Starting phenix.real_space_refine on Fri Jun 13 20:25:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyk_47307/06_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_47307/06_2025/9dyk_47307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_2025/9dyk_47307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyk_47307/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.78, per 1000 atoms: 1.15 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: 3.99 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: 1.31 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: 4.51 Time building geometry restraints manager: 4.70 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: 129.320 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: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 47.020 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.980 ------------------------------------------------------------------------------- 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 : 1.823 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: 1.8121 time to fit residues: 353.4523 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 : 1.765 ------------------------------------------------------------------------------- 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 = 0.117420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.090357 restraints weight = 37331.092| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.18 r_work: 0.2899 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- 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 = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- 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 17.669 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 0.05944 ( 981) hydrogen bonds : angle 4.41722 ( 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 : 1.674 Fit side-chains REVERT: D 13 ARG cc_start: 0.7549 (mtp-110) cc_final: 0.6669 (ptp90) REVERT: D 172 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: D 356 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4395 (ptm160) REVERT: E 13 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.6676 (ptp90) REVERT: E 75 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6712 (mp) REVERT: E 172 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: C 13 ARG cc_start: 0.7209 (ptp90) cc_final: 0.6835 (ptp90) REVERT: C 172 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: A 172 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 172 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 356 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4338 (ptm160) outliers start: 25 outliers final: 9 residues processed: 194 average time/residue: 1.7509 time to fit residues: 366.2087 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 : 1.601 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 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: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.115237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087786 restraints weight = 41923.081| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.28 r_work: 0.2858 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0746 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= 0.192 Angle : 0.550 5.700 21605 Z= 0.305 Chirality : 0.041 0.158 2350 Planarity : 0.004 0.047 2725 Dihedral : 4.384 18.775 2135 Min Nonbonded Distance : 2.313 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: 1.21 (0.18), residues: 1880 helix: 1.24 (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 C 267 PHE 0.023 0.002 PHE D 80 TYR 0.017 0.002 TYR A 97 ARG 0.005 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.06528 ( 981) hydrogen bonds : angle 4.50208 ( 2815) covalent geometry : bond 0.00427 (15905) covalent geometry : angle 0.55041 (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 208 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.655 Fit side-chains REVERT: D 13 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.6684 (ptp90) REVERT: D 172 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: E 13 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.6702 (ptp90) REVERT: E 75 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6789 (mp) REVERT: E 172 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: E 356 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.4311 (ptm160) REVERT: E 375 GLN cc_start: 0.6869 (tp-100) cc_final: 0.6557 (tp40) REVERT: C 13 ARG cc_start: 0.7182 (ptp90) cc_final: 0.6838 (ptp90) REVERT: C 172 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: C 356 ARG cc_start: 0.4764 (OUTLIER) cc_final: 0.4409 (ptm160) REVERT: A 172 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: A 356 ARG cc_start: 0.4886 (OUTLIER) cc_final: 0.4396 (ptm160) REVERT: B 172 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6795 (mp0) outliers start: 26 outliers final: 11 residues processed: 194 average time/residue: 1.7462 time to fit residues: 364.6605 Evaluate side-chains 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.114395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087088 restraints weight = 41066.415| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.26 r_work: 0.2848 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15905 Z= 0.215 Angle : 0.570 5.833 21605 Z= 0.315 Chirality : 0.042 0.159 2350 Planarity : 0.004 0.039 2725 Dihedral : 4.488 19.353 2135 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.71 % Allowed : 10.55 % Favored : 87.74 % 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: 1.03 (0.18), residues: 1880 helix: 1.09 (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 C 93 HIS 0.002 0.001 HIS D 267 PHE 0.018 0.002 PHE B 188 TYR 0.018 0.002 TYR E 97 ARG 0.003 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.06760 ( 981) hydrogen bonds : angle 4.55240 ( 2815) covalent geometry : bond 0.00487 (15905) covalent geometry : angle 0.56999 (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 205 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.938 Fit side-chains REVERT: D 13 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.6683 (ptp90) REVERT: D 172 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: D 356 ARG cc_start: 0.4811 (OUTLIER) cc_final: 0.4338 (ptm160) REVERT: E 13 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.6725 (ptp90) REVERT: E 75 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6835 (mp) REVERT: E 172 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: E 175 ASN cc_start: 0.8850 (t0) cc_final: 0.8477 (m-40) REVERT: E 356 ARG cc_start: 0.4871 (OUTLIER) cc_final: 0.4377 (ptm160) REVERT: E 375 GLN cc_start: 0.6845 (tp-100) cc_final: 0.6541 (tp40) REVERT: C 13 ARG cc_start: 0.7184 (ptp90) cc_final: 0.6860 (ptp90) REVERT: C 172 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: C 356 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.4396 (ptm160) REVERT: A 13 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.6834 (ptp90) REVERT: A 172 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: A 356 ARG cc_start: 0.4958 (OUTLIER) cc_final: 0.4428 (ptm160) REVERT: B 172 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: B 356 ARG cc_start: 0.4857 (OUTLIER) cc_final: 0.4311 (ptm160) outliers start: 28 outliers final: 11 residues processed: 192 average time/residue: 1.7911 time to fit residues: 370.4763 Evaluate side-chains 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0670 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 148 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.089785 restraints weight = 40876.619| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.26 r_work: 0.2889 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15905 Z= 0.141 Angle : 0.496 5.599 21605 Z= 0.278 Chirality : 0.037 0.152 2350 Planarity : 0.003 0.035 2725 Dihedral : 4.242 17.522 2135 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.71 % Allowed : 10.49 % Favored : 87.80 % 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: 1.26 (0.18), residues: 1880 helix: 1.30 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.06 (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 0.021 0.002 PHE E 80 TYR 0.014 0.001 TYR A 97 ARG 0.003 0.000 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 981) hydrogen bonds : angle 4.41443 ( 2815) covalent geometry : bond 0.00291 (15905) covalent geometry : angle 0.49637 (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 207 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.748 Fit side-chains REVERT: D 13 ARG cc_start: 0.7554 (mtp-110) cc_final: 0.6694 (ptp90) REVERT: D 75 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6871 (pp) REVERT: D 172 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: D 356 ARG cc_start: 0.4713 (OUTLIER) cc_final: 0.4322 (ptm160) REVERT: E 13 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6692 (ptp90) REVERT: E 75 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6835 (mp) REVERT: E 172 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: E 175 ASN cc_start: 0.8821 (t0) cc_final: 0.8447 (m-40) REVERT: E 356 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.4326 (ptm160) REVERT: C 13 ARG cc_start: 0.7105 (ptp90) cc_final: 0.6798 (ptp90) REVERT: C 172 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: C 356 ARG cc_start: 0.4778 (OUTLIER) cc_final: 0.4393 (ptm160) REVERT: A 13 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6788 (ptp90) REVERT: A 172 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 356 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.4366 (ptm160) REVERT: B 13 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.6454 (ptp90) REVERT: B 172 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: B 356 ARG cc_start: 0.4815 (OUTLIER) cc_final: 0.4334 (ptm160) outliers start: 28 outliers final: 9 residues processed: 192 average time/residue: 1.8063 time to fit residues: 373.0678 Evaluate side-chains 197 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 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 197 ARG 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 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 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: 5.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086302 restraints weight = 43302.513| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.30 r_work: 0.2834 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- 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 = 0.17 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 = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0953 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= 0.252 Angle : 0.594 6.418 21605 Z= 0.328 Chirality : 0.044 0.161 2350 Planarity : 0.005 0.042 2725 Dihedral : 4.542 19.812 2135 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.95 % Allowed : 10.24 % Favored : 87.80 % 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: 0.98 (0.18), residues: 1880 helix: 1.05 (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 0.017 0.002 TRP B 93 HIS 0.002 0.001 HIS B 226 PHE 0.020 0.003 PHE A 188 TYR 0.020 0.002 TYR A 97 ARG 0.004 0.001 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.07047 ( 981) hydrogen bonds : angle 4.59534 ( 2815) covalent geometry : bond 0.00579 (15905) covalent geometry : angle 0.59449 (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 210 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 1.648 Fit side-chains REVERT: D 13 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.6714 (ptp90) REVERT: D 75 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6970 (pp) REVERT: D 172 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: D 356 ARG cc_start: 0.4807 (OUTLIER) cc_final: 0.4335 (ptm160) REVERT: E 13 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.6755 (ptp90) REVERT: E 75 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6893 (mp) REVERT: E 172 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: E 356 ARG cc_start: 0.4936 (OUTLIER) cc_final: 0.4408 (ptm160) REVERT: C 13 ARG cc_start: 0.7205 (ptp90) cc_final: 0.6909 (ptp90) REVERT: C 172 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: C 356 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.4435 (ptm160) REVERT: A 13 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.6781 (ptp90) REVERT: A 172 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: A 356 ARG cc_start: 0.4939 (OUTLIER) cc_final: 0.4390 (ptm160) REVERT: B 165 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7880 (mtt90) REVERT: B 172 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: B 356 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.4445 (ptm160) outliers start: 32 outliers final: 12 residues processed: 192 average time/residue: 1.8320 time to fit residues: 378.4806 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 : 1.672 ------------------------------------------------------------------------------- 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 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 165 ARG 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: 0.9990 chunk 78 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.117665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.090345 restraints weight = 44085.870| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.34 r_work: 0.2897 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 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 = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0739 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= 0.129 Angle : 0.486 5.661 21605 Z= 0.272 Chirality : 0.037 0.151 2350 Planarity : 0.003 0.037 2725 Dihedral : 4.187 16.945 2135 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.40 % Allowed : 11.10 % 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: 1.29 (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 B 93 HIS 0.002 0.001 HIS A 115 PHE 0.023 0.002 PHE C 80 TYR 0.013 0.001 TYR A 97 ARG 0.003 0.000 ARG E 168 Details of bonding type rmsd hydrogen bonds : bond 0.05597 ( 981) hydrogen bonds : angle 4.38507 ( 2815) covalent geometry : bond 0.00257 (15905) covalent geometry : angle 0.48578 (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: 23 poor density : 178 time to evaluate : 1.641 Fit side-chains REVERT: D 13 ARG cc_start: 0.7526 (mtp-110) cc_final: 0.6672 (ptp90) REVERT: D 75 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6849 (pp) REVERT: D 172 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: D 356 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.4271 (ptm160) REVERT: E 13 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.6661 (ptp90) REVERT: E 175 ASN cc_start: 0.8810 (t0) cc_final: 0.8416 (m-40) REVERT: E 356 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.4323 (ptm160) REVERT: C 13 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6950 (ptp90) REVERT: C 172 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: C 356 ARG cc_start: 0.4702 (OUTLIER) cc_final: 0.4359 (ptm160) REVERT: A 13 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6765 (ptp90) REVERT: A 172 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: A 356 ARG cc_start: 0.4789 (OUTLIER) cc_final: 0.4348 (ptm160) REVERT: B 13 ARG cc_start: 0.7424 (mtp-110) cc_final: 0.6475 (ptp90) REVERT: B 172 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 356 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.4342 (ptm160) REVERT: B 374 MET cc_start: 0.6413 (mtm) cc_final: 0.6121 (mtm) outliers start: 23 outliers final: 8 residues processed: 189 average time/residue: 1.8230 time to fit residues: 370.8229 Evaluate side-chains 192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 78 VAL 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: 0.9990 chunk 18 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 0.0070 chunk 58 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091550 restraints weight = 42690.868| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.31 r_work: 0.2916 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15905 Z= 0.122 Angle : 0.472 5.965 21605 Z= 0.264 Chirality : 0.036 0.149 2350 Planarity : 0.003 0.034 2725 Dihedral : 4.045 16.119 2135 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.29 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: 1.40 (0.18), residues: 1880 helix: 1.43 (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 0.015 0.002 TRP B 93 HIS 0.002 0.001 HIS A 115 PHE 0.027 0.001 PHE A 283 TYR 0.014 0.001 TYR A 97 ARG 0.007 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05388 ( 981) hydrogen bonds : angle 4.34109 ( 2815) covalent geometry : bond 0.00240 (15905) covalent geometry : angle 0.47201 (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 200 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.763 Fit side-chains REVERT: D 13 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.6665 (ptp90) REVERT: D 75 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6881 (pp) REVERT: D 356 ARG cc_start: 0.4620 (OUTLIER) cc_final: 0.4258 (ptm160) REVERT: E 13 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.6637 (ptp90) REVERT: E 175 ASN cc_start: 0.8775 (t0) cc_final: 0.8378 (m-40) REVERT: E 356 ARG cc_start: 0.4735 (OUTLIER) cc_final: 0.4275 (ptm160) REVERT: C 13 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6832 (ptt90) REVERT: C 44 MET cc_start: 0.8900 (mmt) cc_final: 0.8678 (mmm) REVERT: C 172 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: C 356 ARG cc_start: 0.4745 (OUTLIER) cc_final: 0.4388 (ptm160) REVERT: A 13 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.6708 (ptp90) REVERT: A 172 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: A 356 ARG cc_start: 0.4767 (OUTLIER) cc_final: 0.4330 (ptm160) REVERT: B 13 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.6534 (ptp90) REVERT: B 172 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: B 356 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.4294 (ptm160) REVERT: B 374 MET cc_start: 0.6374 (mtm) cc_final: 0.6105 (mtm) outliers start: 20 outliers final: 7 residues processed: 189 average time/residue: 1.8981 time to fit residues: 386.3338 Evaluate side-chains 192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 17 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.115376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088187 restraints weight = 39044.876| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.22 r_work: 0.2867 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15905 Z= 0.188 Angle : 0.542 6.238 21605 Z= 0.300 Chirality : 0.040 0.157 2350 Planarity : 0.004 0.037 2725 Dihedral : 4.320 18.292 2135 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.22 % Allowed : 11.22 % 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: 1.25 (0.18), residues: 1880 helix: 1.29 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 93 HIS 0.002 0.001 HIS A 115 PHE 0.030 0.002 PHE C 80 TYR 0.018 0.002 TYR A 97 ARG 0.005 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.06394 ( 981) hydrogen bonds : angle 4.48294 ( 2815) covalent geometry : bond 0.00417 (15905) covalent geometry : angle 0.54152 (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: 20 poor density : 179 time to evaluate : 2.047 Fit side-chains REVERT: D 13 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.6739 (ptp90) REVERT: D 75 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6922 (pp) REVERT: D 356 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.4301 (ptm160) REVERT: E 13 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.6712 (ptp90) REVERT: E 175 ASN cc_start: 0.8848 (t0) cc_final: 0.8473 (m-40) REVERT: E 356 ARG cc_start: 0.4723 (OUTLIER) cc_final: 0.4322 (ptm160) REVERT: C 13 ARG cc_start: 0.7225 (ptp90) cc_final: 0.7025 (ptp90) REVERT: C 172 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 356 ARG cc_start: 0.4755 (OUTLIER) cc_final: 0.4367 (ptm160) REVERT: A 13 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.6772 (ptp90) REVERT: A 172 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: A 356 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.4373 (ptm160) REVERT: B 13 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6576 (ptp90) REVERT: B 172 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: B 356 ARG cc_start: 0.4847 (OUTLIER) cc_final: 0.4357 (ptm160) REVERT: B 374 MET cc_start: 0.6435 (mtm) cc_final: 0.6151 (mtm) outliers start: 20 outliers final: 8 residues processed: 190 average time/residue: 1.9148 time to fit residues: 391.6631 Evaluate side-chains 192 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 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 172 GLU 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: 0.6980 chunk 93 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN E 71 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 = 0.3402 r_free = 0.3402 target = 0.118468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091255 restraints weight = 41455.505| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.28 r_work: 0.2912 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 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 = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15905 Z= 0.124 Angle : 0.478 5.766 21605 Z= 0.267 Chirality : 0.036 0.149 2350 Planarity : 0.003 0.053 2725 Dihedral : 4.086 16.094 2135 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.10 % Allowed : 11.34 % 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: 1.39 (0.18), residues: 1880 helix: 1.42 (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 0.015 0.002 TRP B 93 HIS 0.002 0.001 HIS A 115 PHE 0.023 0.001 PHE A 283 TYR 0.013 0.001 TYR A 97 ARG 0.006 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.05440 ( 981) hydrogen bonds : angle 4.35780 ( 2815) covalent geometry : bond 0.00245 (15905) covalent geometry : angle 0.47805 (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 195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.713 Fit side-chains REVERT: D 13 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.6644 (ptp90) REVERT: D 75 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6883 (pp) REVERT: D 356 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.4247 (ptm160) REVERT: E 13 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.6641 (ptp90) REVERT: E 175 ASN cc_start: 0.8789 (t0) cc_final: 0.8417 (m-40) REVERT: E 356 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.4264 (ptm160) REVERT: C 13 ARG cc_start: 0.7170 (ptp90) cc_final: 0.6837 (ptp90) REVERT: C 44 MET cc_start: 0.8903 (mmt) cc_final: 0.8675 (mmt) REVERT: C 172 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: C 356 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.4389 (ptm160) REVERT: A 13 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.6705 (ptp90) REVERT: A 172 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: A 356 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4311 (ptm160) REVERT: B 13 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.6544 (ptp90) REVERT: B 172 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: B 356 ARG cc_start: 0.4796 (OUTLIER) cc_final: 0.4297 (ptm160) REVERT: B 374 MET cc_start: 0.6383 (mtm) cc_final: 0.6115 (mtm) outliers start: 18 outliers final: 7 residues processed: 187 average time/residue: 1.8195 time to fit residues: 366.0184 Evaluate side-chains 191 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 100 MET 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 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 37 LEU 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: 0.9990 chunk 7 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.118777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091877 restraints weight = 38017.594| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.20 r_work: 0.2923 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15905 Z= 0.124 Angle : 0.475 6.145 21605 Z= 0.266 Chirality : 0.036 0.149 2350 Planarity : 0.003 0.053 2725 Dihedral : 4.024 16.044 2135 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.98 % Allowed : 11.59 % Favored : 87.44 % 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: 1.44 (0.18), residues: 1880 helix: 1.47 (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 0.015 0.002 TRP B 93 HIS 0.002 0.001 HIS A 115 PHE 0.030 0.002 PHE E 80 TYR 0.014 0.001 TYR A 97 ARG 0.007 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 981) hydrogen bonds : angle 4.33043 ( 2815) covalent geometry : bond 0.00247 (15905) covalent geometry : angle 0.47522 (21605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15318.84 seconds wall clock time: 264 minutes 26.54 seconds (15866.54 seconds total)