Starting phenix.real_space_refine on Sat May 17 07:04:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyk_47307/05_2025/9dyk_47307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyk_47307/05_2025/9dyk_47307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dyk_47307/05_2025/9dyk_47307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyk_47307/05_2025/9dyk_47307.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyk_47307/05_2025/9dyk_47307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyk_47307/05_2025/9dyk_47307.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.115 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 85 5.16 5 Cl 1 4.86 5 C 10130 2.51 5 N 2555 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15486 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 3096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3163 Chain: "E" Number of atoms: 3096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3163 Chain: "C" Number of atoms: 3096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3163 Chain: "A" Number of atoms: 3096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3163 Chain: "B" Number of atoms: 3096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Conformer: "B" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} bond proxies already assigned to first conformer: 3163 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.23, per 1000 atoms: 1.11 Number of scatterers: 15486 At special positions: 0 Unit cell: (105.41, 106.24, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 85 16.00 O 2710 8.00 N 2555 7.00 C 10130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 0 sheets defined 70.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.757A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.782A pdb=" N GLN D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.880A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 19 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.759A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.754A pdb=" N GLN E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.509A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.876A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.754A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.780A pdb=" N GLN C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 4.525A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.884A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.768A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.752A pdb=" N GLN A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 4.547A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.876A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.682A pdb=" N GLN A 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.759A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 removed outlier: 3.795A pdb=" N GLN B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.861A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 981 hydrogen bonds defined for protein. 2815 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: 4.78 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4851 1.34 - 1.46: 3691 1.46 - 1.58: 7233 1.58 - 1.70: 0 1.70 - 1.81: 130 Bond restraints: 15905 Sorted by residual: bond pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.23e-02 6.61e+03 2.78e+00 bond pdb=" C ASP B 155 " pdb=" O ASP B 155 " ideal model delta sigma weight residual 1.237 1.224 0.013 1.19e-02 7.06e+03 1.14e+00 bond pdb=" C ILE B 154 " pdb=" N ASP B 155 " ideal model delta sigma weight residual 1.335 1.323 0.012 1.36e-02 5.41e+03 7.95e-01 bond pdb=" CA ARG A 356 " pdb=" CB ARG A 356 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.50e-01 bond pdb=" CA ARG E 356 " pdb=" CB ARG E 356 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.69e-02 3.50e+03 7.36e-01 ... (remaining 15900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21099 1.41 - 2.82: 402 2.82 - 4.23: 80 4.23 - 5.64: 17 5.64 - 7.05: 7 Bond angle restraints: 21605 Sorted by residual: angle pdb=" C LEU B 355 " pdb=" N ARG B 356 " pdb=" CA ARG B 356 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C LEU A 355 " pdb=" N ARG A 356 " pdb=" CA ARG A 356 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C LEU C 355 " pdb=" N ARG C 356 " pdb=" CA ARG C 356 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C LEU D 355 " pdb=" N ARG D 356 " pdb=" CA ARG D 356 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C LEU E 355 " pdb=" N ARG E 356 " pdb=" CA ARG E 356 " ideal model delta sigma weight residual 121.54 128.46 -6.92 1.91e+00 2.74e-01 1.31e+01 ... (remaining 21600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8459 17.99 - 35.97: 614 35.97 - 53.96: 157 53.96 - 71.94: 40 71.94 - 89.93: 10 Dihedral angle restraints: 9280 sinusoidal: 3685 harmonic: 5595 Sorted by residual: dihedral pdb=" CA ASP B 268 " pdb=" CB ASP B 268 " pdb=" CG ASP B 268 " pdb=" OD1 ASP B 268 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA VAL A 114 " pdb=" C VAL A 114 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA VAL D 114 " pdb=" C VAL D 114 " pdb=" N HIS D 115 " pdb=" CA HIS D 115 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1479 0.029 - 0.058: 629 0.058 - 0.087: 161 0.087 - 0.116: 71 0.116 - 0.144: 10 Chirality restraints: 2350 Sorted by residual: chirality pdb=" CA VAL B 232 " pdb=" N VAL B 232 " pdb=" C VAL B 232 " pdb=" CB VAL B 232 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL E 232 " pdb=" N VAL E 232 " pdb=" C VAL E 232 " pdb=" CB VAL E 232 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA VAL A 232 " pdb=" N VAL A 232 " pdb=" C VAL A 232 " pdb=" CB VAL A 232 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2347 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 154 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ILE B 154 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE B 154 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP B 155 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 80 " -0.012 2.00e-02 2.50e+03 1.01e-02 1.80e+00 pdb=" CG PHE E 80 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE E 80 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE E 80 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 80 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 83 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C GLY E 83 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY E 83 " -0.007 2.00e-02 2.50e+03 pdb=" N PHE E 84 " -0.006 2.00e-02 2.50e+03 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3039 2.77 - 3.30: 15293 3.30 - 3.84: 28653 3.84 - 4.37: 34239 4.37 - 4.90: 55750 Nonbonded interactions: 136974 Sorted by model distance: nonbonded pdb=" OD1 ASP D 155 " pdb=" NH1 ARG D 168 " model vdw 2.240 3.120 nonbonded pdb=" OD1 ASP E 155 " pdb=" NH1 ARG E 168 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASP C 155 " pdb=" NH1 ARG C 168 " model vdw 2.252 3.120 nonbonded pdb=" OD1 ASP A 155 " pdb=" NH2 ARG A 168 " model vdw 2.265 3.120 nonbonded pdb=" OH TYR E 5 " pdb=" O VAL A 232 " model vdw 2.288 3.040 ... (remaining 136969 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 377 or resid 501)) selection = (chain 'B' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 377 or resid 501)) selection = (chain 'C' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 377 or resid 501)) selection = (chain 'D' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 377 or resid 501)) selection = (chain 'E' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 377 or resid 501)) } 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=0.50 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: 4.550 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 46.450 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.002 0.035 15905 Z= 0.133 Angle : 0.526 7.049 21605 Z= 0.304 Chirality : 0.036 0.144 2350 Planarity : 0.003 0.032 2725 Dihedral : 14.111 89.927 5690 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.06 % Allowed : 10.43 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.18), residues: 1880 helix: 1.28 (0.14), residues: 1330 sheet: None (None), residues: 0 loop : -0.31 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 93 HIS 0.002 0.001 HIS B 115 PHE 0.023 0.001 PHE E 80 TYR 0.014 0.001 TYR B 284 ARG 0.007 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.07653 ( 981) hydrogen bonds : angle 4.38847 ( 2815) covalent geometry : bond 0.00249 (15905) covalent geometry : angle 0.52639 (21605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.673 Fit side-chains REVERT: D 13 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7000 (ptp90) REVERT: E 13 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7042 (ptp90) REVERT: C 13 ARG cc_start: 0.7362 (ptp90) cc_final: 0.7056 (ptp90) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 1.7818 time to fit residues: 347.2919 Evaluate side-chains 170 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.090355 restraints weight = 37331.967| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.18 r_work: 0.2900 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15905 Z= 0.154 Angle : 0.513 5.381 21605 Z= 0.286 Chirality : 0.038 0.148 2350 Planarity : 0.004 0.029 2725 Dihedral : 4.213 17.670 2135 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.52 % Allowed : 10.00 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.18), residues: 1880 helix: 1.37 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.05 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 93 HIS 0.002 0.001 HIS C 156 PHE 0.016 0.002 PHE A 171 TYR 0.015 0.002 TYR A 97 ARG 0.005 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.05945 ( 981) hydrogen bonds : angle 4.41725 ( 2815) covalent geometry : bond 0.00325 (15905) covalent geometry : angle 0.51339 (21605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.857 Fit side-chains REVERT: D 13 ARG cc_start: 0.7548 (mtp-110) cc_final: 0.6667 (ptp90) REVERT: D 172 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: D 356 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4392 (ptm160) REVERT: E 13 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.6674 (ptp90) REVERT: E 75 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6710 (mp) REVERT: E 172 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: C 13 ARG cc_start: 0.7208 (ptp90) cc_final: 0.6834 (ptp90) REVERT: C 172 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 172 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: B 172 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 356 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4336 (ptm160) outliers start: 25 outliers final: 9 residues processed: 194 average time/residue: 1.7029 time to fit residues: 356.5756 Evaluate side-chains 195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.087458 restraints weight = 40939.378| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.25 r_work: 0.2852 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15905 Z= 0.203 Angle : 0.563 5.841 21605 Z= 0.311 Chirality : 0.041 0.160 2350 Planarity : 0.004 0.051 2725 Dihedral : 4.435 19.038 2135 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.59 % Allowed : 10.55 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.18), residues: 1880 helix: 1.21 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.04 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 93 HIS 0.001 0.001 HIS A 267 PHE 0.024 0.002 PHE D 80 TYR 0.018 0.002 TYR A 97 ARG 0.006 0.001 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.06669 ( 981) hydrogen bonds : angle 4.52854 ( 2815) covalent geometry : bond 0.00455 (15905) covalent geometry : angle 0.56294 (21605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.739 Fit side-chains REVERT: D 13 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.6683 (ptp90) REVERT: D 172 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: E 13 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.6707 (ptp90) REVERT: E 75 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6804 (mp) REVERT: E 172 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 356 ARG cc_start: 0.4843 (OUTLIER) cc_final: 0.4319 (ptm160) REVERT: E 375 GLN cc_start: 0.6891 (tp-100) cc_final: 0.6583 (tp40) REVERT: C 13 ARG cc_start: 0.7179 (ptp90) cc_final: 0.6832 (ptp90) REVERT: C 172 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: C 356 ARG cc_start: 0.4818 (OUTLIER) cc_final: 0.4437 (ptm160) REVERT: A 172 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: A 356 ARG cc_start: 0.4891 (OUTLIER) cc_final: 0.4398 (ptm160) REVERT: B 172 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.6798 (mp0) outliers start: 26 outliers final: 11 residues processed: 193 average time/residue: 1.8562 time to fit residues: 386.1927 Evaluate side-chains 195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.086380 restraints weight = 39983.674| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.22 r_work: 0.2837 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15905 Z= 0.251 Angle : 0.603 5.867 21605 Z= 0.332 Chirality : 0.044 0.162 2350 Planarity : 0.005 0.039 2725 Dihedral : 4.603 19.908 2135 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.89 % Allowed : 10.49 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.18), residues: 1880 helix: 1.01 (0.14), residues: 1310 sheet: None (None), residues: 0 loop : -0.10 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 93 HIS 0.002 0.001 HIS D 267 PHE 0.020 0.003 PHE B 188 TYR 0.019 0.002 TYR A 97 ARG 0.004 0.001 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.07112 ( 981) hydrogen bonds : angle 4.61702 ( 2815) covalent geometry : bond 0.00578 (15905) covalent geometry : angle 0.60340 (21605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.789 Fit side-chains REVERT: D 13 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.6644 (ptp90) REVERT: D 75 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6941 (pp) REVERT: D 172 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: D 356 ARG cc_start: 0.4841 (OUTLIER) cc_final: 0.4356 (ptm160) REVERT: E 13 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.6760 (ptp90) REVERT: E 75 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6919 (mp) REVERT: E 172 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: E 175 ASN cc_start: 0.8896 (t0) cc_final: 0.8525 (m-40) REVERT: E 356 ARG cc_start: 0.4818 (OUTLIER) cc_final: 0.4291 (ptm160) REVERT: E 375 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6592 (tp40) REVERT: C 13 ARG cc_start: 0.7192 (ptp90) cc_final: 0.6859 (ptp90) REVERT: C 172 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: C 356 ARG cc_start: 0.4941 (OUTLIER) cc_final: 0.4530 (ptm160) REVERT: A 172 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: A 356 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.4506 (ptm160) REVERT: B 172 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: B 356 ARG cc_start: 0.5005 (OUTLIER) cc_final: 0.4474 (ptp-170) outliers start: 31 outliers final: 12 residues processed: 189 average time/residue: 1.7849 time to fit residues: 363.5077 Evaluate side-chains 198 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 375 GLN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 106 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 167 optimal weight: 0.0770 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091115 restraints weight = 41684.491| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.28 r_work: 0.2909 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15905 Z= 0.126 Angle : 0.480 5.673 21605 Z= 0.269 Chirality : 0.036 0.150 2350 Planarity : 0.003 0.031 2725 Dihedral : 4.162 16.656 2135 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.34 % Allowed : 10.73 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.18), residues: 1880 helix: 1.34 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.10 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 93 HIS 0.002 0.001 HIS E 115 PHE 0.020 0.001 PHE C 80 TYR 0.012 0.001 TYR A 97 ARG 0.003 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.05499 ( 981) hydrogen bonds : angle 4.36161 ( 2815) covalent geometry : bond 0.00251 (15905) covalent geometry : angle 0.48012 (21605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.754 Fit side-chains REVERT: D 13 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.6656 (ptp90) REVERT: D 172 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: D 356 ARG cc_start: 0.4669 (OUTLIER) cc_final: 0.4294 (ptm160) REVERT: E 13 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.6664 (ptp90) REVERT: E 175 ASN cc_start: 0.8764 (t0) cc_final: 0.8377 (m-40) REVERT: E 356 ARG cc_start: 0.4857 (OUTLIER) cc_final: 0.4329 (ptm160) REVERT: C 13 ARG cc_start: 0.7159 (ptp90) cc_final: 0.6912 (ptp90) REVERT: C 172 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: C 356 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.4380 (ptm160) REVERT: A 13 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.6800 (ptp90) REVERT: A 172 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 356 ARG cc_start: 0.4781 (OUTLIER) cc_final: 0.4342 (ptm160) REVERT: B 13 ARG cc_start: 0.7409 (mtp-110) cc_final: 0.6434 (ptp90) REVERT: B 172 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: B 356 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.4341 (ptm160) REVERT: B 374 MET cc_start: 0.6435 (mtm) cc_final: 0.6136 (mtm) outliers start: 22 outliers final: 5 residues processed: 192 average time/residue: 1.7633 time to fit residues: 364.8637 Evaluate side-chains 190 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 29 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN B 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.086448 restraints weight = 44581.726| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.34 r_work: 0.2836 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15905 Z= 0.237 Angle : 0.585 6.410 21605 Z= 0.322 Chirality : 0.043 0.161 2350 Planarity : 0.005 0.036 2725 Dihedral : 4.499 19.580 2135 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.77 % Allowed : 10.37 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.18), residues: 1880 helix: 1.08 (0.14), residues: 1310 sheet: None (None), residues: 0 loop : -0.09 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 93 HIS 0.002 0.001 HIS D 267 PHE 0.019 0.002 PHE A 188 TYR 0.020 0.002 TYR A 97 ARG 0.004 0.001 ARG E 125 Details of bonding type rmsd hydrogen bonds : bond 0.06915 ( 981) hydrogen bonds : angle 4.56664 ( 2815) covalent geometry : bond 0.00543 (15905) covalent geometry : angle 0.58486 (21605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.772 Fit side-chains REVERT: D 13 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.6704 (ptp90) REVERT: D 75 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6951 (pp) REVERT: D 172 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: D 356 ARG cc_start: 0.4835 (OUTLIER) cc_final: 0.4348 (ptm160) REVERT: E 13 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.6736 (ptp90) REVERT: E 37 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (mp) REVERT: E 172 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: E 175 ASN cc_start: 0.8871 (t0) cc_final: 0.8503 (m-40) REVERT: E 356 ARG cc_start: 0.4928 (OUTLIER) cc_final: 0.4401 (ptm160) REVERT: C 13 ARG cc_start: 0.7207 (ptp90) cc_final: 0.6913 (ptp90) REVERT: C 172 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: C 356 ARG cc_start: 0.4843 (OUTLIER) cc_final: 0.4413 (ptm160) REVERT: A 13 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.6776 (ptp90) REVERT: A 172 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: A 356 ARG cc_start: 0.4898 (OUTLIER) cc_final: 0.4393 (ptm160) REVERT: B 13 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6547 (ptp90) REVERT: B 172 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: B 356 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.4433 (ptm160) outliers start: 29 outliers final: 11 residues processed: 190 average time/residue: 1.8588 time to fit residues: 380.0911 Evaluate side-chains 197 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.090263 restraints weight = 44315.599| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.34 r_work: 0.2895 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15905 Z= 0.130 Angle : 0.487 5.668 21605 Z= 0.272 Chirality : 0.037 0.150 2350 Planarity : 0.003 0.040 2725 Dihedral : 4.195 17.018 2135 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.52 % Allowed : 10.85 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.18), residues: 1880 helix: 1.33 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.09 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 93 HIS 0.002 0.001 HIS D 115 PHE 0.025 0.001 PHE C 80 TYR 0.013 0.001 TYR A 97 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 981) hydrogen bonds : angle 4.38614 ( 2815) covalent geometry : bond 0.00262 (15905) covalent geometry : angle 0.48723 (21605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 1.639 Fit side-chains REVERT: D 13 ARG cc_start: 0.7508 (mtp-110) cc_final: 0.6665 (ptp90) REVERT: D 75 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6845 (pp) REVERT: D 172 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: D 356 ARG cc_start: 0.4638 (OUTLIER) cc_final: 0.4261 (ptm160) REVERT: E 13 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6655 (ptp90) REVERT: E 175 ASN cc_start: 0.8813 (t0) cc_final: 0.8443 (m-40) REVERT: E 356 ARG cc_start: 0.4828 (OUTLIER) cc_final: 0.4317 (ptm160) REVERT: C 13 ARG cc_start: 0.7169 (ptp90) cc_final: 0.6950 (ptp90) REVERT: C 44 MET cc_start: 0.8893 (mmt) cc_final: 0.8680 (mmt) REVERT: C 172 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: C 356 ARG cc_start: 0.4703 (OUTLIER) cc_final: 0.4356 (ptm160) REVERT: A 13 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6775 (ptp90) REVERT: A 172 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: A 356 ARG cc_start: 0.4786 (OUTLIER) cc_final: 0.4344 (ptm160) REVERT: B 13 ARG cc_start: 0.7428 (mtp-110) cc_final: 0.6474 (ptp90) REVERT: B 172 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: B 356 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.4338 (ptm160) REVERT: B 374 MET cc_start: 0.6404 (mtm) cc_final: 0.6116 (mtm) outliers start: 25 outliers final: 7 residues processed: 188 average time/residue: 1.7850 time to fit residues: 360.9287 Evaluate side-chains 191 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 113 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 173 ASN B 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.116958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.089637 restraints weight = 42224.019| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.30 r_work: 0.2886 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15905 Z= 0.145 Angle : 0.500 6.103 21605 Z= 0.278 Chirality : 0.038 0.151 2350 Planarity : 0.004 0.037 2725 Dihedral : 4.192 17.609 2135 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.22 % Allowed : 11.10 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.18), residues: 1880 helix: 1.34 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.07 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 93 HIS 0.002 0.001 HIS E 115 PHE 0.027 0.002 PHE E 80 TYR 0.016 0.001 TYR A 97 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05839 ( 981) hydrogen bonds : angle 4.40438 ( 2815) covalent geometry : bond 0.00304 (15905) covalent geometry : angle 0.49958 (21605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.700 Fit side-chains REVERT: D 13 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.6696 (ptp90) REVERT: D 75 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6867 (pp) REVERT: D 356 ARG cc_start: 0.4677 (OUTLIER) cc_final: 0.4308 (ptm160) REVERT: E 13 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.6626 (ptp90) REVERT: E 175 ASN cc_start: 0.8829 (t0) cc_final: 0.8454 (m-40) REVERT: E 356 ARG cc_start: 0.4780 (OUTLIER) cc_final: 0.4361 (ptm160) REVERT: C 13 ARG cc_start: 0.7189 (ptp90) cc_final: 0.6854 (ptp90) REVERT: C 172 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 356 ARG cc_start: 0.4742 (OUTLIER) cc_final: 0.4366 (ptm160) REVERT: A 13 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.6735 (ptp90) REVERT: A 172 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 356 ARG cc_start: 0.4767 (OUTLIER) cc_final: 0.4338 (ptm160) REVERT: B 13 ARG cc_start: 0.7450 (mtp-110) cc_final: 0.6514 (ptp90) REVERT: B 172 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: B 356 ARG cc_start: 0.4817 (OUTLIER) cc_final: 0.4325 (ptm160) outliers start: 20 outliers final: 8 residues processed: 189 average time/residue: 1.7852 time to fit residues: 363.6892 Evaluate side-chains 193 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 197 ARG Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 17 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN E 19 GLN A 19 GLN A 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.087967 restraints weight = 38958.693| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.20 r_work: 0.2862 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15905 Z= 0.193 Angle : 0.549 6.558 21605 Z= 0.304 Chirality : 0.040 0.157 2350 Planarity : 0.004 0.054 2725 Dihedral : 4.383 18.924 2135 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.46 % Allowed : 10.98 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.18), residues: 1880 helix: 1.22 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.05 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 93 HIS 0.002 0.001 HIS D 115 PHE 0.028 0.002 PHE C 80 TYR 0.019 0.002 TYR A 97 ARG 0.006 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.06485 ( 981) hydrogen bonds : angle 4.50379 ( 2815) covalent geometry : bond 0.00430 (15905) covalent geometry : angle 0.54895 (21605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 1.899 Fit side-chains REVERT: D 13 ARG cc_start: 0.7573 (mtp-110) cc_final: 0.6732 (ptp90) REVERT: D 75 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6980 (pp) REVERT: D 356 ARG cc_start: 0.4672 (OUTLIER) cc_final: 0.4302 (ptm160) REVERT: E 13 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.6711 (ptp90) REVERT: E 175 ASN cc_start: 0.8848 (t0) cc_final: 0.8482 (m-40) REVERT: E 356 ARG cc_start: 0.4802 (OUTLIER) cc_final: 0.4354 (ptm160) REVERT: C 13 ARG cc_start: 0.7161 (ptp90) cc_final: 0.6887 (ptp90) REVERT: C 172 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: C 356 ARG cc_start: 0.4718 (OUTLIER) cc_final: 0.4363 (ptm160) REVERT: A 13 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6761 (ptp90) REVERT: A 172 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 356 ARG cc_start: 0.4906 (OUTLIER) cc_final: 0.4378 (ptm160) REVERT: B 13 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.6580 (ptp90) REVERT: B 172 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: B 356 ARG cc_start: 0.4877 (OUTLIER) cc_final: 0.4360 (ptm160) outliers start: 24 outliers final: 8 residues processed: 188 average time/residue: 1.7777 time to fit residues: 359.7383 Evaluate side-chains 193 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN E 19 GLN A 19 GLN A 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.090990 restraints weight = 41396.403| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.28 r_work: 0.2908 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15905 Z= 0.126 Angle : 0.482 5.826 21605 Z= 0.269 Chirality : 0.036 0.150 2350 Planarity : 0.003 0.052 2725 Dihedral : 4.133 16.615 2135 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.98 % Allowed : 11.52 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.18), residues: 1880 helix: 1.37 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.07 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 93 HIS 0.002 0.001 HIS A 115 PHE 0.018 0.001 PHE A 80 TYR 0.014 0.001 TYR A 97 ARG 0.007 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05520 ( 981) hydrogen bonds : angle 4.37249 ( 2815) covalent geometry : bond 0.00250 (15905) covalent geometry : angle 0.48219 (21605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.786 Fit side-chains REVERT: D 13 ARG cc_start: 0.7551 (mtp-110) cc_final: 0.6636 (ptp90) REVERT: D 75 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6922 (pp) REVERT: D 356 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.4281 (ptm160) REVERT: E 13 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.6617 (ptp90) REVERT: E 175 ASN cc_start: 0.8804 (t0) cc_final: 0.8434 (m-40) REVERT: E 356 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4283 (ptm160) REVERT: C 13 ARG cc_start: 0.7175 (ptp90) cc_final: 0.6848 (ptp90) REVERT: C 172 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: C 356 ARG cc_start: 0.4735 (OUTLIER) cc_final: 0.4379 (ptm160) REVERT: A 13 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.6717 (ptp90) REVERT: A 172 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: A 356 ARG cc_start: 0.4766 (OUTLIER) cc_final: 0.4329 (ptm160) REVERT: B 13 ARG cc_start: 0.7452 (mtp-110) cc_final: 0.6534 (ptp90) REVERT: B 172 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: B 356 ARG cc_start: 0.4840 (OUTLIER) cc_final: 0.4332 (ptm160) REVERT: B 374 MET cc_start: 0.6383 (mtm) cc_final: 0.6068 (mtm) outliers start: 16 outliers final: 4 residues processed: 189 average time/residue: 1.7710 time to fit residues: 360.3039 Evaluate side-chains 189 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 165 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN E 19 GLN E 71 GLN A 19 GLN A 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091452 restraints weight = 37781.124| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.19 r_work: 0.2917 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15905 Z= 0.127 Angle : 0.480 6.225 21605 Z= 0.268 Chirality : 0.037 0.150 2350 Planarity : 0.003 0.051 2725 Dihedral : 4.068 16.654 2135 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.98 % Allowed : 11.52 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.18), residues: 1880 helix: 1.41 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.07 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 93 HIS 0.002 0.001 HIS D 115 PHE 0.032 0.002 PHE D 80 TYR 0.014 0.001 TYR A 97 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 981) hydrogen bonds : angle 4.35476 ( 2815) covalent geometry : bond 0.00256 (15905) covalent geometry : angle 0.47982 (21605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14586.10 seconds wall clock time: 251 minutes 20.97 seconds (15080.97 seconds total)