Starting phenix.real_space_refine on Thu Sep 18 08:32:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyk_47307/09_2025/9dyk_47307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyk_47307/09_2025/9dyk_47307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dyk_47307/09_2025/9dyk_47307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyk_47307/09_2025/9dyk_47307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyk_47307/09_2025/9dyk_47307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyk_47307/09_2025/9dyk_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-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.14, per 1000 atoms: 0.40 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: 1.40 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 2.53 Time building geometry restraints manager: 1.82 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 18.220 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15905 Z= 0.133 Angle : 0.526 7.049 21605 Z= 0.304 Chirality : 0.036 0.144 2350 Planarity : 0.003 0.032 2725 Dihedral : 14.111 89.927 5690 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.06 % Allowed : 10.43 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00249 (15905) covalent geometry : angle 0.52639 (21605) hydrogen bonds : bond 0.07653 ( 981) hydrogen bonds : angle 4.38847 ( 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 : 0.641 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: 0.9262 time to fit residues: 179.9547 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 : 0.412 ------------------------------------------------------------------------------- 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: 1.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091606 restraints weight = 42618.423| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.32 r_work: 0.2917 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15905 Z= 0.132 Angle : 0.489 5.404 21605 Z= 0.273 Chirality : 0.037 0.146 2350 Planarity : 0.003 0.028 2725 Dihedral : 4.100 16.719 2135 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.65 % Allowed : 9.82 % Favored : 88.54 % 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 aren not related in a simple way. whole: 1.42 (0.18), residues: 1880 helix: 1.44 (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 0.006 0.000 ARG C 13 TYR 0.013 0.001 TYR A 97 PHE 0.015 0.002 PHE A 171 TRP 0.013 0.002 TRP D 93 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00267 (15905) covalent geometry : angle 0.48858 (21605) hydrogen bonds : bond 0.05575 ( 981) hydrogen bonds : angle 4.35963 ( 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 211 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.640 Fit side-chains REVERT: D 13 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.6659 (ptp90) REVERT: D 172 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: D 356 ARG cc_start: 0.4661 (OUTLIER) cc_final: 0.4397 (ptm160) REVERT: E 13 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.6645 (ptp90) REVERT: E 172 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: C 13 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6798 (ptp90) REVERT: C 356 ARG cc_start: 0.4699 (OUTLIER) cc_final: 0.4252 (ptm160) REVERT: A 13 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.6751 (ptp90) REVERT: A 172 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: A 356 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4312 (ptm160) REVERT: B 13 ARG cc_start: 0.7403 (mtp-110) cc_final: 0.6439 (ptp90) REVERT: B 356 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.4326 (ptm160) outliers start: 27 outliers final: 8 residues processed: 197 average time/residue: 0.9092 time to fit residues: 192.3987 Evaluate side-chains 191 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 78 VAL 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: 2.9990 chunk 108 optimal weight: 0.0370 chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 0.2980 chunk 113 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN C 173 ASN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093715 restraints weight = 50317.420| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.51 r_work: 0.2945 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 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 = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 15905 Z= 0.110 Angle : 0.453 5.531 21605 Z= 0.253 Chirality : 0.035 0.148 2350 Planarity : 0.003 0.047 2725 Dihedral : 3.895 15.448 2135 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.04 % Allowed : 10.79 % 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 aren not related in a simple way. whole: 1.52 (0.18), residues: 1880 helix: 1.54 (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 0.006 0.000 ARG B 168 TYR 0.011 0.001 TYR A 97 PHE 0.022 0.001 PHE D 80 TRP 0.013 0.001 TRP B 93 HIS 0.001 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00206 (15905) covalent geometry : angle 0.45309 (21605) hydrogen bonds : bond 0.05060 ( 981) hydrogen bonds : angle 4.26227 ( 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 209 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.738 Fit side-chains REVERT: D 13 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.6657 (ptp90) REVERT: D 356 ARG cc_start: 0.4572 (OUTLIER) cc_final: 0.4241 (ptm160) REVERT: E 13 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.6631 (ptp90) REVERT: E 172 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: E 356 ARG cc_start: 0.4705 (OUTLIER) cc_final: 0.4298 (ptm160) REVERT: C 13 ARG cc_start: 0.7169 (ptp90) cc_final: 0.6876 (ptp90) REVERT: C 75 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7034 (pp) REVERT: C 172 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 13 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6752 (ptp90) REVERT: A 172 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: A 268 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.8008 (p0) REVERT: B 13 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.6419 (ptp90) REVERT: B 172 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 356 ARG cc_start: 0.4648 (OUTLIER) cc_final: 0.4233 (ptm160) outliers start: 17 outliers final: 3 residues processed: 199 average time/residue: 0.9142 time to fit residues: 195.5341 Evaluate side-chains 186 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 268 ASP 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: 6.9990 chunk 128 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN C 173 ASN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.087055 restraints weight = 41876.606| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.27 r_work: 0.2847 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15905 Z= 0.233 Angle : 0.582 6.147 21605 Z= 0.321 Chirality : 0.043 0.161 2350 Planarity : 0.005 0.042 2725 Dihedral : 4.413 18.640 2135 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.52 % Allowed : 11.04 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 1880 helix: 1.23 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.02 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 8 TYR 0.020 0.002 TYR A 97 PHE 0.020 0.003 PHE A 188 TRP 0.015 0.002 TRP D 93 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00530 (15905) covalent geometry : angle 0.58217 (21605) hydrogen bonds : bond 0.06893 ( 981) hydrogen bonds : angle 4.54516 ( 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 204 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.613 Fit side-chains REVERT: D 13 ARG cc_start: 0.7597 (mtp-110) cc_final: 0.6720 (ptp90) REVERT: D 155 ASP cc_start: 0.8908 (m-30) cc_final: 0.8688 (m-30) REVERT: D 172 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: E 13 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.6735 (ptp90) REVERT: E 37 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 172 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: E 356 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4357 (ptm160) REVERT: C 13 ARG cc_start: 0.7181 (ptp90) cc_final: 0.6852 (ptp90) REVERT: C 172 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 356 ARG cc_start: 0.4776 (OUTLIER) cc_final: 0.4406 (ptm160) REVERT: A 172 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: A 356 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.4382 (ptm160) REVERT: B 13 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.6527 (ptp90) REVERT: B 172 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.6912 (mp0) outliers start: 25 outliers final: 12 residues processed: 192 average time/residue: 0.8801 time to fit residues: 181.5552 Evaluate side-chains 194 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 172 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 177 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091286 restraints weight = 41846.053| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.30 r_work: 0.2912 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15905 Z= 0.122 Angle : 0.476 5.637 21605 Z= 0.267 Chirality : 0.036 0.149 2350 Planarity : 0.003 0.038 2725 Dihedral : 4.099 15.997 2135 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.40 % Allowed : 11.16 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.18), residues: 1880 helix: 1.43 (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 C 8 TYR 0.012 0.001 TYR A 97 PHE 0.023 0.001 PHE D 80 TRP 0.015 0.002 TRP C 93 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00240 (15905) covalent geometry : angle 0.47643 (21605) hydrogen bonds : bond 0.05495 ( 981) hydrogen bonds : angle 4.35829 ( 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 203 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.669 Fit side-chains REVERT: D 13 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.6676 (ptp90) REVERT: D 75 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6809 (pp) REVERT: D 172 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: D 356 ARG cc_start: 0.4615 (OUTLIER) cc_final: 0.4282 (ptm160) REVERT: E 13 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.6663 (ptp90) REVERT: E 172 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: E 175 ASN cc_start: 0.8777 (t0) cc_final: 0.8372 (m-40) REVERT: E 356 ARG cc_start: 0.4722 (OUTLIER) cc_final: 0.4277 (ptm160) REVERT: C 13 ARG cc_start: 0.7138 (ptp90) cc_final: 0.6887 (ptp90) REVERT: C 172 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: C 356 ARG cc_start: 0.4664 (OUTLIER) cc_final: 0.4295 (ptm160) REVERT: A 13 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.6799 (ptp90) REVERT: A 172 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: A 268 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (p0) REVERT: A 356 ARG cc_start: 0.4758 (OUTLIER) cc_final: 0.4319 (ptm160) REVERT: B 13 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.6480 (ptp90) REVERT: B 172 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 356 ARG cc_start: 0.4783 (OUTLIER) cc_final: 0.4298 (ptm160) outliers start: 23 outliers final: 6 residues processed: 194 average time/residue: 0.9216 time to fit residues: 191.8011 Evaluate side-chains 195 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 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 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 268 ASP 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: 3.9990 chunk 7 optimal weight: 0.9990 chunk 145 optimal weight: 0.0970 chunk 54 optimal weight: 0.0000 chunk 100 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 183 optimal weight: 0.0070 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096924 restraints weight = 34702.436| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.10 r_work: 0.3000 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0909 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= 0.104 Angle : 0.436 5.447 21605 Z= 0.243 Chirality : 0.035 0.149 2350 Planarity : 0.003 0.033 2725 Dihedral : 3.771 15.055 2135 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.16 % Allowed : 11.59 % Favored : 87.26 % 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 aren not related in a simple way. whole: 1.57 (0.18), residues: 1880 helix: 1.59 (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 0.006 0.000 ARG B 165 TYR 0.010 0.001 TYR A 97 PHE 0.023 0.001 PHE E 80 TRP 0.013 0.001 TRP C 93 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00189 (15905) covalent geometry : angle 0.43622 (21605) hydrogen bonds : bond 0.04732 ( 981) hydrogen bonds : angle 4.21952 ( 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 206 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.626 Fit side-chains REVERT: D 13 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.6633 (ptp90) REVERT: D 75 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6834 (pp) REVERT: D 356 ARG cc_start: 0.4402 (OUTLIER) cc_final: 0.4156 (ptm160) REVERT: E 13 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.6644 (ptp90) REVERT: E 175 ASN cc_start: 0.8696 (t0) cc_final: 0.8283 (m-40) REVERT: E 356 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4234 (ptm160) REVERT: C 13 ARG cc_start: 0.7052 (ptp90) cc_final: 0.6741 (ptt90) REVERT: C 356 ARG cc_start: 0.4588 (OUTLIER) cc_final: 0.4144 (ptm160) REVERT: A 13 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.6706 (ptp90) REVERT: A 172 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: A 356 ARG cc_start: 0.4725 (OUTLIER) cc_final: 0.4329 (ptm160) REVERT: B 13 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.6528 (ptp90) REVERT: B 356 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.4198 (ptm160) REVERT: B 374 MET cc_start: 0.6324 (mtm) cc_final: 0.6008 (mtm) outliers start: 19 outliers final: 2 residues processed: 197 average time/residue: 0.9223 time to fit residues: 195.0346 Evaluate side-chains 186 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG 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: 0.0980 chunk 92 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN E 71 GLN 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 = 0.3423 r_free = 0.3423 target = 0.120156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092302 restraints weight = 50807.650| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.51 r_work: 0.2923 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- 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 = 0.16 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 = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15905 Z= 0.122 Angle : 0.463 5.730 21605 Z= 0.258 Chirality : 0.036 0.150 2350 Planarity : 0.003 0.040 2725 Dihedral : 3.872 15.165 2135 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.10 % Allowed : 11.77 % Favored : 87.13 % 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 aren not related in a simple way. whole: 1.55 (0.18), residues: 1880 helix: 1.55 (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 0.007 0.000 ARG B 165 TYR 0.014 0.001 TYR A 97 PHE 0.029 0.001 PHE D 80 TRP 0.013 0.001 TRP B 93 HIS 0.002 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00245 (15905) covalent geometry : angle 0.46312 (21605) hydrogen bonds : bond 0.05270 ( 981) hydrogen bonds : angle 4.27650 ( 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 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.602 Fit side-chains REVERT: D 13 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.6701 (ptp90) REVERT: D 75 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6911 (pp) REVERT: D 356 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.4158 (ptm160) REVERT: E 13 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.6697 (ptp90) REVERT: E 37 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 175 ASN cc_start: 0.8757 (t0) cc_final: 0.8358 (m-40) REVERT: E 356 ARG cc_start: 0.4662 (OUTLIER) cc_final: 0.4190 (ptm160) REVERT: C 13 ARG cc_start: 0.7116 (ptp90) cc_final: 0.6767 (ptt90) REVERT: C 172 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: C 356 ARG cc_start: 0.4585 (OUTLIER) cc_final: 0.4134 (ptm160) REVERT: A 13 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.6767 (ptp90) REVERT: A 172 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: A 356 ARG cc_start: 0.4802 (OUTLIER) cc_final: 0.4347 (ptm160) REVERT: B 13 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.6631 (ptp90) REVERT: B 172 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: B 356 ARG cc_start: 0.4670 (OUTLIER) cc_final: 0.4201 (ptm160) outliers start: 18 outliers final: 5 residues processed: 189 average time/residue: 0.9296 time to fit residues: 188.3807 Evaluate side-chains 191 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain E residue 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 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: 0.7980 chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3376 r_free = 0.3376 target = 0.116379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088029 restraints weight = 54633.602| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.59 r_work: 0.2857 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15905 Z= 0.174 Angle : 0.526 6.361 21605 Z= 0.293 Chirality : 0.039 0.158 2350 Planarity : 0.004 0.043 2725 Dihedral : 4.198 17.268 2135 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.16 % Allowed : 11.65 % Favored : 87.20 % 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 aren not related in a simple way. whole: 1.35 (0.18), residues: 1880 helix: 1.36 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.01 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.018 0.002 TYR D 97 PHE 0.018 0.002 PHE A 80 TRP 0.014 0.002 TRP B 93 HIS 0.001 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00380 (15905) covalent geometry : angle 0.52601 (21605) hydrogen bonds : bond 0.06237 ( 981) hydrogen bonds : angle 4.44060 ( 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 196 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.604 Fit side-chains REVERT: D 13 ARG cc_start: 0.7621 (mtp-110) cc_final: 0.6724 (ptp90) REVERT: D 75 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6978 (pp) REVERT: D 172 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: D 356 ARG cc_start: 0.4527 (OUTLIER) cc_final: 0.4206 (ptm160) REVERT: E 13 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.6588 (ptp90) REVERT: E 175 ASN cc_start: 0.8866 (t0) cc_final: 0.8485 (m-40) REVERT: E 356 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.4243 (ptm160) REVERT: C 13 ARG cc_start: 0.7215 (ptp90) cc_final: 0.6882 (ptp90) REVERT: C 172 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: C 356 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4287 (ptm160) REVERT: A 13 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.6751 (ptp90) REVERT: A 172 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: A 356 ARG cc_start: 0.4843 (OUTLIER) cc_final: 0.4365 (ptm160) REVERT: B 13 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.6607 (ptp90) REVERT: B 172 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: B 356 ARG cc_start: 0.4701 (OUTLIER) cc_final: 0.4229 (ptm160) outliers start: 18 outliers final: 6 residues processed: 191 average time/residue: 0.9262 time to fit residues: 189.9092 Evaluate side-chains 193 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 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=1.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090438 restraints weight = 50664.454| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.51 r_work: 0.2895 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0792 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= 0.132 Angle : 0.483 5.888 21605 Z= 0.269 Chirality : 0.037 0.150 2350 Planarity : 0.003 0.037 2725 Dihedral : 4.062 16.115 2135 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.10 % Allowed : 11.77 % Favored : 87.13 % 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 aren not related in a simple way. whole: 1.40 (0.18), residues: 1880 helix: 1.42 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.05 (0.24), residues: 580 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 0.024 0.002 PHE C 80 TRP 0.014 0.001 TRP C 93 HIS 0.001 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00268 (15905) covalent geometry : angle 0.48250 (21605) hydrogen bonds : bond 0.05598 ( 981) hydrogen bonds : angle 4.35920 ( 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 194 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.584 Fit side-chains REVERT: D 13 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.6689 (ptp90) REVERT: D 75 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6989 (pp) REVERT: D 172 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: D 356 ARG cc_start: 0.4462 (OUTLIER) cc_final: 0.4170 (ptm160) REVERT: E 13 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.6530 (ptp90) REVERT: E 175 ASN cc_start: 0.8822 (t0) cc_final: 0.8449 (m-40) REVERT: E 356 ARG cc_start: 0.4652 (OUTLIER) cc_final: 0.4191 (ptm160) REVERT: C 13 ARG cc_start: 0.7180 (ptp90) cc_final: 0.6833 (ptt90) REVERT: C 172 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: C 356 ARG cc_start: 0.4642 (OUTLIER) cc_final: 0.4149 (ptm160) REVERT: A 13 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.6712 (ptp90) REVERT: A 172 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 356 ARG cc_start: 0.4794 (OUTLIER) cc_final: 0.4289 (ptm160) REVERT: B 13 ARG cc_start: 0.7495 (mtp-110) cc_final: 0.6614 (ptp90) REVERT: B 172 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: B 356 ARG cc_start: 0.4679 (OUTLIER) cc_final: 0.4218 (ptm160) outliers start: 17 outliers final: 5 residues processed: 189 average time/residue: 0.9044 time to fit residues: 183.1576 Evaluate side-chains 188 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091686 restraints weight = 41622.184| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.29 r_work: 0.2919 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0799 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= 0.126 Angle : 0.473 5.752 21605 Z= 0.265 Chirality : 0.036 0.149 2350 Planarity : 0.003 0.035 2725 Dihedral : 3.997 15.800 2135 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.04 % Allowed : 11.89 % Favored : 87.07 % 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 aren 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 0.007 0.000 ARG B 165 TYR 0.014 0.001 TYR A 97 PHE 0.024 0.001 PHE E 80 TRP 0.014 0.001 TRP C 93 HIS 0.002 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00254 (15905) covalent geometry : angle 0.47308 (21605) hydrogen bonds : bond 0.05440 ( 981) hydrogen bonds : angle 4.33926 ( 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 191 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.575 Fit side-chains REVERT: D 13 ARG cc_start: 0.7592 (mtp-110) cc_final: 0.6723 (ptp90) REVERT: D 172 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: D 356 ARG cc_start: 0.4408 (OUTLIER) cc_final: 0.4150 (ptm160) REVERT: E 13 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.6646 (ptp90) REVERT: E 175 ASN cc_start: 0.8806 (t0) cc_final: 0.8434 (m-40) REVERT: E 356 ARG cc_start: 0.4590 (OUTLIER) cc_final: 0.4146 (ptm160) REVERT: C 13 ARG cc_start: 0.7154 (ptp90) cc_final: 0.6818 (ptt90) REVERT: C 172 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 356 ARG cc_start: 0.4625 (OUTLIER) cc_final: 0.4157 (ptm160) REVERT: A 13 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.6715 (ptp90) REVERT: A 172 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: A 356 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.4312 (ptm160) REVERT: B 13 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.6647 (ptp90) REVERT: B 172 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: B 356 ARG cc_start: 0.4685 (OUTLIER) cc_final: 0.4220 (ptm160) outliers start: 16 outliers final: 5 residues processed: 187 average time/residue: 0.9100 time to fit residues: 182.3402 Evaluate side-chains 187 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 356 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 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 36 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 148 optimal weight: 0.0980 chunk 155 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN A 19 GLN A 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093048 restraints weight = 40769.945| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.27 r_work: 0.2940 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15905 Z= 0.116 Angle : 0.460 6.052 21605 Z= 0.257 Chirality : 0.036 0.148 2350 Planarity : 0.003 0.041 2725 Dihedral : 3.912 15.551 2135 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.04 % Allowed : 11.89 % Favored : 87.07 % 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 aren not related in a simple way. whole: 1.49 (0.18), residues: 1880 helix: 1.51 (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 0.006 0.000 ARG B 165 TYR 0.013 0.001 TYR A 97 PHE 0.035 0.001 PHE D 80 TRP 0.014 0.001 TRP C 93 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00226 (15905) covalent geometry : angle 0.46015 (21605) hydrogen bonds : bond 0.05200 ( 981) hydrogen bonds : angle 4.29934 ( 2815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7763.70 seconds wall clock time: 132 minutes 40.52 seconds (7960.52 seconds total)