Starting phenix.real_space_refine on Fri Jul 3 17:53:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyk_47307/07_2026/9dyk_47307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyk_47307/07_2026/9dyk_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dyk_47307/07_2026/9dyk_47307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyk_47307/07_2026/9dyk_47307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyk_47307/07_2026/9dyk_47307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyk_47307/07_2026/9dyk_47307.map" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.115 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 6.49, per 1000 atoms: 0.42 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: 1.49 Conformation dependent library (CDL) restraints added in 1.1 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: 0.29 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: 2.56 Time building geometry restraints manager: 1.92 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 501)) selection = (chain 'B' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 501)) selection = (chain 'C' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 501)) selection = (chain 'D' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 501)) selection = (chain 'E' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 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: 6.040 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.600 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG C 13 TYR 0.014 0.001 TYR B 284 PHE 0.023 0.001 PHE E 80 TRP 0.014 0.002 TRP D 93 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (15905) covalent geometry : angle 0.52639 / 0.30 (21605) hydrogen bonds : bond 0.07653 / 5.06 ( 981) hydrogen bonds : angle 4.38847 / 3.23 ( 2815) *********************** 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 : 0.598 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: 0.7478 time to fit residues: 146.0642 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 : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3423 r_free = 0.3423 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093076 restraints weight = 42927.105| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.31 r_work: 0.2937 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 15905 Z= 0.124 Angle : 0.477 5.414 21605 Z= 0.267 Chirality : 0.036 0.147 2350 Planarity : 0.003 0.027 2725 Dihedral : 4.032 16.256 2135 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.40 % Allowed : 10.00 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.18), residues: 1880 helix: 1.45 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.06 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.012 0.001 TYR A 97 PHE 0.015 0.001 PHE A 171 TRP 0.013 0.001 TRP D 93 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (15905) covalent geometry : angle 0.47705 / 0.27 (21605) hydrogen bonds : bond 0.05371 / 3.53 ( 981) hydrogen bonds : angle 4.32330 / 3.19 ( 2815) *********************** 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 214 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.546 Fit side-chains REVERT: D 13 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.6636 (ptp90) REVERT: D 301 ASP cc_start: 0.8828 (m-30) cc_final: 0.8219 (m-30) REVERT: D 356 ARG cc_start: 0.4663 (OUTLIER) cc_final: 0.4370 (ptm160) REVERT: E 13 ARG cc_start: 0.7491 (mtm-85) cc_final: 0.6611 (ptp90) REVERT: E 168 ARG cc_start: 0.8465 (tmt90) cc_final: 0.8175 (tmt90) REVERT: E 172 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: E 301 ASP cc_start: 0.8741 (m-30) cc_final: 0.8138 (m-30) REVERT: C 13 ARG cc_start: 0.7120 (ptp90) cc_final: 0.6730 (ptp90) REVERT: C 356 ARG cc_start: 0.4680 (OUTLIER) cc_final: 0.4252 (ptm160) REVERT: A 13 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.6738 (ptp90) REVERT: A 172 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 356 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4302 (ptm160) REVERT: B 13 ARG cc_start: 0.7384 (mtp-110) cc_final: 0.6425 (ptp90) REVERT: B 301 ASP cc_start: 0.8665 (m-30) cc_final: 0.8412 (m-30) REVERT: B 356 ARG cc_start: 0.4776 (OUTLIER) cc_final: 0.4318 (ptm160) outliers start: 23 outliers final: 7 residues processed: 202 average time/residue: 0.7532 time to fit residues: 164.5307 Evaluate side-chains 195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 172 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET 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 356 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 158 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN C 173 ASN 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 = 0.3426 r_free = 0.3426 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092721 restraints weight = 50512.974| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.49 r_work: 0.2930 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15905 Z= 0.119 Angle : 0.465 5.465 21605 Z= 0.260 Chirality : 0.036 0.149 2350 Planarity : 0.003 0.049 2725 Dihedral : 3.949 15.770 2135 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.40 % Allowed : 10.43 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 1880 helix: 1.48 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.09 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 168 TYR 0.012 0.001 TYR A 97 PHE 0.022 0.001 PHE C 80 TRP 0.013 0.001 TRP B 93 HIS 0.001 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (15905) covalent geometry : angle 0.46462 / 0.26 (21605) hydrogen bonds : bond 0.05311 / 3.49 ( 981) hydrogen bonds : angle 4.29254 / 3.17 ( 2815) *********************** 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 211 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.511 Fit side-chains REVERT: D 13 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.6674 (ptp90) REVERT: D 172 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: D 301 ASP cc_start: 0.8815 (m-30) cc_final: 0.8138 (m-30) REVERT: D 356 ARG cc_start: 0.4590 (OUTLIER) cc_final: 0.4245 (ptm160) REVERT: E 13 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.6632 (ptp90) REVERT: E 301 ASP cc_start: 0.8691 (m-30) cc_final: 0.8475 (m-30) REVERT: E 356 ARG cc_start: 0.4714 (OUTLIER) cc_final: 0.4300 (ptm160) REVERT: E 375 GLN cc_start: 0.6911 (tp-100) cc_final: 0.6520 (tp40) REVERT: C 13 ARG cc_start: 0.7194 (ptp90) cc_final: 0.6833 (ptp90) REVERT: C 172 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 13 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.6722 (ptp90) REVERT: A 172 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: B 13 ARG cc_start: 0.7410 (mtp-110) cc_final: 0.6445 (ptp90) REVERT: B 172 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: B 301 ASP cc_start: 0.8687 (m-30) cc_final: 0.8053 (m-30) REVERT: B 356 ARG cc_start: 0.4669 (OUTLIER) cc_final: 0.4242 (ptm160) outliers start: 23 outliers final: 7 residues processed: 200 average time/residue: 0.7436 time to fit residues: 160.8251 Evaluate side-chains 194 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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 172 GLU Chi-restraints excluded: chain B residue 356 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.4980 chunk 147 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN C 173 ASN 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 = 0.3390 r_free = 0.3390 target = 0.117631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089854 restraints weight = 48958.066| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.44 r_work: 0.2888 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15905 Z= 0.151 Angle : 0.502 5.751 21605 Z= 0.280 Chirality : 0.038 0.151 2350 Planarity : 0.004 0.048 2725 Dihedral : 4.114 16.984 2135 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.46 % Allowed : 10.98 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 1880 helix: 1.37 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.08 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.015 0.001 TYR A 97 PHE 0.018 0.002 PHE A 283 TRP 0.014 0.002 TRP D 93 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (15905) covalent geometry : angle 0.50193 / 0.28 (21605) hydrogen bonds : bond 0.05914 / 3.88 ( 981) hydrogen bonds : angle 4.38721 / 3.24 ( 2815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.632 Fit side-chains REVERT: D 13 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.6671 (ptp90) REVERT: D 172 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: D 301 ASP cc_start: 0.8887 (m-30) cc_final: 0.8267 (m-30) REVERT: E 13 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6646 (ptp90) REVERT: E 37 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8191 (mp) REVERT: E 172 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: E 301 ASP cc_start: 0.8803 (m-30) cc_final: 0.8557 (m-30) REVERT: E 356 ARG cc_start: 0.4731 (OUTLIER) cc_final: 0.4293 (ptm160) REVERT: C 13 ARG cc_start: 0.7104 (ptp90) cc_final: 0.6839 (ptp90) REVERT: C 172 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: C 356 ARG cc_start: 0.4718 (OUTLIER) cc_final: 0.4320 (ptm160) REVERT: A 13 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6743 (ptp90) REVERT: A 172 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 356 ARG cc_start: 0.4823 (OUTLIER) cc_final: 0.4376 (ptm160) REVERT: B 13 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.6461 (ptp90) REVERT: B 172 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: B 301 ASP cc_start: 0.8779 (m-30) cc_final: 0.8185 (m-30) REVERT: B 356 ARG cc_start: 0.4677 (OUTLIER) cc_final: 0.4240 (ptm160) outliers start: 24 outliers final: 10 residues processed: 195 average time/residue: 0.7875 time to fit residues: 165.6879 Evaluate side-chains 198 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 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 177 optimal weight: 0.0050 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3431 r_free = 0.3431 target = 0.120821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093588 restraints weight = 42701.617| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.31 r_work: 0.2946 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0698 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= 0.116 Angle : 0.458 5.550 21605 Z= 0.256 Chirality : 0.036 0.148 2350 Planarity : 0.003 0.038 2725 Dihedral : 3.917 15.292 2135 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.28 % Allowed : 11.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.18), residues: 1880 helix: 1.46 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.11 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.012 0.001 TYR A 97 PHE 0.021 0.001 PHE D 80 TRP 0.014 0.001 TRP C 93 HIS 0.001 0.000 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (15905) covalent geometry : angle 0.45850 / 0.26 (21605) hydrogen bonds : bond 0.05245 / 3.45 ( 981) hydrogen bonds : angle 4.28969 / 3.17 ( 2815) *********************** 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 210 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.617 Fit side-chains REVERT: D 13 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.6632 (ptp90) REVERT: D 75 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6791 (pp) REVERT: D 172 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: D 356 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.4222 (ptm160) REVERT: E 13 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.6592 (ptp90) REVERT: E 301 ASP cc_start: 0.8653 (m-30) cc_final: 0.8416 (m-30) REVERT: E 356 ARG cc_start: 0.4678 (OUTLIER) cc_final: 0.4260 (ptm160) REVERT: C 13 ARG cc_start: 0.7096 (ptp90) cc_final: 0.6749 (ptt90) REVERT: C 172 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: C 356 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.4174 (ptm160) REVERT: A 13 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.6679 (ptp90) REVERT: A 172 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: A 356 ARG cc_start: 0.4759 (OUTLIER) cc_final: 0.4329 (ptm160) REVERT: B 13 ARG cc_start: 0.7380 (mtp-110) cc_final: 0.6445 (ptp90) REVERT: B 172 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: B 301 ASP cc_start: 0.8635 (m-30) cc_final: 0.8029 (m-30) REVERT: B 356 ARG cc_start: 0.4641 (OUTLIER) cc_final: 0.4216 (ptm160) outliers start: 21 outliers final: 6 residues processed: 202 average time/residue: 0.8092 time to fit residues: 176.2007 Evaluate side-chains 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 183 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN C 173 ASN 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 = 0.3428 r_free = 0.3428 target = 0.120518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093894 restraints weight = 35071.890| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.12 r_work: 0.2956 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15905 Z= 0.119 Angle : 0.461 5.598 21605 Z= 0.258 Chirality : 0.036 0.150 2350 Planarity : 0.003 0.048 2725 Dihedral : 3.906 15.281 2135 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.52 % Allowed : 10.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 1880 helix: 1.48 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.10 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 168 TYR 0.013 0.001 TYR A 97 PHE 0.016 0.001 PHE A 80 TRP 0.013 0.001 TRP C 93 HIS 0.002 0.000 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (15905) covalent geometry : angle 0.46070 / 0.26 (21605) hydrogen bonds : bond 0.05283 / 3.47 ( 981) hydrogen bonds : angle 4.29113 / 3.17 ( 2815) *********************** 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: 25 poor density : 185 time to evaluate : 0.583 Fit side-chains REVERT: D 13 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.6691 (ptp90) REVERT: D 75 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6896 (pp) REVERT: D 172 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: D 301 ASP cc_start: 0.8979 (m-30) cc_final: 0.8492 (m-30) REVERT: D 356 ARG cc_start: 0.4453 (OUTLIER) cc_final: 0.4186 (ptm160) REVERT: E 13 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.6618 (ptp90) REVERT: E 37 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8203 (mp) REVERT: E 301 ASP cc_start: 0.8677 (m-30) cc_final: 0.8436 (m-30) REVERT: E 356 ARG cc_start: 0.4672 (OUTLIER) cc_final: 0.4245 (ptm160) REVERT: C 13 ARG cc_start: 0.7121 (ptp90) cc_final: 0.6774 (ptt90) REVERT: C 172 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: C 356 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.4153 (ptm160) REVERT: A 13 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.6681 (ptp90) REVERT: A 172 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: A 356 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.4318 (ptm160) REVERT: B 13 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.6470 (ptp90) REVERT: B 172 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: B 356 ARG cc_start: 0.4626 (OUTLIER) cc_final: 0.4207 (ptm160) outliers start: 25 outliers final: 5 residues processed: 199 average time/residue: 0.7644 time to fit residues: 164.4405 Evaluate side-chains 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 11 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN C 173 ASN 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 = 0.3412 r_free = 0.3412 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091155 restraints weight = 51518.765| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.53 r_work: 0.2906 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15905 Z= 0.134 Angle : 0.479 5.939 21605 Z= 0.268 Chirality : 0.037 0.150 2350 Planarity : 0.003 0.043 2725 Dihedral : 3.992 16.048 2135 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.28 % Allowed : 10.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.18), residues: 1880 helix: 1.43 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.07 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.015 0.001 TYR A 97 PHE 0.025 0.002 PHE D 80 TRP 0.014 0.001 TRP B 93 HIS 0.001 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (15905) covalent geometry : angle 0.47910 / 0.27 (21605) hydrogen bonds : bond 0.05582 / 3.67 ( 981) hydrogen bonds : angle 4.33446 / 3.20 ( 2815) *********************** 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 200 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.600 Fit side-chains REVERT: D 13 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.6735 (ptp90) REVERT: D 75 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6911 (pp) REVERT: D 172 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: D 301 ASP cc_start: 0.9047 (m-30) cc_final: 0.8562 (m-30) REVERT: D 356 ARG cc_start: 0.4450 (OUTLIER) cc_final: 0.4173 (ptm160) REVERT: E 13 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.6661 (ptp90) REVERT: E 175 ASN cc_start: 0.8802 (t0) cc_final: 0.8414 (m-40) REVERT: E 301 ASP cc_start: 0.8754 (m-30) cc_final: 0.8503 (m-30) REVERT: E 356 ARG cc_start: 0.4672 (OUTLIER) cc_final: 0.4199 (ptm160) REVERT: C 13 ARG cc_start: 0.7171 (ptp90) cc_final: 0.6805 (ptt90) REVERT: C 172 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: C 356 ARG cc_start: 0.4597 (OUTLIER) cc_final: 0.4138 (ptm160) REVERT: A 13 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6735 (ptp90) REVERT: A 172 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 356 ARG cc_start: 0.4801 (OUTLIER) cc_final: 0.4344 (ptm160) REVERT: B 13 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.6611 (ptp90) REVERT: B 172 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: B 301 ASP cc_start: 0.8926 (m-30) cc_final: 0.8388 (m-30) REVERT: B 356 ARG cc_start: 0.4638 (OUTLIER) cc_final: 0.4200 (ptm160) outliers start: 20 outliers final: 7 residues processed: 193 average time/residue: 0.7473 time to fit residues: 155.5685 Evaluate side-chains 197 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 100 MET 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 10 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN E 19 GLN C 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.087172 restraints weight = 53348.043| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.54 r_work: 0.2843 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0893 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= 0.214 Angle : 0.565 6.436 21605 Z= 0.313 Chirality : 0.042 0.157 2350 Planarity : 0.004 0.041 2725 Dihedral : 4.353 18.334 2135 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.28 % Allowed : 10.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 1880 helix: 1.23 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.12 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 8 TYR 0.020 0.002 TYR A 97 PHE 0.020 0.002 PHE A 80 TRP 0.014 0.002 TRP D 93 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (15905) covalent geometry : angle 0.56474 / 0.31 (21605) hydrogen bonds : bond 0.06693 / 4.40 ( 981) hydrogen bonds : angle 4.52445 / 3.34 ( 2815) *********************** 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 201 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.369 Fit side-chains REVERT: D 13 ARG cc_start: 0.7617 (mtp-110) cc_final: 0.6727 (ptp90) REVERT: D 75 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7085 (pp) REVERT: D 172 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: D 356 ARG cc_start: 0.4575 (OUTLIER) cc_final: 0.4231 (ptm160) REVERT: E 13 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.6738 (ptp90) REVERT: E 356 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.4345 (ptm160) REVERT: C 13 ARG cc_start: 0.7180 (ptp90) cc_final: 0.6975 (ptp90) REVERT: C 172 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: C 356 ARG cc_start: 0.4763 (OUTLIER) cc_final: 0.4377 (ptm160) REVERT: A 13 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.6737 (ptp90) REVERT: A 172 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: A 356 ARG cc_start: 0.4811 (OUTLIER) cc_final: 0.4338 (ptm160) REVERT: B 13 ARG cc_start: 0.7492 (mtp-110) cc_final: 0.6570 (ptp90) REVERT: B 172 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6896 (mp0) outliers start: 20 outliers final: 9 residues processed: 191 average time/residue: 0.7475 time to fit residues: 153.6774 Evaluate side-chains 197 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 100 MET 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 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 100 MET Chi-restraints excluded: chain B residue 172 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3396 r_free = 0.3396 target = 0.117943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.090009 restraints weight = 50365.111| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.50 r_work: 0.2889 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15905 Z= 0.144 Angle : 0.495 5.709 21605 Z= 0.277 Chirality : 0.037 0.153 2350 Planarity : 0.004 0.053 2725 Dihedral : 4.155 16.954 2135 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.28 % Allowed : 11.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 1880 helix: 1.31 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.14 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.014 0.001 TYR A 97 PHE 0.025 0.002 PHE C 80 TRP 0.014 0.002 TRP D 93 HIS 0.001 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (15905) covalent geometry : angle 0.49492 / 0.28 (21605) hydrogen bonds : bond 0.05791 / 3.80 ( 981) hydrogen bonds : angle 4.40218 / 3.25 ( 2815) *********************** 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 200 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.406 Fit side-chains REVERT: D 13 ARG cc_start: 0.7569 (mtp-110) cc_final: 0.6682 (ptp90) REVERT: D 75 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7081 (pp) REVERT: D 172 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: D 356 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.4200 (ptm160) REVERT: E 13 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.6694 (ptp90) REVERT: E 175 ASN cc_start: 0.8807 (t0) cc_final: 0.8413 (m-40) REVERT: E 356 ARG cc_start: 0.4724 (OUTLIER) cc_final: 0.4284 (ptm160) REVERT: C 13 ARG cc_start: 0.7172 (ptp90) cc_final: 0.6955 (ptp90) REVERT: C 172 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 356 ARG cc_start: 0.4679 (OUTLIER) cc_final: 0.4324 (ptm160) REVERT: A 13 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.6688 (ptp90) REVERT: A 172 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 356 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4338 (ptm160) REVERT: B 13 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.6546 (ptp90) REVERT: B 172 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: B 301 ASP cc_start: 0.8917 (m-30) cc_final: 0.8319 (m-30) REVERT: B 356 ARG cc_start: 0.4787 (OUTLIER) cc_final: 0.4283 (ptm160) outliers start: 20 outliers final: 7 residues processed: 191 average time/residue: 0.7964 time to fit residues: 163.9191 Evaluate side-chains 194 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 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 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 99 optimal weight: 0.1980 chunk 84 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3412 r_free = 0.3412 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091858 restraints weight = 41746.133| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.29 r_work: 0.2921 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15905 Z= 0.129 Angle : 0.477 5.641 21605 Z= 0.267 Chirality : 0.037 0.150 2350 Planarity : 0.003 0.061 2725 Dihedral : 4.038 16.156 2135 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.10 % Allowed : 11.52 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.18), residues: 1880 helix: 1.36 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.09 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 168 TYR 0.014 0.001 TYR A 97 PHE 0.018 0.002 PHE A 80 TRP 0.015 0.001 TRP D 93 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (15905) covalent geometry : angle 0.47710 / 0.27 (21605) hydrogen bonds : bond 0.05498 / 3.61 ( 981) hydrogen bonds : angle 4.35837 / 3.22 ( 2815) ********************** 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 199 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.404 Fit side-chains REVERT: D 13 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.6657 (ptp90) REVERT: D 75 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6991 (pp) REVERT: D 172 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: D 301 ASP cc_start: 0.8973 (m-30) cc_final: 0.8519 (m-30) REVERT: D 356 ARG cc_start: 0.4489 (OUTLIER) cc_final: 0.4204 (ptm160) REVERT: E 13 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.6587 (ptp90) REVERT: E 175 ASN cc_start: 0.8781 (t0) cc_final: 0.8386 (m-40) REVERT: E 301 ASP cc_start: 0.8726 (m-30) cc_final: 0.8458 (m-30) REVERT: E 356 ARG cc_start: 0.4715 (OUTLIER) cc_final: 0.4222 (ptm160) REVERT: C 13 ARG cc_start: 0.7115 (ptp90) cc_final: 0.6780 (ptt90) REVERT: C 172 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 356 ARG cc_start: 0.4663 (OUTLIER) cc_final: 0.4304 (ptm160) REVERT: A 13 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.6654 (ptp90) REVERT: A 172 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: A 356 ARG cc_start: 0.4752 (OUTLIER) cc_final: 0.4283 (ptm160) REVERT: B 13 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.6624 (ptp90) REVERT: B 172 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: B 301 ASP cc_start: 0.8870 (m-30) cc_final: 0.8371 (m-30) REVERT: B 356 ARG cc_start: 0.4674 (OUTLIER) cc_final: 0.4246 (ptm160) outliers start: 17 outliers final: 6 residues processed: 193 average time/residue: 0.7740 time to fit residues: 160.9602 Evaluate side-chains 195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 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 36 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 148 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 164 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 ASN E 19 GLN A 19 GLN A 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091687 restraints weight = 40629.916| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.26 r_work: 0.2919 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15905 Z= 0.134 Angle : 0.483 6.191 21605 Z= 0.270 Chirality : 0.037 0.149 2350 Planarity : 0.004 0.060 2725 Dihedral : 4.044 16.333 2135 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.16 % Allowed : 11.46 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.18), residues: 1880 helix: 1.37 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.09 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 168 TYR 0.015 0.001 TYR E 97 PHE 0.034 0.002 PHE D 80 TRP 0.015 0.001 TRP C 93 HIS 0.002 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (15905) covalent geometry : angle 0.48303 / 0.27 (21605) hydrogen bonds : bond 0.05578 / 3.67 ( 981) hydrogen bonds : angle 4.36353 / 3.22 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6779.92 seconds wall clock time: 116 minutes 0.24 seconds (6960.24 seconds total)