Starting phenix.real_space_refine on Sat Jul 4 23:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x84_38135/07_2026/8x84_38135_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x84_38135/07_2026/8x84_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x84_38135/07_2026/8x84_38135_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x84_38135/07_2026/8x84_38135_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x84_38135/07_2026/8x84_38135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x84_38135/07_2026/8x84_38135.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24534 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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, 12 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain breaks: 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} Time building chain proxies: 3.76, per 1000 atoms: 0.15 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: 1.87 Conformation dependent library (CDL) restraints added in 623.9 milliseconds 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: 0.47 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: 4.55 Time building geometry restraints manager: 2.59 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: 0.870 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: 0.150 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.900 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.001 0.000 ARG D 31 TYR 0.005 0.001 TYR B 96 PHE 0.007 0.001 PHE C 315 TRP 0.006 0.001 TRP B 328 HIS 0.001 0.000 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.23 (12316) covalent geometry : angle 0.52744 / 0.32 (16712) hydrogen bonds : bond 0.09482 / 6.20 ( 1064) hydrogen bonds : angle 4.94729 / 3.58 ( 3180) *********************** 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 : 0.544 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: 0.2631 time to fit residues: 33.9302 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 : 0.543 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 421 GLN C 421 GLN D 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108363 restraints weight = 38746.905| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.59 r_work: 0.3032 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12316 Z= 0.168 Angle : 0.457 4.122 16712 Z= 0.251 Chirality : 0.034 0.129 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.575 21.692 1760 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.91 % Allowed : 8.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.21), residues: 1508 helix: 2.63 (0.14), residues: 1264 sheet: 0.35 (0.85), residues: 48 loop : -0.70 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.007 0.001 TYR A 175 PHE 0.007 0.001 PHE C 40 TRP 0.007 0.001 TRP A 328 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (12316) covalent geometry : angle 0.45680 / 0.25 (16712) hydrogen bonds : bond 0.04211 / 2.82 ( 1064) hydrogen bonds : angle 4.00741 / 2.93 ( 3180) *********************** 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 136 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.615 Fit side-chains REVERT: A 209 MET cc_start: 0.8176 (ttt) cc_final: 0.7902 (ttm) REVERT: B 209 MET cc_start: 0.8143 (ttt) cc_final: 0.7863 (ttm) REVERT: C 209 MET cc_start: 0.8157 (ttt) cc_final: 0.7870 (ttm) REVERT: D 209 MET cc_start: 0.8122 (ttt) cc_final: 0.7847 (ttm) outliers start: 12 outliers final: 0 residues processed: 136 average time/residue: 0.1938 time to fit residues: 40.3709 Evaluate side-chains 104 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106706 restraints weight = 39049.518| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.65 r_work: 0.3010 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12316 Z= 0.134 Angle : 0.415 4.045 16712 Z= 0.229 Chirality : 0.033 0.133 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.237 10.485 1756 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.61 % Allowed : 9.45 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.21), residues: 1508 helix: 2.86 (0.14), residues: 1264 sheet: 0.16 (0.85), residues: 48 loop : -0.70 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 402 TYR 0.007 0.001 TYR A 96 PHE 0.007 0.001 PHE D 11 TRP 0.005 0.001 TRP D 328 HIS 0.002 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12316) covalent geometry : angle 0.41511 / 0.23 (16712) hydrogen bonds : bond 0.04005 / 2.67 ( 1064) hydrogen bonds : angle 3.82901 / 2.79 ( 3180) *********************** 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 128 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.533 Fit side-chains REVERT: A 126 ARG cc_start: 0.7476 (ttt180) cc_final: 0.6519 (ttp-110) REVERT: A 130 TRP cc_start: 0.6983 (m100) cc_final: 0.6361 (m100) REVERT: A 209 MET cc_start: 0.8223 (ttt) cc_final: 0.7907 (ttm) REVERT: B 126 ARG cc_start: 0.7470 (ttt180) cc_final: 0.6511 (ttp-110) REVERT: B 130 TRP cc_start: 0.6971 (m100) cc_final: 0.6346 (m100) REVERT: B 209 MET cc_start: 0.8195 (ttt) cc_final: 0.7867 (ttm) REVERT: C 126 ARG cc_start: 0.7477 (ttt180) cc_final: 0.6518 (ttp-110) REVERT: C 130 TRP cc_start: 0.6966 (m100) cc_final: 0.6340 (m100) REVERT: C 209 MET cc_start: 0.8209 (ttt) cc_final: 0.7878 (ttm) REVERT: D 126 ARG cc_start: 0.7456 (ttt180) cc_final: 0.6494 (ttp-110) REVERT: D 130 TRP cc_start: 0.6971 (m100) cc_final: 0.6350 (m100) REVERT: D 209 MET cc_start: 0.8220 (ttt) cc_final: 0.7908 (ttm) outliers start: 8 outliers final: 8 residues processed: 128 average time/residue: 0.2706 time to fit residues: 48.6481 Evaluate side-chains 119 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER 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 117 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 148 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN C 171 ASN D 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103223 restraints weight = 39749.420| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.65 r_work: 0.2962 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2054 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= 0.168 Angle : 0.440 4.186 16712 Z= 0.245 Chirality : 0.033 0.134 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.418 18.362 1756 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.91 % Allowed : 9.98 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.21), residues: 1508 helix: 2.73 (0.14), residues: 1268 sheet: -0.09 (0.88), residues: 48 loop : -0.55 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 402 TYR 0.008 0.001 TYR C 96 PHE 0.007 0.001 PHE A 11 TRP 0.007 0.001 TRP C 328 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (12316) covalent geometry : angle 0.44001 / 0.25 (16712) hydrogen bonds : bond 0.04198 / 2.80 ( 1064) hydrogen bonds : angle 3.85840 / 2.82 ( 3180) *********************** 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 150 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.501 Fit side-chains REVERT: A 75 THR cc_start: 0.8071 (m) cc_final: 0.7771 (t) REVERT: A 110 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 126 ARG cc_start: 0.7515 (ttt180) cc_final: 0.6999 (ttt90) REVERT: A 130 TRP cc_start: 0.6915 (m100) cc_final: 0.6389 (m100) REVERT: B 75 THR cc_start: 0.8059 (m) cc_final: 0.7762 (t) REVERT: B 110 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: B 126 ARG cc_start: 0.7501 (ttt180) cc_final: 0.6983 (ttt90) REVERT: B 130 TRP cc_start: 0.6902 (m100) cc_final: 0.6380 (m100) REVERT: C 75 THR cc_start: 0.8065 (m) cc_final: 0.7775 (t) REVERT: C 110 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: C 126 ARG cc_start: 0.7509 (ttt180) cc_final: 0.6515 (ttp80) REVERT: C 130 TRP cc_start: 0.6887 (m100) cc_final: 0.6389 (m100) REVERT: D 75 THR cc_start: 0.8049 (m) cc_final: 0.7751 (t) REVERT: D 110 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: D 126 ARG cc_start: 0.7503 (ttt180) cc_final: 0.6983 (ttt90) REVERT: D 130 TRP cc_start: 0.6901 (m100) cc_final: 0.6377 (m100) outliers start: 12 outliers final: 8 residues processed: 150 average time/residue: 0.2491 time to fit residues: 52.3481 Evaluate side-chains 142 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP 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 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP 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 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 66 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101845 restraints weight = 40086.505| |-----------------------------------------------------------------------------| r_work (start): 0.3076 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: 0.8086 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12316 Z= 0.196 Angle : 0.451 4.269 16712 Z= 0.252 Chirality : 0.035 0.136 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.441 16.362 1756 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.13 % Allowed : 9.15 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.21), residues: 1508 helix: 2.56 (0.14), residues: 1268 sheet: -0.24 (0.89), residues: 48 loop : -0.59 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 402 TYR 0.007 0.001 TYR B 182 PHE 0.010 0.001 PHE A 315 TRP 0.007 0.001 TRP A 328 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (12316) covalent geometry : angle 0.45076 / 0.25 (16712) hydrogen bonds : bond 0.04371 / 2.92 ( 1064) hydrogen bonds : angle 3.92391 / 2.87 ( 3180) *********************** 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 180 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.638 Fit side-chains REVERT: A 75 THR cc_start: 0.8215 (m) cc_final: 0.7893 (t) REVERT: A 110 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: A 126 ARG cc_start: 0.7564 (ttt180) cc_final: 0.7037 (ttt90) REVERT: A 130 TRP cc_start: 0.7009 (m100) cc_final: 0.6473 (m100) REVERT: B 75 THR cc_start: 0.8206 (m) cc_final: 0.7885 (t) REVERT: B 110 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: B 126 ARG cc_start: 0.7524 (ttt180) cc_final: 0.6630 (ttp80) REVERT: B 130 TRP cc_start: 0.6986 (m100) cc_final: 0.6474 (m100) REVERT: C 75 THR cc_start: 0.8214 (m) cc_final: 0.7895 (t) REVERT: C 110 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: C 126 ARG cc_start: 0.7565 (ttt180) cc_final: 0.6567 (ttp80) REVERT: C 130 TRP cc_start: 0.6984 (m100) cc_final: 0.6471 (m100) REVERT: D 75 THR cc_start: 0.8201 (m) cc_final: 0.7885 (t) REVERT: D 110 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: D 126 ARG cc_start: 0.7559 (ttt180) cc_final: 0.6557 (ttp80) REVERT: D 130 TRP cc_start: 0.7000 (m100) cc_final: 0.6490 (m100) outliers start: 28 outliers final: 13 residues processed: 168 average time/residue: 0.2722 time to fit residues: 64.1447 Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 A residue 371 GLU 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 98 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101641 restraints weight = 40252.917| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.59 r_work: 0.2939 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12316 Z= 0.191 Angle : 0.450 4.218 16712 Z= 0.251 Chirality : 0.034 0.136 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.495 16.018 1756 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 10.29 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.21), residues: 1508 helix: 2.50 (0.14), residues: 1268 sheet: -0.28 (0.89), residues: 48 loop : -0.66 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 402 TYR 0.007 0.001 TYR A 182 PHE 0.006 0.001 PHE B 315 TRP 0.007 0.001 TRP C 328 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (12316) covalent geometry : angle 0.45001 / 0.25 (16712) hydrogen bonds : bond 0.04332 / 2.89 ( 1064) hydrogen bonds : angle 3.91192 / 2.86 ( 3180) *********************** 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 171 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.629 Fit side-chains REVERT: A 75 THR cc_start: 0.8222 (m) cc_final: 0.7896 (t) REVERT: A 110 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: A 126 ARG cc_start: 0.7546 (ttt180) cc_final: 0.6585 (ttp80) REVERT: A 130 TRP cc_start: 0.6997 (m100) cc_final: 0.6481 (m100) REVERT: B 75 THR cc_start: 0.8212 (m) cc_final: 0.7886 (t) REVERT: B 110 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: B 126 ARG cc_start: 0.7543 (ttt180) cc_final: 0.6577 (ttp80) REVERT: B 130 TRP cc_start: 0.6983 (m100) cc_final: 0.6450 (m100) REVERT: C 75 THR cc_start: 0.8223 (m) cc_final: 0.7898 (t) REVERT: C 110 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: C 126 ARG cc_start: 0.7572 (ttt180) cc_final: 0.6590 (ttp80) REVERT: C 130 TRP cc_start: 0.6980 (m100) cc_final: 0.6463 (m100) REVERT: D 75 THR cc_start: 0.8206 (m) cc_final: 0.7884 (t) REVERT: D 110 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: D 126 ARG cc_start: 0.7524 (ttt180) cc_final: 0.6576 (ttp80) REVERT: D 130 TRP cc_start: 0.6994 (m100) cc_final: 0.6482 (m100) outliers start: 24 outliers final: 19 residues processed: 159 average time/residue: 0.2776 time to fit residues: 61.5574 Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 B residue 371 GLU 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 C residue 371 GLU 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 Chi-restraints excluded: chain D residue 371 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103222 restraints weight = 40032.956| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.59 r_work: 0.2968 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12316 Z= 0.140 Angle : 0.428 5.368 16712 Z= 0.235 Chirality : 0.033 0.131 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.366 13.434 1756 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 10.59 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.22), residues: 1508 helix: 2.67 (0.14), residues: 1268 sheet: -0.27 (0.89), residues: 48 loop : -0.59 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 367 TYR 0.006 0.001 TYR D 96 PHE 0.007 0.001 PHE D 40 TRP 0.006 0.001 TRP A 328 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (12316) covalent geometry : angle 0.42754 / 0.23 (16712) hydrogen bonds : bond 0.04084 / 2.72 ( 1064) hydrogen bonds : angle 3.79419 / 2.78 ( 3180) *********************** 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 166 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.409 Fit side-chains REVERT: A 75 THR cc_start: 0.8194 (m) cc_final: 0.7883 (t) REVERT: A 110 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: A 126 ARG cc_start: 0.7542 (ttt180) cc_final: 0.6568 (ttp80) REVERT: A 127 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7320 (ttt180) REVERT: A 130 TRP cc_start: 0.6967 (m100) cc_final: 0.6444 (m100) REVERT: B 75 THR cc_start: 0.8176 (m) cc_final: 0.7866 (t) REVERT: B 110 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: B 126 ARG cc_start: 0.7520 (ttt180) cc_final: 0.6541 (ttp80) REVERT: B 127 ARG cc_start: 0.7566 (ttt180) cc_final: 0.7327 (ttt180) REVERT: B 130 TRP cc_start: 0.6953 (m100) cc_final: 0.6425 (m100) REVERT: C 75 THR cc_start: 0.8195 (m) cc_final: 0.7886 (t) REVERT: C 110 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: C 126 ARG cc_start: 0.7526 (ttt180) cc_final: 0.6547 (ttp80) REVERT: C 127 ARG cc_start: 0.7550 (ttt180) cc_final: 0.7318 (ttt180) REVERT: C 130 TRP cc_start: 0.6960 (m100) cc_final: 0.6441 (m100) REVERT: D 75 THR cc_start: 0.8177 (m) cc_final: 0.7870 (t) REVERT: D 110 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: D 126 ARG cc_start: 0.7515 (ttt180) cc_final: 0.6546 (ttp80) REVERT: D 127 ARG cc_start: 0.7540 (ttt180) cc_final: 0.7312 (ttt180) REVERT: D 130 TRP cc_start: 0.6978 (m100) cc_final: 0.6460 (m100) outliers start: 16 outliers final: 12 residues processed: 158 average time/residue: 0.2808 time to fit residues: 60.1080 Evaluate side-chains 166 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 16 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.101229 restraints weight = 40469.898| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.60 r_work: 0.2932 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12316 Z= 0.199 Angle : 0.462 5.390 16712 Z= 0.255 Chirality : 0.034 0.135 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.504 16.379 1756 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.37 % Allowed : 10.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.21), residues: 1508 helix: 2.50 (0.14), residues: 1268 sheet: -0.31 (0.89), residues: 48 loop : -0.71 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.008 0.001 TYR C 182 PHE 0.006 0.001 PHE D 315 TRP 0.007 0.001 TRP C 328 HIS 0.004 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (12316) covalent geometry : angle 0.46165 / 0.25 (16712) hydrogen bonds : bond 0.04373 / 2.92 ( 1064) hydrogen bonds : angle 3.91146 / 2.87 ( 3180) *********************** 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 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.658 Fit side-chains REVERT: A 110 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: A 126 ARG cc_start: 0.7573 (ttt180) cc_final: 0.6618 (ttp80) REVERT: A 130 TRP cc_start: 0.7007 (m100) cc_final: 0.6472 (m100) REVERT: B 110 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: B 126 ARG cc_start: 0.7560 (ttt180) cc_final: 0.6591 (ttp80) REVERT: B 130 TRP cc_start: 0.6999 (m100) cc_final: 0.6457 (m100) REVERT: C 110 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: C 126 ARG cc_start: 0.7569 (ttt180) cc_final: 0.6604 (ttp80) REVERT: C 130 TRP cc_start: 0.7002 (m100) cc_final: 0.6467 (m100) REVERT: D 110 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: D 126 ARG cc_start: 0.7550 (ttt180) cc_final: 0.6597 (ttp80) REVERT: D 130 TRP cc_start: 0.7017 (m100) cc_final: 0.6484 (m100) outliers start: 18 outliers final: 12 residues processed: 148 average time/residue: 0.2681 time to fit residues: 54.7736 Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103089 restraints weight = 40084.390| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.61 r_work: 0.2963 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12316 Z= 0.141 Angle : 0.430 5.966 16712 Z= 0.235 Chirality : 0.033 0.138 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.355 12.711 1756 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 10.75 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.22), residues: 1508 helix: 2.70 (0.14), residues: 1268 sheet: -0.24 (0.89), residues: 48 loop : -0.67 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 367 TYR 0.006 0.001 TYR D 96 PHE 0.007 0.001 PHE D 40 TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12316) covalent geometry : angle 0.43013 / 0.23 (16712) hydrogen bonds : bond 0.04058 / 2.70 ( 1064) hydrogen bonds : angle 3.77427 / 2.77 ( 3180) *********************** 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 162 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.658 Fit side-chains REVERT: A 75 THR cc_start: 0.8190 (m) cc_final: 0.7869 (t) REVERT: A 110 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: A 126 ARG cc_start: 0.7536 (ttt180) cc_final: 0.6538 (ttp80) REVERT: A 127 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7320 (ttt180) REVERT: A 130 TRP cc_start: 0.6954 (m100) cc_final: 0.6425 (m100) REVERT: B 75 THR cc_start: 0.8180 (m) cc_final: 0.7858 (t) REVERT: B 110 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: B 126 ARG cc_start: 0.7515 (ttt180) cc_final: 0.6522 (ttp80) REVERT: B 127 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7315 (ttt180) REVERT: B 130 TRP cc_start: 0.6937 (m100) cc_final: 0.6404 (m100) REVERT: C 75 THR cc_start: 0.8192 (m) cc_final: 0.7870 (t) REVERT: C 110 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: C 126 ARG cc_start: 0.7525 (ttt180) cc_final: 0.6529 (ttp80) REVERT: C 127 ARG cc_start: 0.7510 (ttt180) cc_final: 0.7299 (ttt180) REVERT: C 130 TRP cc_start: 0.6959 (m100) cc_final: 0.6429 (m100) REVERT: D 75 THR cc_start: 0.8180 (m) cc_final: 0.7863 (t) REVERT: D 110 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: D 126 ARG cc_start: 0.7504 (ttt180) cc_final: 0.6511 (ttp80) REVERT: D 127 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7301 (ttt180) REVERT: D 130 TRP cc_start: 0.6968 (m100) cc_final: 0.6442 (m100) outliers start: 16 outliers final: 12 residues processed: 158 average time/residue: 0.3228 time to fit residues: 70.0110 Evaluate side-chains 158 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 12 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099541 restraints weight = 40634.215| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.60 r_work: 0.2910 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12316 Z= 0.261 Angle : 0.513 6.218 16712 Z= 0.283 Chirality : 0.037 0.141 2008 Planarity : 0.003 0.022 2040 Dihedral : 3.663 17.710 1756 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.52 % Allowed : 10.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.21), residues: 1508 helix: 2.29 (0.14), residues: 1268 sheet: -0.37 (0.88), residues: 48 loop : -0.76 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.012 0.002 TYR A 182 PHE 0.008 0.002 PHE A 392 TRP 0.010 0.001 TRP C 328 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 (12316) covalent geometry : angle 0.51273 / 0.28 (16712) hydrogen bonds : bond 0.04711 / 3.15 ( 1064) hydrogen bonds : angle 4.04618 / 2.97 ( 3180) ********************** 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 161 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.664 Fit side-chains REVERT: A 110 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: A 126 ARG cc_start: 0.7556 (ttt180) cc_final: 0.6584 (ttp80) REVERT: A 130 TRP cc_start: 0.6996 (m100) cc_final: 0.6449 (m100) REVERT: A 364 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6887 (tt0) REVERT: B 110 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: B 126 ARG cc_start: 0.7564 (ttt180) cc_final: 0.6575 (ttp80) REVERT: B 130 TRP cc_start: 0.7009 (m100) cc_final: 0.6462 (m100) REVERT: B 364 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6911 (tt0) REVERT: C 110 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: C 126 ARG cc_start: 0.7543 (ttt180) cc_final: 0.6569 (ttp80) REVERT: C 130 TRP cc_start: 0.6984 (m100) cc_final: 0.6433 (m100) REVERT: D 110 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: D 126 ARG cc_start: 0.7549 (ttt180) cc_final: 0.6566 (ttp80) REVERT: D 130 TRP cc_start: 0.7015 (m100) cc_final: 0.6471 (m100) REVERT: D 364 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6910 (tt0) outliers start: 20 outliers final: 12 residues processed: 157 average time/residue: 0.2628 time to fit residues: 57.5756 Evaluate side-chains 149 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 120 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 148 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104393 restraints weight = 39963.481| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.59 r_work: 0.2980 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12316 Z= 0.109 Angle : 0.424 6.615 16712 Z= 0.230 Chirality : 0.033 0.137 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.314 11.331 1756 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.07 % Allowed : 11.20 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.22), residues: 1508 helix: 2.76 (0.14), residues: 1268 sheet: -0.31 (0.89), residues: 48 loop : -0.57 (0.48), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 367 TYR 0.008 0.001 TYR D 96 PHE 0.009 0.001 PHE D 40 TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (12316) covalent geometry : angle 0.42412 / 0.23 (16712) hydrogen bonds : bond 0.03924 / 2.61 ( 1064) hydrogen bonds : angle 3.72447 / 2.74 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4557.80 seconds wall clock time: 78 minutes 18.36 seconds (4698.36 seconds total)