Starting phenix.real_space_refine on Thu Sep 18 08:29:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyo_47311/09_2025/9dyo_47311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyo_47311/09_2025/9dyo_47311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dyo_47311/09_2025/9dyo_47311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyo_47311/09_2025/9dyo_47311.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyo_47311/09_2025/9dyo_47311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyo_47311/09_2025/9dyo_47311.cif" } resolution = 2.57 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= 0.002 sd= 0.095 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 10100 2.51 5 N 2555 2.21 5 O 2705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 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: 15451 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Chain: "C" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Chain: "E" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Chain: "A" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} Chain: "B" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3089 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 11, 'TRANS': 364} 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: "C" 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: "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: 3.62, per 1000 atoms: 0.23 Number of scatterers: 15451 At special positions: 0 Unit cell: (106.795, 108.438, 109.26, 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 2705 8.00 N 2555 7.00 C 10100 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: 1.36 Conformation dependent library (CDL) restraints added in 749.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 0 sheets defined 71.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.915A pdb=" N LEU D 20 " --> pdb=" O GLY D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.669A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.706A pdb=" N GLN D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 4.489A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) 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: 3.813A 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 'D' and resid 371 through 375 removed outlier: 3.620A pdb=" N GLN D 375 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.891A pdb=" N LEU C 20 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.684A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.720A pdb=" N GLN C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 4.499A 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: 3.848A 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 'C' and resid 371 through 375 removed outlier: 3.649A pdb=" N GLN C 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.692A pdb=" N ALA E 10 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.991A pdb=" N LEU E 20 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.745A pdb=" N GLN E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.412A 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: 3.811A 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 'E' and resid 371 through 375 Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.899A pdb=" N LEU A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.675A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.737A pdb=" N GLN A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 4.495A 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: 3.808A 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: 3.574A pdb=" N GLN A 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.943A pdb=" N LEU B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.720A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 removed outlier: 3.739A pdb=" N GLN B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.523A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) 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: 3.816A 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 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.683A pdb=" N GLN B 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2835 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: 2.70 Time building geometry restraints manager: 1.74 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: 4853 1.34 - 1.46: 2706 1.46 - 1.57: 8171 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 15860 Sorted by residual: bond pdb=" N LEU D 329 " pdb=" CA LEU D 329 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 5.98e+00 bond pdb=" N GLU D 324 " pdb=" CA GLU D 324 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.26e-02 6.30e+03 5.32e+00 bond pdb=" N LYS E 170 " pdb=" CA LYS E 170 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 bond pdb=" N TYR D 326 " pdb=" CA TYR D 326 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.28e-02 6.10e+03 5.00e+00 bond pdb=" N MET D 325 " pdb=" CA MET D 325 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.25e-02 6.40e+03 4.94e+00 ... (remaining 15855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 20657 0.99 - 1.99: 697 1.99 - 2.98: 126 2.98 - 3.98: 35 3.98 - 4.97: 10 Bond angle restraints: 21525 Sorted by residual: angle pdb=" CA ASP D 327 " pdb=" C ASP D 327 " pdb=" O ASP D 327 " ideal model delta sigma weight residual 121.54 118.04 3.50 1.16e+00 7.43e-01 9.10e+00 angle pdb=" CA LYS E 170 " pdb=" C LYS E 170 " pdb=" O LYS E 170 " ideal model delta sigma weight residual 120.55 117.43 3.12 1.06e+00 8.90e-01 8.66e+00 angle pdb=" CA MET D 325 " pdb=" C MET D 325 " pdb=" O MET D 325 " ideal model delta sigma weight residual 120.10 116.80 3.30 1.13e+00 7.83e-01 8.52e+00 angle pdb=" CA TRP E 187 " pdb=" C TRP E 187 " pdb=" O TRP E 187 " ideal model delta sigma weight residual 120.55 117.64 2.91 1.06e+00 8.90e-01 7.52e+00 angle pdb=" CA ASN E 190 " pdb=" C ASN E 190 " pdb=" O ASN E 190 " ideal model delta sigma weight residual 120.42 117.66 2.76 1.06e+00 8.90e-01 6.78e+00 ... (remaining 21520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8205 17.96 - 35.91: 759 35.91 - 53.87: 200 53.87 - 71.83: 47 71.83 - 89.78: 19 Dihedral angle restraints: 9230 sinusoidal: 3675 harmonic: 5555 Sorted by residual: dihedral pdb=" CB GLU A 333 " pdb=" CG GLU A 333 " pdb=" CD GLU A 333 " pdb=" OE1 GLU A 333 " ideal model delta sinusoidal sigma weight residual 0.00 -88.32 88.32 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ARG D 51 " pdb=" C ARG D 51 " pdb=" N PHE D 52 " pdb=" CA PHE D 52 " ideal model delta harmonic sigma weight residual -180.00 -164.19 -15.81 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CB GLU C 333 " pdb=" CG GLU C 333 " pdb=" CD GLU C 333 " pdb=" OE1 GLU C 333 " ideal model delta sinusoidal sigma weight residual 0.00 -86.30 86.30 1 3.00e+01 1.11e-03 9.98e+00 ... (remaining 9227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1683 0.034 - 0.067: 506 0.067 - 0.100: 110 0.100 - 0.134: 34 0.134 - 0.167: 2 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA LEU D 329 " pdb=" N LEU D 329 " pdb=" C LEU D 329 " pdb=" CB LEU D 329 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA ASP D 327 " pdb=" N ASP D 327 " pdb=" C ASP D 327 " pdb=" CB ASP D 327 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE C 201 " pdb=" N ILE C 201 " pdb=" C ILE C 201 " pdb=" CB ILE C 201 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2332 not shown) Planarity restraints: 2715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 102 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 103 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 102 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO E 103 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 345 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 346 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " 0.022 5.00e-02 4.00e+02 ... (remaining 2712 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 155 2.57 - 3.15: 12944 3.15 - 3.73: 25815 3.73 - 4.32: 37523 4.32 - 4.90: 60763 Nonbonded interactions: 137200 Sorted by model distance: nonbonded pdb=" OH TYR D 337 " pdb=" O ALA E 160 " model vdw 1.984 3.040 nonbonded pdb=" OH TYR A 337 " pdb=" O ALA B 160 " model vdw 2.035 3.040 nonbonded pdb=" O ALA C 160 " pdb=" OH TYR B 337 " model vdw 2.049 3.040 nonbonded pdb=" O ALA D 160 " pdb=" OH TYR C 337 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR D 5 " pdb=" O VAL E 232 " model vdw 2.128 3.040 ... (remaining 137195 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 601) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.230 Find NCS groups from input model: 0.340 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:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.003 0.030 15860 Z= 0.139 Angle : 0.452 4.971 21525 Z= 0.272 Chirality : 0.035 0.167 2335 Planarity : 0.003 0.048 2715 Dihedral : 15.828 89.784 5660 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.86 % Allowed : 14.66 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.19), residues: 1870 helix: 1.57 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.21 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 313 TYR 0.010 0.001 TYR E 97 PHE 0.015 0.001 PHE B 171 TRP 0.016 0.002 TRP E 93 HIS 0.002 0.000 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00254 (15860) covalent geometry : angle 0.45169 (21525) hydrogen bonds : bond 0.06553 ( 974) hydrogen bonds : angle 4.10687 ( 2835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.598 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.6995 time to fit residues: 120.9740 Evaluate side-chains 148 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 71 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0030 chunk 149 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN A 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107925 restraints weight = 16508.994| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.49 r_work: 0.3125 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15860 Z= 0.159 Angle : 0.507 5.130 21525 Z= 0.280 Chirality : 0.038 0.153 2335 Planarity : 0.004 0.041 2715 Dihedral : 4.650 53.068 2131 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.82 % Allowed : 12.09 % Favored : 85.09 % 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: 1870 helix: 1.45 (0.14), residues: 1275 sheet: None (None), residues: 0 loop : -0.20 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 13 TYR 0.013 0.001 TYR E 97 PHE 0.016 0.002 PHE B 171 TRP 0.014 0.002 TRP A 93 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00349 (15860) covalent geometry : angle 0.50718 (21525) hydrogen bonds : bond 0.05461 ( 974) hydrogen bonds : angle 4.32462 ( 2835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.639 Fit side-chains REVERT: D 25 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8149 (ttt-90) REVERT: D 155 ASP cc_start: 0.7998 (m-30) cc_final: 0.7796 (m-30) REVERT: D 169 LYS cc_start: 0.7823 (mttt) cc_final: 0.7374 (mtpp) REVERT: D 303 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7681 (t0) REVERT: C 306 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: E 159 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: E 175 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 71 GLN cc_start: 0.7960 (pt0) cc_final: 0.7601 (pp30) outliers start: 46 outliers final: 6 residues processed: 196 average time/residue: 0.6800 time to fit residues: 145.7654 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 71 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 0.0000 chunk 144 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106345 restraints weight = 16782.169| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.49 r_work: 0.3111 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15860 Z= 0.178 Angle : 0.505 5.301 21525 Z= 0.279 Chirality : 0.039 0.157 2335 Planarity : 0.004 0.043 2715 Dihedral : 4.575 55.602 2120 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.07 % Allowed : 13.01 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.21 (0.18), residues: 1870 helix: 1.36 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.38 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 13 TYR 0.014 0.001 TYR E 97 PHE 0.020 0.002 PHE D 283 TRP 0.016 0.002 TRP C 93 HIS 0.002 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00402 (15860) covalent geometry : angle 0.50476 (21525) hydrogen bonds : bond 0.05651 ( 974) hydrogen bonds : angle 4.37628 ( 2835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.637 Fit side-chains REVERT: D 25 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8125 (ttt-90) REVERT: D 102 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8409 (mt) REVERT: D 169 LYS cc_start: 0.7884 (mttt) cc_final: 0.7428 (mtpp) REVERT: D 303 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7717 (t0) REVERT: C 80 PHE cc_start: 0.8206 (m-80) cc_final: 0.7993 (m-80) REVERT: E 25 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7266 (ttp-110) REVERT: E 159 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: E 175 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8030 (t0) REVERT: E 306 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: A 71 GLN cc_start: 0.7906 (pt0) cc_final: 0.7625 (pp30) REVERT: B 203 ASP cc_start: 0.8205 (p0) cc_final: 0.7994 (p0) outliers start: 50 outliers final: 7 residues processed: 198 average time/residue: 0.7202 time to fit residues: 155.3869 Evaluate side-chains 155 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 171 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108462 restraints weight = 16652.333| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.49 r_work: 0.3139 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 15860 Z= 0.137 Angle : 0.473 6.113 21525 Z= 0.263 Chirality : 0.037 0.157 2335 Planarity : 0.003 0.041 2715 Dihedral : 4.222 47.214 2117 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.39 % Allowed : 13.37 % Favored : 84.23 % 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: 1.36 (0.18), residues: 1870 helix: 1.50 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.36 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 13 TYR 0.013 0.001 TYR E 97 PHE 0.015 0.001 PHE A 80 TRP 0.015 0.001 TRP C 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00292 (15860) covalent geometry : angle 0.47266 (21525) hydrogen bonds : bond 0.05195 ( 974) hydrogen bonds : angle 4.31877 ( 2835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.548 Fit side-chains REVERT: D 25 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8124 (ttt-90) REVERT: D 169 LYS cc_start: 0.7841 (mttt) cc_final: 0.7394 (mtpp) REVERT: D 303 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7661 (t0) REVERT: C 80 PHE cc_start: 0.8211 (m-80) cc_final: 0.7976 (m-80) REVERT: E 25 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7119 (ttp-170) REVERT: E 169 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7338 (mtpm) REVERT: E 306 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8223 (mp0) REVERT: A 71 GLN cc_start: 0.7900 (pt0) cc_final: 0.7664 (pp30) REVERT: A 203 ASP cc_start: 0.8038 (p0) cc_final: 0.7661 (p0) REVERT: B 25 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8048 (ttp-170) outliers start: 39 outliers final: 9 residues processed: 190 average time/residue: 0.6827 time to fit residues: 141.5549 Evaluate side-chains 154 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 137 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104825 restraints weight = 17602.050| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.72 r_work: 0.3089 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15860 Z= 0.177 Angle : 0.501 5.112 21525 Z= 0.277 Chirality : 0.039 0.160 2335 Planarity : 0.004 0.045 2715 Dihedral : 4.329 48.334 2117 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.45 % Allowed : 14.05 % Favored : 83.50 % 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 aren not related in a simple way. whole: 1.24 (0.18), residues: 1870 helix: 1.43 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.44 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.014 0.001 TYR E 97 PHE 0.016 0.002 PHE B 171 TRP 0.016 0.002 TRP C 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00401 (15860) covalent geometry : angle 0.50058 (21525) hydrogen bonds : bond 0.05601 ( 974) hydrogen bonds : angle 4.38945 ( 2835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.583 Fit side-chains REVERT: D 25 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8169 (ttt-90) REVERT: D 303 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7755 (t0) REVERT: D 374 MET cc_start: 0.5959 (mtt) cc_final: 0.5682 (mtt) REVERT: C 80 PHE cc_start: 0.8343 (m-80) cc_final: 0.8128 (m-80) REVERT: C 249 LEU cc_start: 0.8119 (tp) cc_final: 0.7908 (tp) REVERT: E 25 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7353 (ttp-110) REVERT: E 169 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7493 (mtpm) REVERT: E 306 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: A 71 GLN cc_start: 0.7942 (pt0) cc_final: 0.7730 (pp30) outliers start: 40 outliers final: 14 residues processed: 181 average time/residue: 0.6833 time to fit residues: 135.1027 Evaluate side-chains 163 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.0060 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 267 HIS E 280 GLN B 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109402 restraints weight = 17520.149| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.70 r_work: 0.3152 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15860 Z= 0.117 Angle : 0.448 5.048 21525 Z= 0.250 Chirality : 0.036 0.159 2335 Planarity : 0.003 0.042 2715 Dihedral : 4.116 46.684 2117 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.02 % Allowed : 15.09 % Favored : 82.88 % 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: 1.41 (0.18), residues: 1870 helix: 1.57 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.43 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.012 0.001 TYR E 97 PHE 0.018 0.001 PHE A 80 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00238 (15860) covalent geometry : angle 0.44829 (21525) hydrogen bonds : bond 0.04908 ( 974) hydrogen bonds : angle 4.27915 ( 2835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.585 Fit side-chains REVERT: D 25 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8171 (ttt-90) REVERT: D 102 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 169 LYS cc_start: 0.7895 (mttt) cc_final: 0.7479 (mtpp) REVERT: D 303 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7695 (t0) REVERT: D 374 MET cc_start: 0.5928 (mtt) cc_final: 0.5700 (mtt) REVERT: C 13 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7245 (mtp85) REVERT: C 80 PHE cc_start: 0.8288 (m-80) cc_final: 0.8068 (m-80) REVERT: C 374 MET cc_start: 0.5430 (mtt) cc_final: 0.5188 (mtm) REVERT: E 25 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7207 (ttp-170) REVERT: E 169 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7525 (mtpm) REVERT: E 306 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8326 (mp0) REVERT: A 203 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7705 (p0) outliers start: 33 outliers final: 10 residues processed: 184 average time/residue: 0.6794 time to fit residues: 136.3410 Evaluate side-chains 162 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105589 restraints weight = 16278.072| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.70 r_work: 0.3091 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15860 Z= 0.182 Angle : 0.501 5.093 21525 Z= 0.278 Chirality : 0.039 0.160 2335 Planarity : 0.004 0.046 2715 Dihedral : 4.304 48.617 2117 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.09 % Allowed : 14.97 % Favored : 82.94 % 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: 1.25 (0.18), residues: 1870 helix: 1.45 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.49 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 13 TYR 0.015 0.001 TYR E 97 PHE 0.016 0.002 PHE B 171 TRP 0.016 0.002 TRP C 93 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00413 (15860) covalent geometry : angle 0.50126 (21525) hydrogen bonds : bond 0.05662 ( 974) hydrogen bonds : angle 4.40146 ( 2835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.582 Fit side-chains REVERT: D 25 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8158 (ttt-90) REVERT: D 102 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8389 (mt) REVERT: D 169 LYS cc_start: 0.7907 (mttt) cc_final: 0.7477 (mtpp) REVERT: D 303 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7802 (t0) REVERT: D 374 MET cc_start: 0.5773 (mtt) cc_final: 0.5536 (mtt) REVERT: C 13 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7340 (mtp85) REVERT: C 80 PHE cc_start: 0.8321 (m-80) cc_final: 0.8055 (m-80) REVERT: E 25 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7684 (ttp-170) REVERT: E 169 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7466 (mtpm) REVERT: E 306 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8307 (mp0) REVERT: A 253 ILE cc_start: 0.8454 (mm) cc_final: 0.8249 (mt) outliers start: 34 outliers final: 8 residues processed: 179 average time/residue: 0.7179 time to fit residues: 139.9649 Evaluate side-chains 158 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 178 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109565 restraints weight = 16251.607| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.69 r_work: 0.3148 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15860 Z= 0.114 Angle : 0.446 5.069 21525 Z= 0.248 Chirality : 0.036 0.158 2335 Planarity : 0.003 0.041 2715 Dihedral : 4.070 46.897 2117 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.17 % Allowed : 16.01 % Favored : 82.82 % 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: 1.39 (0.18), residues: 1870 helix: 1.59 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.52 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.012 0.001 TYR E 97 PHE 0.014 0.001 PHE C 171 TRP 0.014 0.001 TRP D 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00230 (15860) covalent geometry : angle 0.44619 (21525) hydrogen bonds : bond 0.04840 ( 974) hydrogen bonds : angle 4.27794 ( 2835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.610 Fit side-chains REVERT: D 25 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8164 (ttt-90) REVERT: D 102 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8339 (mt) REVERT: D 169 LYS cc_start: 0.7832 (mttt) cc_final: 0.7404 (mtpp) REVERT: D 303 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7674 (t0) REVERT: C 13 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7292 (mtp85) REVERT: C 80 PHE cc_start: 0.8274 (m-80) cc_final: 0.8024 (m-80) REVERT: C 374 MET cc_start: 0.5336 (mtt) cc_final: 0.5108 (mtm) REVERT: E 169 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7468 (mtpm) REVERT: E 306 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8294 (mp0) outliers start: 19 outliers final: 9 residues processed: 170 average time/residue: 0.6799 time to fit residues: 126.3480 Evaluate side-chains 157 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108542 restraints weight = 16247.688| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.69 r_work: 0.3124 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15860 Z= 0.132 Angle : 0.460 5.045 21525 Z= 0.256 Chirality : 0.037 0.159 2335 Planarity : 0.003 0.042 2715 Dihedral : 4.085 46.534 2117 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 16.13 % Favored : 82.45 % 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: 1.38 (0.18), residues: 1870 helix: 1.59 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.013 0.001 TYR E 97 PHE 0.029 0.001 PHE D 283 TRP 0.014 0.001 TRP D 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00282 (15860) covalent geometry : angle 0.46009 (21525) hydrogen bonds : bond 0.05059 ( 974) hydrogen bonds : angle 4.29487 ( 2835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.603 Fit side-chains REVERT: D 25 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8170 (ttt-90) REVERT: D 169 LYS cc_start: 0.7839 (mttt) cc_final: 0.7435 (mtpp) REVERT: D 303 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7715 (t0) REVERT: C 13 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7310 (mtp85) REVERT: C 80 PHE cc_start: 0.8284 (m-80) cc_final: 0.8022 (m-80) REVERT: C 249 LEU cc_start: 0.8124 (tp) cc_final: 0.7905 (tp) REVERT: E 25 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7232 (ttp-170) REVERT: E 169 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7458 (mtpm) REVERT: E 306 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8304 (mp0) outliers start: 23 outliers final: 9 residues processed: 163 average time/residue: 0.7018 time to fit residues: 124.5104 Evaluate side-chains 157 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108686 restraints weight = 16311.323| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.70 r_work: 0.3134 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15860 Z= 0.128 Angle : 0.459 5.021 21525 Z= 0.255 Chirality : 0.037 0.158 2335 Planarity : 0.003 0.041 2715 Dihedral : 4.073 46.150 2117 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.10 % Allowed : 16.69 % Favored : 82.21 % 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: 1.39 (0.18), residues: 1870 helix: 1.60 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.55 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.013 0.001 TYR E 97 PHE 0.027 0.001 PHE D 283 TRP 0.014 0.001 TRP E 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00272 (15860) covalent geometry : angle 0.45857 (21525) hydrogen bonds : bond 0.05009 ( 974) hydrogen bonds : angle 4.28786 ( 2835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.610 Fit side-chains REVERT: D 25 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8188 (ttt-90) REVERT: D 169 LYS cc_start: 0.7828 (mttt) cc_final: 0.7424 (mtpp) REVERT: D 303 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7722 (t0) REVERT: C 13 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7298 (mtp85) REVERT: C 80 PHE cc_start: 0.8258 (m-80) cc_final: 0.7988 (m-80) REVERT: C 249 LEU cc_start: 0.8107 (tp) cc_final: 0.7895 (tp) REVERT: E 25 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7241 (ttp-170) REVERT: E 169 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7475 (mtpm) REVERT: E 306 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8296 (mp0) outliers start: 18 outliers final: 8 residues processed: 162 average time/residue: 0.6851 time to fit residues: 121.1809 Evaluate side-chains 156 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN C 280 GLN E 280 GLN B 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109851 restraints weight = 16182.061| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.69 r_work: 0.3149 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15860 Z= 0.118 Angle : 0.448 4.984 21525 Z= 0.249 Chirality : 0.036 0.158 2335 Planarity : 0.003 0.039 2715 Dihedral : 3.997 45.043 2117 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.17 % Allowed : 16.75 % Favored : 82.09 % 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: 1.45 (0.18), residues: 1870 helix: 1.66 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.55 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.012 0.001 TYR E 97 PHE 0.026 0.001 PHE D 283 TRP 0.013 0.001 TRP D 93 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00242 (15860) covalent geometry : angle 0.44753 (21525) hydrogen bonds : bond 0.04830 ( 974) hydrogen bonds : angle 4.25046 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5136.69 seconds wall clock time: 88 minutes 31.52 seconds (5311.52 seconds total)