Starting phenix.real_space_refine on Thu Nov 14 13:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jub_61826/11_2024/9jub_61826_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jub_61826/11_2024/9jub_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jub_61826/11_2024/9jub_61826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jub_61826/11_2024/9jub_61826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jub_61826/11_2024/9jub_61826_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jub_61826/11_2024/9jub_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-5513/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: 5.35, per 1000 atoms: 0.83 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: 1.81 Conformation dependent library (CDL) restraints added in 1.5 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: 0.84 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: 1.93 Time building geometry restraints manager: 1.91 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: 7.380 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: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- 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 : 0.757 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: 0.1903 time to fit residues: 36.2525 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 : 0.934 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 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 : 0.697 Fit side-chains revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7432 (mttp) cc_final: 0.6895 (mtpt) REVERT: B 78 LYS cc_start: 0.7647 (tttt) cc_final: 0.7342 (ttpt) REVERT: B 142 THR cc_start: 0.7727 (p) cc_final: 0.7513 (t) REVERT: C 135 ILE cc_start: 0.7922 (mm) cc_final: 0.7568 (mt) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.1676 time to fit residues: 22.8147 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 : 0.690 ------------------------------------------------------------------------------- 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 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 0.0470 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6634 Z= 0.155 Angle : 0.560 9.650 9051 Z= 0.286 Chirality : 0.046 0.322 1053 Planarity : 0.004 0.045 1140 Dihedral : 6.188 58.890 995 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.81 % Allowed : 10.43 % Favored : 87.76 % 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: -1.00 (0.29), residues: 819 helix: 0.02 (0.40), residues: 154 sheet: 0.46 (0.36), residues: 231 loop : -1.61 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.003 0.001 HIS A 228 PHE 0.019 0.001 PHE A 133 TYR 0.013 0.001 TYR A 323 ARG 0.005 0.000 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 96 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.6297 (t0) cc_final: 0.6034 (t0) REVERT: B 42 LYS cc_start: 0.7455 (mttp) cc_final: 0.6929 (mtpt) REVERT: B 78 LYS cc_start: 0.7645 (tttt) cc_final: 0.6994 (mtpt) REVERT: C 135 ILE cc_start: 0.7956 (mm) cc_final: 0.7620 (mt) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.1883 time to fit residues: 22.4805 Evaluate side-chains 82 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 386 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 52 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6634 Z= 0.277 Angle : 0.645 10.347 9051 Z= 0.327 Chirality : 0.049 0.349 1053 Planarity : 0.005 0.046 1140 Dihedral : 6.298 57.873 993 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.09 % Allowed : 11.96 % Favored : 85.95 % 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: -0.25 (0.40), residues: 160 sheet: 0.44 (0.37), residues: 223 loop : -1.55 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 150 HIS 0.004 0.001 HIS A 228 PHE 0.021 0.002 PHE C 71 TYR 0.017 0.002 TYR C 49 ARG 0.008 0.001 ARG C 61 *********************** 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 96 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7528 (mttp) cc_final: 0.6981 (mtpt) REVERT: B 78 LYS cc_start: 0.7657 (tttt) cc_final: 0.7253 (ttpt) REVERT: C 135 ILE cc_start: 0.8007 (mm) cc_final: 0.7715 (mt) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.1889 time to fit residues: 22.9906 Evaluate side-chains 84 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 20 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 C 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6634 Z= 0.185 Angle : 0.565 9.912 9051 Z= 0.287 Chirality : 0.046 0.339 1053 Planarity : 0.004 0.045 1140 Dihedral : 5.799 58.553 993 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.53 % Allowed : 13.49 % Favored : 84.98 % 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: -0.98 (0.29), residues: 819 helix: -0.02 (0.40), residues: 160 sheet: 0.52 (0.38), residues: 219 loop : -1.55 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 35 HIS 0.002 0.001 HIS A 228 PHE 0.019 0.002 PHE A 133 TYR 0.013 0.001 TYR A 323 ARG 0.005 0.000 ARG C 61 *********************** 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: 11 poor density : 82 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 PHE cc_start: 0.7600 (m-80) cc_final: 0.7209 (m-80) REVERT: B 78 LYS cc_start: 0.7625 (tttt) cc_final: 0.6927 (mtpt) REVERT: C 135 ILE cc_start: 0.7964 (mm) cc_final: 0.7662 (mt) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.1800 time to fit residues: 21.7561 Evaluate side-chains 83 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 310 ASP Chi-restraints excluded: chain A residue 337 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6634 Z= 0.204 Angle : 0.572 10.070 9051 Z= 0.289 Chirality : 0.046 0.335 1053 Planarity : 0.004 0.045 1140 Dihedral : 5.836 59.855 993 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.36 % Allowed : 12.80 % Favored : 84.84 % 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: -0.95 (0.29), residues: 819 helix: 0.13 (0.41), residues: 160 sheet: 0.47 (0.37), residues: 219 loop : -1.55 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 154 HIS 0.002 0.001 HIS A 227 PHE 0.018 0.002 PHE A 133 TYR 0.013 0.002 TYR C 49 ARG 0.005 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 90 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7468 (mttp) cc_final: 0.6978 (mtpt) REVERT: B 78 LYS cc_start: 0.7612 (tttt) cc_final: 0.6913 (mtpt) REVERT: C 135 ILE cc_start: 0.7947 (mm) cc_final: 0.7646 (mt) outliers start: 17 outliers final: 15 residues processed: 84 average time/residue: 0.1940 time to fit residues: 21.9507 Evaluate side-chains 86 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 334 SER Chi-restraints excluded: chain A residue 336 ILE 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 83 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 79 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6634 Z= 0.189 Angle : 0.557 9.974 9051 Z= 0.280 Chirality : 0.046 0.330 1053 Planarity : 0.004 0.045 1140 Dihedral : 5.740 59.431 993 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.81 % Allowed : 13.35 % Favored : 84.84 % 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: -0.89 (0.29), residues: 819 helix: 0.18 (0.40), residues: 160 sheet: 0.49 (0.37), residues: 219 loop : -1.50 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.002 0.001 HIS A 214 PHE 0.017 0.001 PHE A 133 TYR 0.012 0.001 TYR C 49 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 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 85 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.7614 (tttt) cc_final: 0.6923 (mtpt) REVERT: C 135 ILE cc_start: 0.7961 (mm) cc_final: 0.7650 (mt) outliers start: 13 outliers final: 13 residues processed: 80 average time/residue: 0.1880 time to fit residues: 20.6757 Evaluate side-chains 81 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 83 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.0020 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6634 Z= 0.166 Angle : 0.536 9.929 9051 Z= 0.270 Chirality : 0.045 0.319 1053 Planarity : 0.004 0.044 1140 Dihedral : 5.546 58.977 993 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.81 % Allowed : 13.77 % Favored : 84.42 % 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: -0.83 (0.29), residues: 819 helix: 0.13 (0.40), residues: 166 sheet: 0.64 (0.38), residues: 211 loop : -1.47 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.001 0.001 HIS A 214 PHE 0.023 0.001 PHE A 133 TYR 0.012 0.001 TYR C 49 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 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 88 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7402 (mttp) cc_final: 0.6954 (mtpt) REVERT: B 78 LYS cc_start: 0.7603 (tttt) cc_final: 0.6922 (mtpt) REVERT: C 135 ILE cc_start: 0.7968 (mm) cc_final: 0.7654 (mt) outliers start: 13 outliers final: 13 residues processed: 83 average time/residue: 0.1803 time to fit residues: 20.5701 Evaluate side-chains 81 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER 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 83 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6634 Z= 0.143 Angle : 0.519 9.792 9051 Z= 0.262 Chirality : 0.044 0.308 1053 Planarity : 0.004 0.044 1140 Dihedral : 5.353 58.481 993 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.67 % Allowed : 14.19 % Favored : 84.14 % 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: -0.70 (0.30), residues: 819 helix: 0.30 (0.41), residues: 166 sheet: 0.53 (0.37), residues: 223 loop : -1.34 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.002 0.001 HIS A 123 PHE 0.011 0.001 PHE A 199 TYR 0.012 0.001 TYR A 277 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 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 82 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.7599 (tttt) cc_final: 0.6929 (mtpt) REVERT: C 135 ILE cc_start: 0.7949 (mm) cc_final: 0.7629 (mt) outliers start: 12 outliers final: 12 residues processed: 78 average time/residue: 0.1715 time to fit residues: 18.5267 Evaluate side-chains 81 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 334 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 83 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 0.0050 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3576 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= 0.186 Angle : 0.549 9.988 9051 Z= 0.277 Chirality : 0.045 0.316 1053 Planarity : 0.004 0.045 1140 Dihedral : 5.556 59.879 993 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.95 % Allowed : 14.05 % Favored : 84.01 % 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: -0.80 (0.29), residues: 819 helix: 0.24 (0.41), residues: 166 sheet: 0.34 (0.37), residues: 223 loop : -1.34 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 154 HIS 0.002 0.001 HIS A 214 PHE 0.021 0.001 PHE A 133 TYR 0.013 0.002 TYR C 49 ARG 0.004 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 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 91 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7397 (mttp) cc_final: 0.6978 (mtpt) REVERT: B 78 LYS cc_start: 0.7589 (tttt) cc_final: 0.6928 (mtpt) REVERT: C 4 MET cc_start: 0.6592 (mtp) cc_final: 0.6382 (ttm) REVERT: C 135 ILE cc_start: 0.7943 (mm) cc_final: 0.7627 (mt) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.1795 time to fit residues: 21.2643 Evaluate side-chains 86 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 83 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.238394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.202798 restraints weight = 6662.751| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.00 r_work: 0.3976 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6634 Z= 0.152 Angle : 0.524 9.847 9051 Z= 0.264 Chirality : 0.045 0.310 1053 Planarity : 0.004 0.044 1140 Dihedral : 5.371 58.461 993 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.67 % Allowed : 14.46 % Favored : 83.87 % 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: -0.74 (0.30), residues: 819 helix: 0.31 (0.41), residues: 166 sheet: 0.31 (0.37), residues: 233 loop : -1.30 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 53 HIS 0.001 0.000 HIS A 214 PHE 0.023 0.001 PHE A 133 TYR 0.014 0.001 TYR C 49 ARG 0.005 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.76 seconds wall clock time: 35 minutes 24.79 seconds (2124.79 seconds total)