Starting phenix.real_space_refine on Tue Jan 14 10:24:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jub_61826/01_2025/9jub_61826_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jub_61826/01_2025/9jub_61826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jub_61826/01_2025/9jub_61826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jub_61826/01_2025/9jub_61826.map" model { file = "/net/cci-nas-00/data/ceres_data/9jub_61826/01_2025/9jub_61826_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jub_61826/01_2025/9jub_61826_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 29 5.16 5 C 4127 2.51 5 N 1059 2.21 5 O 1264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6479 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3286 Classifications: {'peptide': 406} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 382} Chain: "B" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1561 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 2 Chain: "C" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1562 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.75, per 1000 atoms: 0.89 Number of scatterers: 6479 At special positions: 0 Unit cell: (68.392, 73.04, 162.68, 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 29 16.00 O 1264 8.00 N 1059 7.00 C 4127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 351 " distance=2.26 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 238 " distance=0.71 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 387 " distance=2.04 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 435 " distance=1.15 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 198 " distance=1.78 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 196 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 501 " - " ASN A 166 " " NAG A 502 " - " ASN A 235 " " NAG A 503 " - " ASN A 393 " " NAG D 1 " - " ASN A 368 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 15 sheets defined 20.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 121 through 135 removed outlier: 3.602A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 176 removed outlier: 3.821A pdb=" N SER A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.696A pdb=" N LYS A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.731A pdb=" N GLU A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.605A pdb=" N ILE A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.329A pdb=" N TRP A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.515A pdb=" N TYR A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLU A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'A' and resid 422 through 432 removed outlier: 3.607A pdb=" N LEU A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 4.191A pdb=" N THR B 87 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'C' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 77 removed outlier: 7.016A pdb=" N TRP A 51 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY A 77 " --> pdb=" O TRP A 51 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP A 53 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ALA A 302 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TRP A 339 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 304 " --> pdb=" O TRP A 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 409 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.642A pdb=" N VAL B 36 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE B 33 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE B 49 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TRP B 35 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.703A pdb=" N LEU B 107 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.557A pdb=" N ILE C 48 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 16 through 24 removed outlier: 7.500A pdb=" N GLY C 17 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY C 77 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 75 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 67 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.808A pdb=" N VAL C 136 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR C 134 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU C 183 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL C 136 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU C 181 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL C 138 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER C 179 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN C 140 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 177 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 147 through 152 238 hydrogen bonds defined for protein. 645 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: 1.91 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1052 1.31 - 1.44: 1847 1.44 - 1.57: 3697 1.57 - 1.71: 0 1.71 - 1.84: 38 Bond restraints: 6634 Sorted by residual: bond pdb=" C CYS A 381 " pdb=" O CYS A 381 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.28e-02 6.10e+03 2.16e+01 bond pdb=" CZ TYR A 225 " pdb=" OH TYR A 225 " ideal model delta sigma weight residual 1.376 1.282 0.094 2.10e-02 2.27e+03 2.00e+01 bond pdb=" CA CYS A 238 " pdb=" C CYS A 238 " ideal model delta sigma weight residual 1.524 1.470 0.054 1.26e-02 6.30e+03 1.83e+01 bond pdb=" C GLU A 148 " pdb=" O GLU A 148 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.29e-02 6.01e+03 1.73e+01 bond pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta sigma weight residual 1.455 1.404 0.050 1.29e-02 6.01e+03 1.51e+01 ... (remaining 6629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 8835 2.19 - 4.37: 184 4.37 - 6.56: 21 6.56 - 8.74: 8 8.74 - 10.93: 3 Bond angle restraints: 9051 Sorted by residual: angle pdb=" N ASN A 240 " pdb=" CA ASN A 240 " pdb=" C ASN A 240 " ideal model delta sigma weight residual 111.28 119.85 -8.57 1.09e+00 8.42e-01 6.19e+01 angle pdb=" N LEU A 342 " pdb=" CA LEU A 342 " pdb=" C LEU A 342 " ideal model delta sigma weight residual 113.89 102.96 10.93 1.58e+00 4.01e-01 4.79e+01 angle pdb=" C ARG A 95 " pdb=" CA ARG A 95 " pdb=" CB ARG A 95 " ideal model delta sigma weight residual 112.44 102.93 9.51 2.07e+00 2.33e-01 2.11e+01 angle pdb=" C CYS A 224 " pdb=" N TYR A 225 " pdb=" CA TYR A 225 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CB ARG A 95 " pdb=" CG ARG A 95 " pdb=" CD ARG A 95 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 ... (remaining 9046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.96: 3820 19.96 - 39.91: 150 39.91 - 59.87: 25 59.87 - 79.83: 5 79.83 - 99.79: 7 Dihedral angle restraints: 4007 sinusoidal: 1603 harmonic: 2404 Sorted by residual: dihedral pdb=" C TYR A 225 " pdb=" N TYR A 225 " pdb=" CA TYR A 225 " pdb=" CB TYR A 225 " ideal model delta harmonic sigma weight residual -122.60 -139.99 17.39 0 2.50e+00 1.60e-01 4.84e+01 dihedral pdb=" N TYR A 225 " pdb=" C TYR A 225 " pdb=" CA TYR A 225 " pdb=" CB TYR A 225 " ideal model delta harmonic sigma weight residual 122.80 139.54 -16.74 0 2.50e+00 1.60e-01 4.48e+01 dihedral pdb=" CB CYS A 381 " pdb=" SG CYS A 381 " pdb=" SG CYS A 435 " pdb=" CB CYS A 435 " ideal model delta sinusoidal sigma weight residual 93.00 145.74 -52.74 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 4004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1045 0.165 - 0.330: 6 0.330 - 0.494: 0 0.494 - 0.659: 0 0.659 - 0.824: 2 Chirality restraints: 1053 Sorted by residual: chirality pdb=" CA TYR A 225 " pdb=" N TYR A 225 " pdb=" C TYR A 225 " pdb=" CB TYR A 225 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 393 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.30 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 1050 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 393 " -0.230 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" CG ASN A 393 " 0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN A 393 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN A 393 " 0.516 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " -0.319 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 235 " 0.069 2.00e-02 2.50e+03 6.91e-02 5.97e+01 pdb=" CG ASN A 235 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 235 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 235 " -0.103 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 239 " 0.012 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C PHE A 239 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 239 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 240 " 0.013 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 54 2.53 - 3.12: 4869 3.12 - 3.71: 9111 3.71 - 4.31: 12877 4.31 - 4.90: 21959 Nonbonded interactions: 48870 Sorted by model distance: nonbonded pdb=" O ASP A 223 " pdb=" ND2 ASN A 246 " model vdw 1.934 3.120 nonbonded pdb=" OD1 ASN A 240 " pdb=" N VAL A 241 " model vdw 2.071 3.120 nonbonded pdb=" O ASN A 235 " pdb=" OD1 ASN A 235 " model vdw 2.083 3.040 nonbonded pdb=" CD2 LEU A 398 " pdb=" CE2 PHE A 433 " model vdw 2.092 3.760 nonbonded pdb=" CD2 LEU A 398 " pdb=" CZ PHE A 433 " model vdw 2.120 3.760 ... (remaining 48865 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: 8.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 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 0.094 6634 Z= 0.448 Angle : 0.788 10.931 9051 Z= 0.443 Chirality : 0.060 0.824 1053 Planarity : 0.005 0.046 1140 Dihedral : 11.954 99.786 2440 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.57 % Favored : 92.31 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.89 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.28), residues: 819 helix: -0.91 (0.39), residues: 157 sheet: 0.37 (0.37), residues: 217 loop : -2.14 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 339 HIS 0.004 0.001 HIS A 228 PHE 0.022 0.002 PHE A 199 TYR 0.022 0.003 TYR A 277 ARG 0.003 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 PHE cc_start: 0.7696 (m-80) cc_final: 0.7320 (m-80) REVERT: B 42 LYS cc_start: 0.7502 (mttp) cc_final: 0.6937 (mtpt) REVERT: B 78 LYS cc_start: 0.7640 (tttt) cc_final: 0.7422 (ttpt) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.1838 time to fit residues: 35.0422 Evaluate side-chains 90 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 438 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.240335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.200888 restraints weight = 6655.209| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.44 r_work: 0.3969 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6634 Z= 0.205 Angle : 0.635 9.481 9051 Z= 0.326 Chirality : 0.047 0.267 1053 Planarity : 0.005 0.043 1140 Dihedral : 7.408 59.931 998 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.81 % Allowed : 7.65 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.28), residues: 819 helix: -0.54 (0.40), residues: 160 sheet: 0.51 (0.38), residues: 211 loop : -1.85 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 35 HIS 0.003 0.001 HIS A 399 PHE 0.014 0.002 PHE A 199 TYR 0.014 0.001 TYR A 323 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7693 (mttp) cc_final: 0.7221 (mtpt) REVERT: B 78 LYS cc_start: 0.8265 (tttt) cc_final: 0.7995 (ttpt) REVERT: B 142 THR cc_start: 0.7486 (p) cc_final: 0.7224 (t) REVERT: C 135 ILE cc_start: 0.7921 (mm) cc_final: 0.7598 (mt) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.1744 time to fit residues: 23.5894 Evaluate side-chains 92 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS C 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.229560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190519 restraints weight = 6734.154| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.38 r_work: 0.3934 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 6634 Z= 0.410 Angle : 0.769 10.981 9051 Z= 0.392 Chirality : 0.053 0.320 1053 Planarity : 0.006 0.062 1140 Dihedral : 7.153 58.219 995 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.36 % Allowed : 10.71 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 819 helix: -0.85 (0.38), residues: 159 sheet: 0.11 (0.37), residues: 233 loop : -1.85 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 35 HIS 0.006 0.002 HIS A 228 PHE 0.025 0.003 PHE A 199 TYR 0.019 0.002 TYR A 219 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 VAL cc_start: 0.7789 (m) cc_final: 0.7568 (p) REVERT: B 42 LYS cc_start: 0.7735 (mttp) cc_final: 0.7252 (mtpt) REVERT: B 78 LYS cc_start: 0.8167 (tttt) cc_final: 0.7828 (ttpt) REVERT: C 135 ILE cc_start: 0.7905 (mm) cc_final: 0.7544 (mt) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.1905 time to fit residues: 23.5460 Evaluate side-chains 88 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.237347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.197775 restraints weight = 6762.798| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.55 r_work: 0.3996 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.171 Angle : 0.575 9.827 9051 Z= 0.292 Chirality : 0.046 0.343 1053 Planarity : 0.004 0.044 1140 Dihedral : 6.003 57.692 993 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.81 % Allowed : 12.10 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.29), residues: 819 helix: -0.38 (0.39), residues: 160 sheet: 0.47 (0.37), residues: 219 loop : -1.69 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 35 HIS 0.002 0.001 HIS A 228 PHE 0.015 0.001 PHE A 133 TYR 0.014 0.001 TYR A 323 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 LYS cc_start: 0.8090 (tttt) cc_final: 0.7465 (mtpt) REVERT: B 142 THR cc_start: 0.7514 (p) cc_final: 0.7282 (t) REVERT: C 135 ILE cc_start: 0.7800 (mm) cc_final: 0.7514 (mt) outliers start: 13 outliers final: 8 residues processed: 88 average time/residue: 0.2000 time to fit residues: 23.3869 Evaluate side-chains 83 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN C 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.235882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.196030 restraints weight = 6739.491| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.66 r_work: 0.3981 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6634 Z= 0.209 Angle : 0.595 10.152 9051 Z= 0.301 Chirality : 0.047 0.342 1053 Planarity : 0.004 0.046 1140 Dihedral : 6.021 58.829 993 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.95 % Allowed : 12.52 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 819 helix: -0.17 (0.40), residues: 160 sheet: 0.45 (0.37), residues: 219 loop : -1.56 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 154 HIS 0.003 0.001 HIS A 227 PHE 0.017 0.002 PHE C 71 TYR 0.016 0.002 TYR A 323 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7746 (mttp) cc_final: 0.7262 (mtpt) REVERT: B 78 LYS cc_start: 0.8128 (tttt) cc_final: 0.7785 (ttpt) REVERT: B 142 THR cc_start: 0.7615 (p) cc_final: 0.7357 (t) REVERT: C 135 ILE cc_start: 0.7856 (mm) cc_final: 0.7545 (mt) outliers start: 14 outliers final: 13 residues processed: 87 average time/residue: 0.1795 time to fit residues: 21.2321 Evaluate side-chains 88 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN C 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.237434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.201562 restraints weight = 6689.693| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.98 r_work: 0.3958 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6634 Z= 0.163 Angle : 0.541 9.875 9051 Z= 0.274 Chirality : 0.045 0.331 1053 Planarity : 0.004 0.044 1140 Dihedral : 5.654 58.568 993 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.39 % Allowed : 14.05 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.29), residues: 819 helix: -0.13 (0.40), residues: 166 sheet: 0.56 (0.38), residues: 211 loop : -1.55 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.001 0.001 HIS A 214 PHE 0.021 0.001 PHE A 133 TYR 0.015 0.001 TYR A 323 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 260 TYR cc_start: 0.7542 (m-80) cc_final: 0.7199 (m-80) REVERT: B 78 LYS cc_start: 0.8207 (tttt) cc_final: 0.7598 (mtpt) REVERT: C 135 ILE cc_start: 0.7938 (mm) cc_final: 0.7633 (mt) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.1915 time to fit residues: 23.3945 Evaluate side-chains 79 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3549 > 50: distance: 22 - 27: 9.760 distance: 27 - 28: 22.365 distance: 28 - 29: 12.293 distance: 28 - 31: 12.085 distance: 29 - 30: 34.446 distance: 29 - 36: 35.586 distance: 31 - 32: 3.180 distance: 32 - 33: 3.969 distance: 33 - 34: 26.464 distance: 34 - 35: 11.454 distance: 36 - 37: 12.245 distance: 37 - 38: 5.139 distance: 38 - 39: 19.708 distance: 38 - 40: 20.712 distance: 40 - 41: 12.838 distance: 41 - 42: 14.683 distance: 41 - 44: 23.509 distance: 42 - 43: 4.362 distance: 42 - 48: 41.137 distance: 44 - 45: 16.618 distance: 45 - 46: 9.300 distance: 45 - 47: 26.699 distance: 48 - 49: 5.445 distance: 48 - 54: 13.527 distance: 49 - 50: 8.683 distance: 49 - 52: 7.321 distance: 50 - 51: 7.707 distance: 50 - 55: 11.332 distance: 52 - 53: 4.975 distance: 53 - 54: 11.655 distance: 55 - 56: 16.741 distance: 56 - 57: 15.007 distance: 56 - 59: 14.679 distance: 57 - 58: 14.011 distance: 57 - 62: 23.612 distance: 59 - 60: 25.722 distance: 59 - 61: 32.902 distance: 62 - 63: 12.300 distance: 63 - 64: 30.301 distance: 63 - 66: 36.491 distance: 64 - 65: 16.104 distance: 64 - 67: 21.812 distance: 67 - 68: 16.221 distance: 67 - 73: 20.361 distance: 68 - 69: 24.396 distance: 68 - 71: 26.130 distance: 69 - 74: 35.560 distance: 71 - 72: 28.607 distance: 72 - 73: 29.326 distance: 74 - 75: 8.249 distance: 75 - 76: 12.000 distance: 75 - 78: 28.572 distance: 76 - 77: 18.425 distance: 76 - 81: 9.703 distance: 78 - 79: 18.422 distance: 78 - 80: 14.810 distance: 81 - 82: 12.736 distance: 82 - 83: 14.223 distance: 82 - 85: 21.980 distance: 83 - 84: 12.439 distance: 83 - 88: 11.830 distance: 85 - 86: 17.563 distance: 85 - 87: 33.369 distance: 88 - 89: 27.558 distance: 88 - 119: 16.277 distance: 89 - 90: 9.768 distance: 89 - 92: 23.216 distance: 90 - 91: 10.721 distance: 90 - 96: 12.719 distance: 91 - 116: 12.341 distance: 92 - 93: 14.924 distance: 93 - 94: 26.381 distance: 93 - 95: 40.961