Starting phenix.real_space_refine on Sat May 17 06:38:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyo_47311/05_2025/9dyo_47311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyo_47311/05_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_47311/05_2025/9dyo_47311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyo_47311/05_2025/9dyo_47311.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyo_47311/05_2025/9dyo_47311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyo_47311/05_2025/9dyo_47311.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.92, per 1000 atoms: 0.64 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: 3.94 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.53 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: 4.73 Time building geometry restraints manager: 4.52 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 377 or resid 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.240 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.120 ------------------------------------------------------------------------------- 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 : 16.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (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 TRP 0.016 0.002 TRP E 93 HIS 0.002 0.000 HIS E 226 PHE 0.015 0.001 PHE B 171 TYR 0.010 0.001 TYR E 97 ARG 0.002 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.06553 ( 974) hydrogen bonds : angle 4.10687 ( 2835) covalent geometry : bond 0.00254 (15860) covalent geometry : angle 0.45169 (21525) *********************** 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 : 2.078 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 1.4255 time to fit residues: 247.6522 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 : 1.641 ------------------------------------------------------------------------------- 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 156 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.129494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104290 restraints weight = 16915.152| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.48 r_work: 0.3084 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.006 0.033 15860 Z= 0.239 Angle : 0.566 5.233 21525 Z= 0.311 Chirality : 0.042 0.157 2335 Planarity : 0.004 0.043 2715 Dihedral : 4.887 54.082 2131 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.07 % Allowed : 12.09 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1870 helix: 1.23 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -0.32 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.003 0.001 HIS B 115 PHE 0.019 0.002 PHE A 171 TYR 0.015 0.002 TYR E 97 ARG 0.004 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.06227 ( 974) hydrogen bonds : angle 4.46345 ( 2835) covalent geometry : bond 0.00557 (15860) covalent geometry : angle 0.56573 (21525) *********************** 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 208 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 1.781 Fit side-chains REVERT: D 25 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8142 (ttt-90) REVERT: D 169 LYS cc_start: 0.7893 (mttt) cc_final: 0.7660 (mtmm) REVERT: D 303 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7762 (t0) REVERT: C 13 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7726 (mtp85) REVERT: E 19 GLN cc_start: 0.7585 (pt0) cc_final: 0.7381 (pp30) REVERT: E 175 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 71 GLN cc_start: 0.7981 (pt0) cc_final: 0.7598 (pp30) outliers start: 50 outliers final: 9 residues processed: 196 average time/residue: 1.3338 time to fit residues: 288.2388 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG 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 175 ASN Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 252 LEU 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 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 0.0050 chunk 179 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.133144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107514 restraints weight = 16517.789| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.52 r_work: 0.3126 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15860 Z= 0.148 Angle : 0.483 5.472 21525 Z= 0.269 Chirality : 0.038 0.158 2335 Planarity : 0.003 0.041 2715 Dihedral : 4.555 56.840 2120 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.25 % Allowed : 12.39 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1295 sheet: None (None), residues: 0 loop : -0.38 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 93 HIS 0.002 0.001 HIS B 115 PHE 0.016 0.001 PHE C 80 TYR 0.012 0.001 TYR E 97 ARG 0.004 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05344 ( 974) hydrogen bonds : angle 4.34588 ( 2835) covalent geometry : bond 0.00322 (15860) covalent geometry : angle 0.48302 (21525) *********************** 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 220 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 1.702 Fit side-chains REVERT: D 25 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (ttt-90) REVERT: D 102 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8380 (mt) REVERT: D 169 LYS cc_start: 0.7822 (mttt) cc_final: 0.7371 (mtpp) REVERT: D 303 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7692 (t0) REVERT: C 306 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: E 25 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7188 (ttp-170) REVERT: E 80 PHE cc_start: 0.8138 (m-80) cc_final: 0.7931 (m-80) REVERT: E 169 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7277 (mtpm) REVERT: E 306 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8210 (mp0) REVERT: A 71 GLN cc_start: 0.7874 (pt0) cc_final: 0.7550 (pp30) REVERT: B 25 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8023 (ttp-170) REVERT: B 175 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8318 (m-40) REVERT: B 203 ASP cc_start: 0.8148 (p0) cc_final: 0.7935 (p0) outliers start: 53 outliers final: 9 residues processed: 203 average time/residue: 1.4147 time to fit residues: 314.8002 Evaluate side-chains 161 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 C residue 306 GLU Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 71 GLN 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 13 ARG Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 175 ASN 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 107 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.133303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107816 restraints weight = 16406.798| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.49 r_work: 0.3126 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15860 Z= 0.147 Angle : 0.484 5.762 21525 Z= 0.269 Chirality : 0.038 0.158 2335 Planarity : 0.003 0.043 2715 Dihedral : 4.282 48.234 2117 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.33 % Allowed : 13.62 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 1870 helix: 1.46 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.37 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 93 HIS 0.002 0.000 HIS B 115 PHE 0.020 0.001 PHE D 283 TYR 0.014 0.001 TYR E 97 ARG 0.004 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05321 ( 974) hydrogen bonds : angle 4.34687 ( 2835) covalent geometry : bond 0.00319 (15860) covalent geometry : angle 0.48415 (21525) *********************** 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 196 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.608 Fit side-chains REVERT: D 25 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8102 (ttt-90) REVERT: D 71 GLN cc_start: 0.7989 (pt0) cc_final: 0.7777 (pp30) REVERT: D 169 LYS cc_start: 0.7838 (mttt) cc_final: 0.7396 (mtpp) REVERT: D 303 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7680 (t0) REVERT: C 13 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7644 (mtp85) REVERT: C 306 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: E 25 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7215 (ttp-170) REVERT: E 71 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7603 (pp30) REVERT: E 169 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7360 (mtpm) REVERT: E 306 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: A 71 GLN cc_start: 0.7885 (pt0) cc_final: 0.7678 (pp30) REVERT: B 25 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7944 (ttp-110) REVERT: B 175 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8284 (m-40) outliers start: 38 outliers final: 10 residues processed: 186 average time/residue: 1.4603 time to fit residues: 296.7493 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 : 1.738 ------------------------------------------------------------------------------- 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 25 ARG Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 306 GLU 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 13 ARG Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 175 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.133286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106489 restraints weight = 17579.374| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.72 r_work: 0.3112 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15860 Z= 0.157 Angle : 0.487 5.138 21525 Z= 0.270 Chirality : 0.038 0.159 2335 Planarity : 0.003 0.043 2715 Dihedral : 4.297 48.318 2117 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.82 % Allowed : 13.80 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 1870 helix: 1.44 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.46 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 93 HIS 0.003 0.000 HIS B 115 PHE 0.016 0.002 PHE B 171 TYR 0.014 0.001 TYR E 97 ARG 0.004 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 974) hydrogen bonds : angle 4.36291 ( 2835) covalent geometry : bond 0.00349 (15860) covalent geometry : angle 0.48667 (21525) *********************** 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 199 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.868 Fit side-chains REVERT: D 25 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8175 (ttt-90) REVERT: D 169 LYS cc_start: 0.7996 (mttt) cc_final: 0.7571 (mtpp) REVERT: D 303 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7751 (t0) REVERT: C 306 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: E 25 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7329 (ttp-170) REVERT: E 169 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7505 (mtpm) REVERT: E 306 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: A 71 GLN cc_start: 0.7948 (pt0) cc_final: 0.7710 (pp30) REVERT: A 149 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8384 (mmtp) outliers start: 46 outliers final: 12 residues processed: 184 average time/residue: 1.4288 time to fit residues: 288.4638 Evaluate side-chains 162 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 C residue 306 GLU Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 149 LYS 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 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 131 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.134978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108258 restraints weight = 16222.869| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.69 r_work: 0.3122 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15860 Z= 0.128 Angle : 0.459 5.062 21525 Z= 0.255 Chirality : 0.036 0.158 2335 Planarity : 0.003 0.042 2715 Dihedral : 4.166 47.195 2117 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.15 % Allowed : 15.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 1870 helix: 1.53 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.47 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.002 0.000 HIS B 115 PHE 0.018 0.001 PHE A 80 TYR 0.013 0.001 TYR E 97 ARG 0.005 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 974) hydrogen bonds : angle 4.30229 ( 2835) covalent geometry : bond 0.00270 (15860) covalent geometry : angle 0.45854 (21525) *********************** 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 188 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 1.667 Fit side-chains REVERT: D 25 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8166 (ttt-90) REVERT: D 102 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8365 (mt) REVERT: D 169 LYS cc_start: 0.7928 (mttt) cc_final: 0.7506 (mtpp) REVERT: D 303 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7729 (t0) REVERT: C 306 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: E 25 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7276 (ttp-170) REVERT: E 169 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7487 (mtpm) REVERT: E 306 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8344 (mp0) REVERT: A 71 GLN cc_start: 0.7922 (pt0) cc_final: 0.7703 (pp30) REVERT: A 203 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 169 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7646 (mtpp) outliers start: 35 outliers final: 10 residues processed: 179 average time/residue: 1.4624 time to fit residues: 285.9621 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 303 ASP Chi-restraints excluded: chain C residue 306 GLU 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 177 SER 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 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 117 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108759 restraints weight = 16363.609| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.70 r_work: 0.3135 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15860 Z= 0.123 Angle : 0.451 5.128 21525 Z= 0.251 Chirality : 0.036 0.158 2335 Planarity : 0.003 0.040 2715 Dihedral : 4.093 46.249 2117 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.96 % Allowed : 15.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 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 TRP 0.014 0.001 TRP D 93 HIS 0.002 0.000 HIS B 115 PHE 0.014 0.001 PHE C 171 TYR 0.013 0.001 TYR E 97 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.04942 ( 974) hydrogen bonds : angle 4.28168 ( 2835) covalent geometry : bond 0.00256 (15860) covalent geometry : angle 0.45051 (21525) *********************** 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 183 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 1.696 Fit side-chains REVERT: D 25 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8182 (ttt-90) REVERT: D 169 LYS cc_start: 0.7919 (mttt) cc_final: 0.7505 (mtpp) REVERT: D 303 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7714 (t0) REVERT: C 306 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: E 25 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7203 (ttp-170) REVERT: E 169 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7490 (mtpm) REVERT: E 306 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8307 (mp0) REVERT: A 149 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8350 (mttp) REVERT: A 203 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7825 (p0) outliers start: 32 outliers final: 10 residues processed: 175 average time/residue: 1.3988 time to fit residues: 268.1209 Evaluate side-chains 159 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 25 ARG Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 177 SER 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 71 GLN 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 139 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.130585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103809 restraints weight = 16357.690| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.69 r_work: 0.3066 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 15860 Z= 0.242 Angle : 0.547 5.186 21525 Z= 0.302 Chirality : 0.042 0.162 2335 Planarity : 0.004 0.048 2715 Dihedral : 4.495 50.622 2117 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.15 % Allowed : 15.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 1870 helix: 1.27 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.58 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 93 HIS 0.002 0.001 HIS B 115 PHE 0.025 0.002 PHE D 283 TYR 0.019 0.002 TYR C 97 ARG 0.003 0.001 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.06202 ( 974) hydrogen bonds : angle 4.50717 ( 2835) covalent geometry : bond 0.00566 (15860) covalent geometry : angle 0.54746 (21525) *********************** 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 186 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.843 Fit side-chains REVERT: D 25 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8165 (ttt-90) REVERT: D 102 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8408 (mt) REVERT: D 303 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7851 (t0) REVERT: E 25 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: A 203 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7861 (p0) REVERT: B 303 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7653 (t0) outliers start: 35 outliers final: 9 residues processed: 175 average time/residue: 1.4327 time to fit residues: 274.7637 Evaluate side-chains 158 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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 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 319 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 325 MET 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 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 HIS D 280 GLN C 280 GLN E 267 HIS E 280 GLN B 280 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107884 restraints weight = 16220.581| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.70 r_work: 0.3123 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15860 Z= 0.128 Angle : 0.465 5.033 21525 Z= 0.260 Chirality : 0.037 0.158 2335 Planarity : 0.003 0.041 2715 Dihedral : 4.241 49.231 2117 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.23 % Allowed : 16.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 1870 helix: 1.50 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.60 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 93 HIS 0.002 0.001 HIS B 115 PHE 0.024 0.001 PHE D 283 TYR 0.013 0.001 TYR E 97 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 974) hydrogen bonds : angle 4.35643 ( 2835) covalent geometry : bond 0.00269 (15860) covalent geometry : angle 0.46535 (21525) *********************** 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 169 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.668 Fit side-chains REVERT: D 25 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8156 (ttt-90) REVERT: D 102 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8359 (mt) REVERT: D 169 LYS cc_start: 0.7912 (mttt) cc_final: 0.7496 (mtpp) REVERT: D 303 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7713 (t0) REVERT: E 25 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7254 (ttp-170) REVERT: E 169 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7435 (mtpm) REVERT: E 306 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8382 (mp0) outliers start: 20 outliers final: 6 residues processed: 165 average time/residue: 1.4903 time to fit residues: 268.7764 Evaluate side-chains 151 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 303 ASP 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 177 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.133960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107226 restraints weight = 16244.397| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.69 r_work: 0.3115 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15860 Z= 0.142 Angle : 0.474 5.123 21525 Z= 0.264 Chirality : 0.037 0.159 2335 Planarity : 0.003 0.042 2715 Dihedral : 4.222 49.038 2117 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.80 % Allowed : 17.30 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 1870 helix: 1.50 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.60 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 93 HIS 0.002 0.000 HIS B 115 PHE 0.023 0.001 PHE D 283 TYR 0.017 0.001 TYR C 97 ARG 0.005 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 974) hydrogen bonds : angle 4.36415 ( 2835) covalent geometry : bond 0.00308 (15860) covalent geometry : angle 0.47373 (21525) ********************** 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 158 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 2.029 Fit side-chains REVERT: D 25 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8166 (ttt-90) REVERT: D 102 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8358 (mt) REVERT: D 169 LYS cc_start: 0.7875 (mttt) cc_final: 0.7469 (mtpp) REVERT: D 303 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7734 (t0) REVERT: C 107 MET cc_start: 0.8765 (ptt) cc_final: 0.8115 (ptt) REVERT: E 25 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7334 (ttp-170) REVERT: E 159 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7815 (mp0) REVERT: E 169 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7463 (mtpm) REVERT: E 306 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8352 (mp0) outliers start: 13 outliers final: 6 residues processed: 154 average time/residue: 1.5781 time to fit residues: 265.4182 Evaluate side-chains 150 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 303 ASP 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 177 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 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 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 = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108736 restraints weight = 16238.531| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.69 r_work: 0.3137 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15860 Z= 0.124 Angle : 0.456 5.042 21525 Z= 0.254 Chirality : 0.036 0.159 2335 Planarity : 0.003 0.040 2715 Dihedral : 4.119 47.992 2117 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.86 % Allowed : 17.24 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 1870 helix: 1.57 (0.14), residues: 1285 sheet: None (None), residues: 0 loop : -0.60 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.002 0.000 HIS B 115 PHE 0.023 0.001 PHE D 283 TYR 0.015 0.001 TYR C 97 ARG 0.005 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 974) hydrogen bonds : angle 4.31123 ( 2835) covalent geometry : bond 0.00259 (15860) covalent geometry : angle 0.45606 (21525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10046.24 seconds wall clock time: 174 minutes 7.89 seconds (10447.89 seconds total)