Starting phenix.real_space_refine on Fri Jun 20 23:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x84_38135/06_2025/8x84_38135_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x84_38135/06_2025/8x84_38135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x84_38135/06_2025/8x84_38135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x84_38135/06_2025/8x84_38135.map" model { file = "/net/cci-nas-00/data/ceres_data/8x84_38135/06_2025/8x84_38135_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x84_38135/06_2025/8x84_38135_neut_trim.cif" } resolution = 3.1 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= 0.000 sd= 0.004 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 2 9.91 5 S 72 5.16 5 C 7836 2.51 5 N 2056 2.21 5 O 2124 1.98 5 H 12444 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24534 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 15.61, per 1000 atoms: 0.64 Number of scatterers: 24534 At special positions: 0 Unit cell: (110.67, 110.67, 106.02, 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 2 19.99 S 72 16.00 O 2124 8.00 N 2056 7.00 C 7836 6.00 H 12444 1.00 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: 6.44 Conformation dependent library (CDL) restraints added in 2.1 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3180 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: 9.97 Time building geometry restraints manager: 7.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12412 1.03 - 1.23: 32 1.23 - 1.42: 5120 1.42 - 1.61: 7084 1.61 - 1.81: 112 Bond restraints: 24760 Sorted by residual: bond pdb=" C LEU A 419 " pdb=" N ILE A 420 " ideal model delta sigma weight residual 1.335 1.426 -0.092 1.26e-02 6.30e+03 5.31e+01 bond pdb=" C LEU B 419 " pdb=" N ILE B 420 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.26e-02 6.30e+03 5.23e+01 bond pdb=" C LEU C 419 " pdb=" N ILE C 420 " ideal model delta sigma weight residual 1.335 1.424 -0.089 1.26e-02 6.30e+03 5.03e+01 bond pdb=" C LEU D 419 " pdb=" N ILE D 420 " ideal model delta sigma weight residual 1.335 1.424 -0.089 1.26e-02 6.30e+03 5.03e+01 bond pdb=" C2 FRU A 503 " pdb=" O5 FRU A 503 " ideal model delta sigma weight residual 1.412 1.486 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 24755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 42718 1.15 - 2.30: 1854 2.30 - 3.45: 88 3.45 - 4.60: 34 4.60 - 5.75: 18 Bond angle restraints: 44712 Sorted by residual: angle pdb=" C TYR A 175 " pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 120.24 122.86 -2.62 6.30e-01 2.52e+00 1.73e+01 angle pdb=" C TYR B 175 " pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 120.24 122.86 -2.62 6.30e-01 2.52e+00 1.73e+01 angle pdb=" C TYR C 175 " pdb=" N ILE C 176 " pdb=" CA ILE C 176 " ideal model delta sigma weight residual 120.24 122.86 -2.62 6.30e-01 2.52e+00 1.73e+01 angle pdb=" C TYR D 175 " pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 120.24 122.86 -2.62 6.30e-01 2.52e+00 1.73e+01 angle pdb=" C VAL B 345 " pdb=" N GLU B 346 " pdb=" CA GLU B 346 " ideal model delta sigma weight residual 120.09 124.19 -4.10 1.25e+00 6.40e-01 1.07e+01 ... (remaining 44707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10548 17.92 - 35.84: 752 35.84 - 53.77: 208 53.77 - 71.69: 60 71.69 - 89.61: 20 Dihedral angle restraints: 11588 sinusoidal: 6256 harmonic: 5332 Sorted by residual: dihedral pdb=" CG ARG D 367 " pdb=" CD ARG D 367 " pdb=" NE ARG D 367 " pdb=" CZ ARG D 367 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 367 " pdb=" CD ARG A 367 " pdb=" NE ARG A 367 " pdb=" CZ ARG A 367 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C 367 " pdb=" CD ARG C 367 " pdb=" NE ARG C 367 " pdb=" CZ ARG C 367 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 11585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1356 0.025 - 0.051: 389 0.051 - 0.076: 187 0.076 - 0.101: 56 0.101 - 0.126: 20 Chirality restraints: 2008 Sorted by residual: chirality pdb=" CA ILE B 420 " pdb=" N ILE B 420 " pdb=" C ILE B 420 " pdb=" CB ILE B 420 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE A 420 " pdb=" N ILE A 420 " pdb=" C ILE A 420 " pdb=" CB ILE A 420 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE C 420 " pdb=" N ILE C 420 " pdb=" C ILE C 420 " pdb=" CB ILE C 420 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 2005 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 419 " -0.010 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU B 419 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU B 419 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 420 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 419 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU D 419 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU D 419 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE D 420 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 419 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU C 419 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU C 419 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE C 420 " 0.010 2.00e-02 2.50e+03 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1272 2.20 - 2.80: 51400 2.80 - 3.40: 72468 3.40 - 4.00: 91870 4.00 - 4.60: 146603 Nonbonded interactions: 363613 Sorted by model distance: nonbonded pdb=" HE2 PHE A 422 " pdb="HG12 VAL B 417 " model vdw 1.596 2.270 nonbonded pdb=" HE2 PHE B 422 " pdb="HG12 VAL C 417 " model vdw 1.596 2.270 nonbonded pdb="HG12 VAL A 417 " pdb=" HE2 PHE D 422 " model vdw 1.599 2.270 nonbonded pdb=" HE2 PHE C 422 " pdb="HG12 VAL D 417 " model vdw 1.599 2.270 nonbonded pdb=" OD1 ASN C 401 " pdb=" HG1 THR C 403 " model vdw 1.653 2.450 ... (remaining 363608 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 1 through 426) selection = (chain 'B' and resid 1 through 426) selection = (chain 'C' and resid 1 through 426) selection = (chain 'D' and resid 1 through 426) } 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: 0.990 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: 0.420 Extract box with map and model: 0.830 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 57.220 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.004 0.092 12316 Z= 0.230 Angle : 0.527 5.753 16712 Z= 0.316 Chirality : 0.033 0.126 2008 Planarity : 0.002 0.022 2040 Dihedral : 14.451 89.610 4464 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.30 % Allowed : 7.93 % Favored : 91.77 % 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: 3.21 (0.22), residues: 1508 helix: 2.52 (0.14), residues: 1248 sheet: 0.73 (0.81), residues: 48 loop : -0.01 (0.51), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.001 0.000 HIS C 349 PHE 0.007 0.001 PHE C 315 TYR 0.005 0.001 TYR B 96 ARG 0.001 0.000 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.09482 ( 1064) hydrogen bonds : angle 4.94729 ( 3180) covalent geometry : bond 0.00411 (12316) covalent geometry : angle 0.52744 (16712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.6652 time to fit residues: 85.6093 Evaluate side-chains 84 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain D residue 25 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103550 restraints weight = 39363.602| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.60 r_work: 0.2967 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12316 Z= 0.239 Angle : 0.517 4.444 16712 Z= 0.286 Chirality : 0.036 0.132 2008 Planarity : 0.003 0.029 2040 Dihedral : 3.726 23.100 1760 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.30 % Allowed : 9.15 % Favored : 90.55 % 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: 2.77 (0.21), residues: 1508 helix: 2.26 (0.14), residues: 1264 sheet: 0.23 (0.86), residues: 48 loop : -0.62 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 328 HIS 0.004 0.001 HIS D 349 PHE 0.008 0.001 PHE D 338 TYR 0.010 0.002 TYR B 182 ARG 0.003 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1064) hydrogen bonds : angle 4.20106 ( 3180) covalent geometry : bond 0.00532 (12316) covalent geometry : angle 0.51736 (16712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 2.066 Fit side-chains REVERT: A 75 THR cc_start: 0.8015 (m) cc_final: 0.7716 (t) REVERT: A 126 ARG cc_start: 0.7489 (ttt180) cc_final: 0.6775 (ttp-110) REVERT: B 75 THR cc_start: 0.8005 (m) cc_final: 0.7710 (t) REVERT: B 126 ARG cc_start: 0.7501 (ttt180) cc_final: 0.6796 (ttp-110) REVERT: C 75 THR cc_start: 0.8006 (m) cc_final: 0.7718 (t) REVERT: C 126 ARG cc_start: 0.7495 (ttt180) cc_final: 0.6780 (ttp-110) REVERT: D 75 THR cc_start: 0.7994 (m) cc_final: 0.7702 (t) REVERT: D 126 ARG cc_start: 0.7493 (ttt180) cc_final: 0.6480 (ttp-110) REVERT: D 130 TRP cc_start: 0.6988 (m100) cc_final: 0.6570 (m100) outliers start: 4 outliers final: 0 residues processed: 144 average time/residue: 0.8969 time to fit residues: 185.6378 Evaluate side-chains 124 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN B 370 HIS B 421 GLN C 370 HIS C 421 GLN D 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105052 restraints weight = 39046.820| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.58 r_work: 0.2986 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12316 Z= 0.157 Angle : 0.439 4.120 16712 Z= 0.241 Chirality : 0.033 0.132 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.355 11.459 1756 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.52 % Allowed : 10.37 % Favored : 88.11 % 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: 3.20 (0.21), residues: 1508 helix: 2.57 (0.14), residues: 1268 sheet: 0.07 (0.87), residues: 48 loop : -0.60 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE A 11 TYR 0.008 0.001 TYR B 96 ARG 0.002 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1064) hydrogen bonds : angle 3.93923 ( 3180) covalent geometry : bond 0.00334 (12316) covalent geometry : angle 0.43877 (16712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 2.003 Fit side-chains REVERT: A 75 THR cc_start: 0.8029 (m) cc_final: 0.7758 (t) REVERT: A 110 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: A 126 ARG cc_start: 0.7610 (ttt180) cc_final: 0.6850 (ttp-110) REVERT: B 75 THR cc_start: 0.8014 (m) cc_final: 0.7749 (t) REVERT: B 110 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: B 126 ARG cc_start: 0.7609 (ttt180) cc_final: 0.6845 (ttp-110) REVERT: C 75 THR cc_start: 0.8021 (m) cc_final: 0.7763 (t) REVERT: C 110 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: C 126 ARG cc_start: 0.7605 (ttt180) cc_final: 0.6846 (ttp-110) REVERT: D 75 THR cc_start: 0.8008 (m) cc_final: 0.7744 (t) REVERT: D 110 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: D 126 ARG cc_start: 0.7531 (ttt180) cc_final: 0.6534 (ttp80) REVERT: D 130 TRP cc_start: 0.6996 (m100) cc_final: 0.6557 (m100) outliers start: 20 outliers final: 12 residues processed: 136 average time/residue: 0.6238 time to fit residues: 119.8367 Evaluate side-chains 136 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101960 restraints weight = 40058.889| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.60 r_work: 0.2944 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12316 Z= 0.191 Angle : 0.460 4.264 16712 Z= 0.254 Chirality : 0.034 0.135 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.481 17.208 1756 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.83 % Allowed : 9.53 % Favored : 88.64 % 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: 3.11 (0.21), residues: 1508 helix: 2.51 (0.14), residues: 1268 sheet: -0.17 (0.88), residues: 48 loop : -0.56 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 328 HIS 0.003 0.001 HIS A 337 PHE 0.009 0.001 PHE C 315 TYR 0.010 0.001 TYR D 182 ARG 0.003 0.000 ARG D 402 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 1064) hydrogen bonds : angle 3.94862 ( 3180) covalent geometry : bond 0.00423 (12316) covalent geometry : angle 0.45995 (16712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.757 Fit side-chains REVERT: A 75 THR cc_start: 0.8184 (m) cc_final: 0.7874 (t) REVERT: A 110 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: A 126 ARG cc_start: 0.7624 (ttt180) cc_final: 0.6943 (ttp80) REVERT: B 75 THR cc_start: 0.8173 (m) cc_final: 0.7864 (t) REVERT: B 110 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: B 126 ARG cc_start: 0.7606 (ttt180) cc_final: 0.6936 (ttp80) REVERT: C 75 THR cc_start: 0.8184 (m) cc_final: 0.7877 (t) REVERT: C 110 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: C 126 ARG cc_start: 0.7608 (ttt180) cc_final: 0.6931 (ttp80) REVERT: D 75 THR cc_start: 0.8170 (m) cc_final: 0.7856 (t) REVERT: D 110 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: D 126 ARG cc_start: 0.7548 (ttt180) cc_final: 0.7034 (ttt90) REVERT: D 130 TRP cc_start: 0.6991 (m100) cc_final: 0.6460 (m100) outliers start: 24 outliers final: 12 residues processed: 155 average time/residue: 0.6306 time to fit residues: 134.8449 Evaluate side-chains 151 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 114 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101934 restraints weight = 40154.692| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.61 r_work: 0.2947 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12316 Z= 0.183 Angle : 0.451 4.194 16712 Z= 0.249 Chirality : 0.034 0.136 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.441 14.410 1756 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 10.98 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.21), residues: 1508 helix: 2.49 (0.14), residues: 1268 sheet: -0.20 (0.89), residues: 48 loop : -0.62 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE A 11 TYR 0.008 0.001 TYR A 182 ARG 0.002 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1064) hydrogen bonds : angle 3.91812 ( 3180) covalent geometry : bond 0.00401 (12316) covalent geometry : angle 0.45143 (16712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.829 Fit side-chains REVERT: A 75 THR cc_start: 0.8189 (m) cc_final: 0.7871 (t) REVERT: A 110 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: A 126 ARG cc_start: 0.7614 (ttt180) cc_final: 0.6903 (ttp80) REVERT: B 75 THR cc_start: 0.8184 (m) cc_final: 0.7865 (t) REVERT: B 110 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: B 126 ARG cc_start: 0.7619 (ttt180) cc_final: 0.6910 (ttp80) REVERT: C 75 THR cc_start: 0.8191 (m) cc_final: 0.7878 (t) REVERT: C 110 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: C 126 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6901 (ttp80) REVERT: D 75 THR cc_start: 0.8182 (m) cc_final: 0.7869 (t) REVERT: D 110 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: D 126 ARG cc_start: 0.7565 (ttt180) cc_final: 0.6570 (ttp80) REVERT: D 130 TRP cc_start: 0.7002 (m100) cc_final: 0.6485 (m100) outliers start: 16 outliers final: 12 residues processed: 152 average time/residue: 0.6518 time to fit residues: 136.9545 Evaluate side-chains 150 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100960 restraints weight = 40253.025| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.60 r_work: 0.2931 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12316 Z= 0.202 Angle : 0.463 4.243 16712 Z= 0.257 Chirality : 0.034 0.141 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.533 15.755 1756 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.52 % Allowed : 11.28 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.95 (0.21), residues: 1508 helix: 2.41 (0.14), residues: 1268 sheet: -0.22 (0.89), residues: 48 loop : -0.66 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 328 HIS 0.004 0.001 HIS B 337 PHE 0.007 0.001 PHE C 11 TYR 0.010 0.001 TYR B 182 ARG 0.002 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 1064) hydrogen bonds : angle 3.95893 ( 3180) covalent geometry : bond 0.00448 (12316) covalent geometry : angle 0.46295 (16712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.736 Fit side-chains REVERT: A 110 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: A 126 ARG cc_start: 0.7604 (ttt180) cc_final: 0.6921 (ttp80) REVERT: B 110 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: B 126 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6922 (ttp80) REVERT: C 110 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: C 126 ARG cc_start: 0.7617 (ttt180) cc_final: 0.6923 (ttp80) REVERT: D 110 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: D 126 ARG cc_start: 0.7520 (ttt180) cc_final: 0.6581 (ttp80) REVERT: D 130 TRP cc_start: 0.7009 (m100) cc_final: 0.6475 (m100) outliers start: 20 outliers final: 16 residues processed: 148 average time/residue: 0.6429 time to fit residues: 130.7996 Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101507 restraints weight = 40386.683| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.60 r_work: 0.2936 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12316 Z= 0.183 Angle : 0.460 5.465 16712 Z= 0.251 Chirality : 0.034 0.139 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.483 14.137 1756 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.52 % Allowed : 11.59 % Favored : 86.89 % 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: 3.01 (0.21), residues: 1508 helix: 2.46 (0.14), residues: 1268 sheet: -0.21 (0.89), residues: 48 loop : -0.72 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 328 HIS 0.004 0.001 HIS C 337 PHE 0.007 0.001 PHE C 40 TYR 0.007 0.001 TYR C 182 ARG 0.001 0.000 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 1064) hydrogen bonds : angle 3.91304 ( 3180) covalent geometry : bond 0.00400 (12316) covalent geometry : angle 0.45971 (16712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.864 Fit side-chains REVERT: A 110 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: A 126 ARG cc_start: 0.7611 (ttt180) cc_final: 0.6917 (ttp80) REVERT: B 110 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: B 126 ARG cc_start: 0.7620 (ttt180) cc_final: 0.6923 (ttp80) REVERT: C 75 THR cc_start: 0.8220 (m) cc_final: 0.7891 (t) REVERT: C 110 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: C 126 ARG cc_start: 0.7634 (ttt180) cc_final: 0.6554 (ttp80) REVERT: C 130 TRP cc_start: 0.7023 (m100) cc_final: 0.6416 (m100) REVERT: D 110 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: D 126 ARG cc_start: 0.7555 (ttt180) cc_final: 0.6564 (ttp80) REVERT: D 130 TRP cc_start: 0.7012 (m100) cc_final: 0.6487 (m100) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.6494 time to fit residues: 136.7652 Evaluate side-chains 148 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100923 restraints weight = 40259.110| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.58 r_work: 0.2931 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12316 Z= 0.202 Angle : 0.472 5.537 16712 Z= 0.258 Chirality : 0.035 0.138 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.523 14.719 1756 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.52 % Allowed : 11.36 % Favored : 87.12 % 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: 2.92 (0.21), residues: 1508 helix: 2.40 (0.14), residues: 1268 sheet: -0.22 (0.90), residues: 48 loop : -0.76 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.004 0.001 HIS D 337 PHE 0.007 0.001 PHE B 40 TYR 0.009 0.001 TYR A 182 ARG 0.002 0.000 ARG D 402 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 1064) hydrogen bonds : angle 3.95395 ( 3180) covalent geometry : bond 0.00448 (12316) covalent geometry : angle 0.47239 (16712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.805 Fit side-chains REVERT: A 110 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: A 126 ARG cc_start: 0.7590 (ttt180) cc_final: 0.6916 (ttp80) REVERT: B 110 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: B 126 ARG cc_start: 0.7622 (ttt180) cc_final: 0.6911 (ttp80) REVERT: C 110 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: C 126 ARG cc_start: 0.7601 (ttt180) cc_final: 0.6920 (ttp80) REVERT: D 110 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: D 126 ARG cc_start: 0.7540 (ttt180) cc_final: 0.6590 (ttp80) REVERT: D 130 TRP cc_start: 0.7014 (m100) cc_final: 0.6489 (m100) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.6586 time to fit residues: 130.5327 Evaluate side-chains 148 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.102515 restraints weight = 40316.657| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.61 r_work: 0.2952 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12316 Z= 0.148 Angle : 0.443 6.052 16712 Z= 0.240 Chirality : 0.033 0.134 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.393 12.495 1756 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.22 % Allowed : 11.66 % Favored : 87.12 % 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: 3.21 (0.22), residues: 1508 helix: 2.60 (0.14), residues: 1268 sheet: -0.22 (0.90), residues: 48 loop : -0.71 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS D 337 PHE 0.008 0.001 PHE C 40 TYR 0.007 0.001 TYR C 96 ARG 0.002 0.000 ARG D 367 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1064) hydrogen bonds : angle 3.82580 ( 3180) covalent geometry : bond 0.00311 (12316) covalent geometry : angle 0.44266 (16712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.8187 (m) cc_final: 0.7861 (t) REVERT: A 110 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 126 ARG cc_start: 0.7565 (ttt180) cc_final: 0.6505 (ttp80) REVERT: A 127 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7321 (ttt180) REVERT: A 130 TRP cc_start: 0.7018 (m100) cc_final: 0.6405 (m100) REVERT: B 75 THR cc_start: 0.8185 (m) cc_final: 0.7861 (t) REVERT: B 110 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: B 126 ARG cc_start: 0.7599 (ttt180) cc_final: 0.6513 (ttp80) REVERT: B 127 ARG cc_start: 0.7528 (ttt180) cc_final: 0.7320 (ttt180) REVERT: B 130 TRP cc_start: 0.6995 (m100) cc_final: 0.6382 (m100) REVERT: C 75 THR cc_start: 0.8194 (m) cc_final: 0.7873 (t) REVERT: C 110 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: C 126 ARG cc_start: 0.7574 (ttt180) cc_final: 0.6511 (ttp80) REVERT: C 127 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7309 (ttt180) REVERT: C 130 TRP cc_start: 0.7008 (m100) cc_final: 0.6397 (m100) REVERT: D 75 THR cc_start: 0.8184 (m) cc_final: 0.7860 (t) REVERT: D 110 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: D 126 ARG cc_start: 0.7498 (ttt180) cc_final: 0.6504 (ttp80) REVERT: D 130 TRP cc_start: 0.6977 (m100) cc_final: 0.6459 (m100) REVERT: D 364 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6808 (tt0) outliers start: 16 outliers final: 12 residues processed: 157 average time/residue: 0.6815 time to fit residues: 145.4932 Evaluate side-chains 155 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101289 restraints weight = 40499.095| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.62 r_work: 0.2933 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12316 Z= 0.188 Angle : 0.467 6.297 16712 Z= 0.254 Chirality : 0.034 0.134 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.476 14.882 1756 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.22 % Allowed : 11.89 % Favored : 86.89 % 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: 3.05 (0.22), residues: 1508 helix: 2.50 (0.14), residues: 1268 sheet: -0.33 (0.90), residues: 48 loop : -0.78 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 328 HIS 0.004 0.001 HIS D 337 PHE 0.007 0.001 PHE C 40 TYR 0.009 0.001 TYR D 182 ARG 0.002 0.000 ARG B 402 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1064) hydrogen bonds : angle 3.89101 ( 3180) covalent geometry : bond 0.00414 (12316) covalent geometry : angle 0.46704 (16712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.753 Fit side-chains REVERT: A 110 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: A 126 ARG cc_start: 0.7548 (ttt180) cc_final: 0.6522 (ttp80) REVERT: A 127 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7308 (ttt180) REVERT: A 130 TRP cc_start: 0.7031 (m100) cc_final: 0.6408 (m100) REVERT: A 364 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6837 (tt0) REVERT: B 110 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: B 126 ARG cc_start: 0.7539 (ttt180) cc_final: 0.6527 (ttp80) REVERT: B 127 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7317 (ttt180) REVERT: B 130 TRP cc_start: 0.7000 (m100) cc_final: 0.6376 (m100) REVERT: B 364 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6834 (tt0) REVERT: C 110 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: C 126 ARG cc_start: 0.7540 (ttt180) cc_final: 0.6527 (ttp80) REVERT: C 127 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7310 (ttt180) REVERT: C 130 TRP cc_start: 0.7002 (m100) cc_final: 0.6380 (m100) REVERT: C 364 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6818 (tt0) REVERT: D 110 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: D 126 ARG cc_start: 0.7517 (ttt180) cc_final: 0.6543 (ttp80) REVERT: D 127 ARG cc_start: 0.7516 (ttt180) cc_final: 0.7308 (ttt180) REVERT: D 130 TRP cc_start: 0.6990 (m100) cc_final: 0.6458 (m100) REVERT: D 364 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6881 (tt0) outliers start: 16 outliers final: 12 residues processed: 152 average time/residue: 0.7091 time to fit residues: 146.9882 Evaluate side-chains 153 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102237 restraints weight = 40073.255| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.59 r_work: 0.2946 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12316 Z= 0.164 Angle : 0.451 6.336 16712 Z= 0.244 Chirality : 0.034 0.133 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.412 13.226 1756 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.22 % Allowed : 11.97 % Favored : 86.81 % 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: 3.16 (0.22), residues: 1508 helix: 2.58 (0.14), residues: 1268 sheet: -0.38 (0.89), residues: 48 loop : -0.76 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.004 0.001 HIS B 337 PHE 0.007 0.001 PHE D 40 TYR 0.006 0.001 TYR A 182 ARG 0.002 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 1064) hydrogen bonds : angle 3.83282 ( 3180) covalent geometry : bond 0.00353 (12316) covalent geometry : angle 0.45066 (16712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10622.52 seconds wall clock time: 184 minutes 33.43 seconds (11073.43 seconds total)