Starting phenix.real_space_refine on Fri Feb 6 08:32:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x84_38135/02_2026/8x84_38135_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x84_38135/02_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_38135/02_2026/8x84_38135_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x84_38135/02_2026/8x84_38135_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x84_38135/02_2026/8x84_38135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x84_38135/02_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 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} Time building chain proxies: 4.87, per 1000 atoms: 0.20 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 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: 0.62 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: 6.30 Time building geometry restraints manager: 3.62 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: 0.970 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: 0.170 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.530 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.00411 (12316) covalent geometry : angle 0.52744 (16712) hydrogen bonds : bond 0.09482 ( 1064) hydrogen bonds : angle 4.94729 ( 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 : 0.634 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: 0.3351 time to fit residues: 42.1091 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 : 0.648 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3481 r_free = 0.3481 target = 0.134107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108830 restraints weight = 38666.864| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.59 r_work: 0.3042 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1127 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 : 0.453 4.089 16712 Z= 0.249 Chirality : 0.034 0.129 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.578 20.943 1760 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.58 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: 3.29 (0.21), residues: 1508 helix: 2.65 (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 0.002 0.000 ARG A 424 TYR 0.007 0.001 TYR C 175 PHE 0.007 0.001 PHE D 40 TRP 0.007 0.001 TRP D 328 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00359 (12316) covalent geometry : angle 0.45277 (16712) hydrogen bonds : bond 0.04202 ( 1064) hydrogen bonds : angle 4.01321 ( 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 128 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.666 Fit side-chains REVERT: A 209 MET cc_start: 0.8169 (ttt) cc_final: 0.7901 (ttm) REVERT: B 209 MET cc_start: 0.8145 (ttt) cc_final: 0.7860 (ttm) REVERT: C 209 MET cc_start: 0.8159 (ttt) cc_final: 0.7868 (ttm) REVERT: D 209 MET cc_start: 0.8115 (ttt) cc_final: 0.7850 (ttm) outliers start: 12 outliers final: 0 residues processed: 128 average time/residue: 0.2372 time to fit residues: 45.7179 Evaluate side-chains 96 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 3.9990 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3489 r_free = 0.3489 target = 0.134936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109790 restraints weight = 38777.138| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.59 r_work: 0.3053 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12316 Z= 0.111 Angle : 0.407 3.928 16712 Z= 0.222 Chirality : 0.032 0.131 2008 Planarity : 0.002 0.028 2040 Dihedral : 3.172 10.379 1756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.30 % Allowed : 9.76 % 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: 3.65 (0.21), residues: 1508 helix: 2.92 (0.13), residues: 1264 sheet: 0.19 (0.85), residues: 48 loop : -0.74 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 367 TYR 0.009 0.001 TYR B 96 PHE 0.007 0.001 PHE B 11 TRP 0.004 0.001 TRP A 328 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00222 (12316) covalent geometry : angle 0.40704 (16712) hydrogen bonds : bond 0.03834 ( 1064) hydrogen bonds : angle 3.76964 ( 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 116 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.621 Fit side-chains REVERT: A 126 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6678 (ttp-110) REVERT: A 209 MET cc_start: 0.8203 (ttt) cc_final: 0.7928 (ttm) REVERT: B 126 ARG cc_start: 0.7433 (ttt180) cc_final: 0.6663 (ttp-110) REVERT: B 209 MET cc_start: 0.8183 (ttt) cc_final: 0.7895 (ttm) REVERT: C 126 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6679 (ttp-110) REVERT: C 209 MET cc_start: 0.8201 (ttt) cc_final: 0.7911 (ttm) REVERT: D 126 ARG cc_start: 0.7438 (ttt180) cc_final: 0.6660 (ttp-110) REVERT: D 209 MET cc_start: 0.8169 (ttt) cc_final: 0.7890 (ttm) outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.3362 time to fit residues: 51.2047 Evaluate side-chains 112 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain D residue 182 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.131084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105402 restraints weight = 39476.818| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.61 r_work: 0.2992 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1861 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= 0.147 Angle : 0.433 5.203 16712 Z= 0.238 Chirality : 0.033 0.133 2008 Planarity : 0.003 0.029 2040 Dihedral : 3.296 15.666 1756 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.61 % Allowed : 9.76 % Favored : 89.63 % 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: 3.61 (0.21), residues: 1508 helix: 2.89 (0.14), residues: 1264 sheet: -0.01 (0.86), residues: 48 loop : -0.60 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.007 0.001 TYR D 56 PHE 0.007 0.001 PHE B 11 TRP 0.007 0.001 TRP C 328 HIS 0.002 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00317 (12316) covalent geometry : angle 0.43274 (16712) hydrogen bonds : bond 0.04027 ( 1064) hydrogen bonds : angle 3.79136 ( 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 140 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.636 Fit side-chains REVERT: A 75 THR cc_start: 0.8046 (m) cc_final: 0.7756 (t) REVERT: A 126 ARG cc_start: 0.7483 (ttt180) cc_final: 0.7008 (ttt90) REVERT: A 130 TRP cc_start: 0.6936 (m100) cc_final: 0.6243 (m100) REVERT: A 209 MET cc_start: 0.8218 (ttt) cc_final: 0.7892 (ttm) REVERT: B 75 THR cc_start: 0.8035 (m) cc_final: 0.7747 (t) REVERT: B 126 ARG cc_start: 0.7468 (ttt180) cc_final: 0.7000 (ttt90) REVERT: B 130 TRP cc_start: 0.6926 (m100) cc_final: 0.6234 (m100) REVERT: C 75 THR cc_start: 0.8038 (m) cc_final: 0.7759 (t) REVERT: C 126 ARG cc_start: 0.7496 (ttt180) cc_final: 0.7022 (ttt90) REVERT: C 130 TRP cc_start: 0.6919 (m100) cc_final: 0.6222 (m100) REVERT: D 75 THR cc_start: 0.8026 (m) cc_final: 0.7742 (t) REVERT: D 126 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7002 (ttt90) REVERT: D 130 TRP cc_start: 0.6937 (m100) cc_final: 0.6246 (m100) REVERT: D 209 MET cc_start: 0.8169 (ttt) cc_final: 0.7854 (ttm) outliers start: 8 outliers final: 8 residues processed: 140 average time/residue: 0.3001 time to fit residues: 58.8129 Evaluate side-chains 130 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.127107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101273 restraints weight = 40086.913| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.61 r_work: 0.2937 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12316 Z= 0.216 Angle : 0.471 4.401 16712 Z= 0.263 Chirality : 0.035 0.137 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.580 19.423 1756 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.44 % Allowed : 8.16 % Favored : 89.41 % 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: 3.10 (0.21), residues: 1508 helix: 2.51 (0.14), residues: 1268 sheet: -0.19 (0.88), residues: 48 loop : -0.64 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 402 TYR 0.009 0.001 TYR B 182 PHE 0.011 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 covalent geometry : bond 0.00484 (12316) covalent geometry : angle 0.47067 (16712) hydrogen bonds : bond 0.04483 ( 1064) hydrogen bonds : angle 3.98315 ( 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 181 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.631 Fit side-chains REVERT: A 75 THR cc_start: 0.8188 (m) cc_final: 0.7871 (t) REVERT: A 110 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 126 ARG cc_start: 0.7555 (ttt180) cc_final: 0.6623 (ttp80) REVERT: A 130 TRP cc_start: 0.6993 (m100) cc_final: 0.6488 (m100) REVERT: B 75 THR cc_start: 0.8178 (m) cc_final: 0.7861 (t) REVERT: B 110 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: B 126 ARG cc_start: 0.7553 (ttt180) cc_final: 0.6618 (ttp80) REVERT: B 130 TRP cc_start: 0.6983 (m100) cc_final: 0.6482 (m100) REVERT: C 75 THR cc_start: 0.8193 (m) cc_final: 0.7881 (t) REVERT: C 110 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: C 126 ARG cc_start: 0.7553 (ttt180) cc_final: 0.6621 (ttp80) REVERT: C 130 TRP cc_start: 0.6979 (m100) cc_final: 0.6474 (m100) REVERT: D 75 THR cc_start: 0.8175 (m) cc_final: 0.7860 (t) REVERT: D 110 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: D 126 ARG cc_start: 0.7554 (ttt180) cc_final: 0.6617 (ttp80) REVERT: D 130 TRP cc_start: 0.6994 (m100) cc_final: 0.6487 (m100) outliers start: 32 outliers final: 20 residues processed: 171 average time/residue: 0.2816 time to fit residues: 66.4993 Evaluate side-chains 161 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 A residue 404 ILE 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 404 ILE 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 404 ILE 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 404 ILE 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: 8.9990 chunk 53 optimal weight: 2.9990 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: 0.5980 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.126034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100639 restraints weight = 40478.237| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.60 r_work: 0.2927 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12316 Z= 0.220 Angle : 0.472 4.325 16712 Z= 0.263 Chirality : 0.035 0.139 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.567 16.140 1756 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.83 % Allowed : 9.76 % Favored : 88.41 % 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: 2.85 (0.21), residues: 1508 helix: 2.35 (0.14), residues: 1268 sheet: -0.24 (0.89), residues: 48 loop : -0.73 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.008 0.001 TYR B 182 PHE 0.008 0.001 PHE B 315 TRP 0.007 0.001 TRP D 328 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00491 (12316) covalent geometry : angle 0.47166 (16712) hydrogen bonds : bond 0.04492 ( 1064) hydrogen bonds : angle 3.99679 ( 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 : 0.690 Fit side-chains REVERT: A 110 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 126 ARG cc_start: 0.7550 (ttt180) cc_final: 0.6580 (ttp80) REVERT: A 130 TRP cc_start: 0.7012 (m100) cc_final: 0.6497 (m100) REVERT: B 110 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: B 126 ARG cc_start: 0.7590 (ttt180) cc_final: 0.6589 (ttp80) REVERT: B 130 TRP cc_start: 0.6980 (m100) cc_final: 0.6448 (m100) REVERT: C 110 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: C 126 ARG cc_start: 0.7587 (ttt180) cc_final: 0.6580 (ttp80) REVERT: C 130 TRP cc_start: 0.6983 (m100) cc_final: 0.6453 (m100) REVERT: D 110 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: D 126 ARG cc_start: 0.7565 (ttt180) cc_final: 0.6581 (ttp80) REVERT: D 130 TRP cc_start: 0.7001 (m100) cc_final: 0.6494 (m100) outliers start: 24 outliers final: 20 residues processed: 159 average time/residue: 0.3256 time to fit residues: 71.2413 Evaluate side-chains 167 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 A residue 371 GLU 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: 0.7980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.127063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101719 restraints weight = 40173.187| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.60 r_work: 0.2940 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2631 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= 0.181 Angle : 0.444 4.145 16712 Z= 0.248 Chirality : 0.034 0.134 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.489 14.574 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 : 1.52 % 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 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: 3.03 (0.21), residues: 1508 helix: 2.47 (0.14), residues: 1268 sheet: -0.22 (0.89), residues: 48 loop : -0.70 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 402 TYR 0.007 0.001 TYR D 96 PHE 0.007 0.001 PHE B 11 TRP 0.007 0.001 TRP B 328 HIS 0.004 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00395 (12316) covalent geometry : angle 0.44373 (16712) hydrogen bonds : bond 0.04283 ( 1064) hydrogen bonds : angle 3.90557 ( 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 167 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.564 Fit side-chains REVERT: A 110 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: A 126 ARG cc_start: 0.7543 (ttt180) cc_final: 0.6564 (ttp80) REVERT: A 130 TRP cc_start: 0.7006 (m100) cc_final: 0.6489 (m100) REVERT: B 110 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: B 126 ARG cc_start: 0.7525 (ttt180) cc_final: 0.6547 (ttp80) REVERT: B 130 TRP cc_start: 0.6976 (m100) cc_final: 0.6450 (m100) REVERT: C 110 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: C 126 ARG cc_start: 0.7526 (ttt180) cc_final: 0.6546 (ttp80) REVERT: C 130 TRP cc_start: 0.6973 (m100) cc_final: 0.6450 (m100) REVERT: D 110 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: D 126 ARG cc_start: 0.7519 (ttt180) cc_final: 0.6544 (ttp80) REVERT: D 130 TRP cc_start: 0.6995 (m100) cc_final: 0.6478 (m100) outliers start: 20 outliers final: 16 residues processed: 159 average time/residue: 0.3085 time to fit residues: 67.5935 Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 12 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 128 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.129846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.104405 restraints weight = 39766.098| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.2979 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12316 Z= 0.121 Angle : 0.405 3.924 16712 Z= 0.224 Chirality : 0.033 0.130 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.288 11.706 1756 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.91 % Allowed : 10.67 % Favored : 88.41 % 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: 3.43 (0.22), residues: 1508 helix: 2.76 (0.14), residues: 1268 sheet: -0.26 (0.88), residues: 48 loop : -0.63 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.006 0.001 TYR C 96 PHE 0.008 0.001 PHE B 40 TRP 0.006 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00244 (12316) covalent geometry : angle 0.40467 (16712) hydrogen bonds : bond 0.03897 ( 1064) hydrogen bonds : angle 3.71445 ( 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 159 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.674 Fit side-chains REVERT: A 75 THR cc_start: 0.8174 (m) cc_final: 0.7871 (t) REVERT: A 126 ARG cc_start: 0.7490 (ttt180) cc_final: 0.6511 (ttp80) REVERT: A 127 ARG cc_start: 0.7507 (ttt180) cc_final: 0.7294 (ttt180) REVERT: A 130 TRP cc_start: 0.6932 (m100) cc_final: 0.6405 (m100) REVERT: B 75 THR cc_start: 0.8158 (m) cc_final: 0.7852 (t) REVERT: B 126 ARG cc_start: 0.7514 (ttt180) cc_final: 0.6530 (ttp80) REVERT: B 127 ARG cc_start: 0.7525 (ttt180) cc_final: 0.7313 (ttt180) REVERT: B 130 TRP cc_start: 0.6928 (m100) cc_final: 0.6396 (m100) REVERT: C 75 THR cc_start: 0.8179 (m) cc_final: 0.7874 (t) REVERT: C 126 ARG cc_start: 0.7507 (ttt180) cc_final: 0.6520 (ttp80) REVERT: C 127 ARG cc_start: 0.7507 (ttt180) cc_final: 0.7297 (ttt180) REVERT: C 130 TRP cc_start: 0.6917 (m100) cc_final: 0.6386 (m100) REVERT: D 75 THR cc_start: 0.8160 (m) cc_final: 0.7861 (t) REVERT: D 126 ARG cc_start: 0.7509 (ttt180) cc_final: 0.6520 (ttp80) REVERT: D 127 ARG cc_start: 0.7503 (ttt180) cc_final: 0.7292 (ttt180) REVERT: D 130 TRP cc_start: 0.6934 (m100) cc_final: 0.6413 (m100) outliers start: 12 outliers final: 12 residues processed: 155 average time/residue: 0.3008 time to fit residues: 62.9111 Evaluate side-chains 155 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER 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 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: 1.9990 chunk 86 optimal weight: 1.9990 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: 2.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.128628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103136 restraints weight = 40021.710| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.61 r_work: 0.2961 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12316 Z= 0.159 Angle : 0.435 6.127 16712 Z= 0.238 Chirality : 0.033 0.133 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.354 14.120 1756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 10.37 % Favored : 88.41 % 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: 3.36 (0.21), residues: 1508 helix: 2.71 (0.14), residues: 1268 sheet: -0.37 (0.87), residues: 48 loop : -0.66 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.009 0.001 TYR D 96 PHE 0.007 0.001 PHE D 40 TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00345 (12316) covalent geometry : angle 0.43524 (16712) hydrogen bonds : bond 0.04079 ( 1064) hydrogen bonds : angle 3.75428 ( 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 160 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.598 Fit side-chains REVERT: A 75 THR cc_start: 0.8193 (m) cc_final: 0.7880 (t) REVERT: A 110 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: A 126 ARG cc_start: 0.7523 (ttt180) cc_final: 0.6563 (ttp80) REVERT: A 127 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7312 (ttt180) REVERT: A 130 TRP cc_start: 0.6963 (m100) cc_final: 0.6416 (m100) REVERT: B 75 THR cc_start: 0.8182 (m) cc_final: 0.7871 (t) REVERT: B 110 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: B 126 ARG cc_start: 0.7513 (ttt180) cc_final: 0.6564 (ttp80) REVERT: B 127 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7320 (ttt180) REVERT: B 130 TRP cc_start: 0.6914 (m100) cc_final: 0.6363 (m100) REVERT: C 75 THR cc_start: 0.8196 (m) cc_final: 0.7886 (t) REVERT: C 110 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: C 126 ARG cc_start: 0.7509 (ttt180) cc_final: 0.6559 (ttp80) REVERT: C 127 ARG cc_start: 0.7516 (ttt180) cc_final: 0.7311 (ttt180) REVERT: C 130 TRP cc_start: 0.6929 (m100) cc_final: 0.6381 (m100) REVERT: D 75 THR cc_start: 0.8182 (m) cc_final: 0.7876 (t) REVERT: D 110 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: D 126 ARG cc_start: 0.7511 (ttt180) cc_final: 0.6558 (ttp80) REVERT: D 127 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7303 (ttt180) REVERT: D 130 TRP cc_start: 0.6956 (m100) cc_final: 0.6418 (m100) outliers start: 16 outliers final: 12 residues processed: 156 average time/residue: 0.3346 time to fit residues: 70.5566 Evaluate side-chains 160 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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: 0.0980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.128609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103079 restraints weight = 40023.483| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.60 r_work: 0.2959 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2724 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= 0.154 Angle : 0.436 6.414 16712 Z= 0.238 Chirality : 0.033 0.139 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.346 13.997 1756 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.14 % Allowed : 10.44 % Favored : 88.41 % 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: 3.36 (0.21), residues: 1508 helix: 2.72 (0.14), residues: 1268 sheet: -0.41 (0.88), residues: 48 loop : -0.63 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.006 0.001 TYR C 96 PHE 0.007 0.001 PHE D 40 TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00328 (12316) covalent geometry : angle 0.43589 (16712) hydrogen bonds : bond 0.04080 ( 1064) hydrogen bonds : angle 3.75007 ( 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 165 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.786 Fit side-chains REVERT: A 75 THR cc_start: 0.8190 (m) cc_final: 0.7878 (t) REVERT: A 126 ARG cc_start: 0.7529 (ttt180) cc_final: 0.6556 (ttp80) REVERT: A 127 ARG cc_start: 0.7514 (ttt180) cc_final: 0.7303 (ttt180) REVERT: A 130 TRP cc_start: 0.6942 (m100) cc_final: 0.6398 (m100) REVERT: B 75 THR cc_start: 0.8181 (m) cc_final: 0.7868 (t) REVERT: B 100 PHE cc_start: 0.8621 (m-10) cc_final: 0.8420 (m-80) REVERT: B 110 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: B 126 ARG cc_start: 0.7538 (ttt180) cc_final: 0.6574 (ttp80) REVERT: B 127 ARG cc_start: 0.7514 (ttt180) cc_final: 0.7311 (ttt180) REVERT: B 130 TRP cc_start: 0.6927 (m100) cc_final: 0.6375 (m100) REVERT: C 75 THR cc_start: 0.8188 (m) cc_final: 0.7875 (t) REVERT: C 110 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: C 126 ARG cc_start: 0.7533 (ttt180) cc_final: 0.6560 (ttp80) REVERT: C 127 ARG cc_start: 0.7506 (ttt180) cc_final: 0.7303 (ttt180) REVERT: C 130 TRP cc_start: 0.6935 (m100) cc_final: 0.6383 (m100) REVERT: D 75 THR cc_start: 0.8180 (m) cc_final: 0.7871 (t) REVERT: D 110 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: D 126 ARG cc_start: 0.7522 (ttt180) cc_final: 0.6550 (ttp80) REVERT: D 127 ARG cc_start: 0.7502 (ttt180) cc_final: 0.7293 (ttt180) REVERT: D 130 TRP cc_start: 0.6946 (m100) cc_final: 0.6403 (m100) outliers start: 15 outliers final: 12 residues processed: 161 average time/residue: 0.2991 time to fit residues: 64.8071 Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 148 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: 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 = 0.3398 r_free = 0.3398 target = 0.127323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101674 restraints weight = 40268.554| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.61 r_work: 0.2944 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2836 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= 0.188 Angle : 0.459 6.112 16712 Z= 0.252 Chirality : 0.034 0.133 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.458 15.689 1756 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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 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: 3.22 (0.21), residues: 1508 helix: 2.61 (0.14), residues: 1268 sheet: -0.48 (0.88), residues: 48 loop : -0.63 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 402 TYR 0.008 0.001 TYR B 182 PHE 0.006 0.001 PHE D 40 TRP 0.008 0.001 TRP A 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00416 (12316) covalent geometry : angle 0.45918 (16712) hydrogen bonds : bond 0.04289 ( 1064) hydrogen bonds : angle 3.83855 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5064.46 seconds wall clock time: 87 minutes 1.86 seconds (5221.86 seconds total)