 146 - 152: 17.084 distance: 148 - 149: 18.123 distance: 149 - 150: 18.640 distance: 149 - 151: 13.860 distance: 152 - 153: 11.308 distance: 153 - 154: 9.799 distance: 153 - 156: 5.534 distance: 154 - 155: 9.929 distance: 154 - 160: 24.951 distance: 156 - 157: 12.633 distance: 157 - 158: 10.061 distance: 157 - 159: 7.472 distance: 160 - 161: 8.789 distance: 161 - 162: 12.420 distance: 161 - 164: 10.594 distance: 162 - 163: 9.052 distance: 162 - 169: 8.008 distance: 164 - 165: 15.299 distance: 165 - 166: 15.413 distance: 166 - 167: 13.992 distance: 167 - 168: 18.129