Starting phenix.real_space_refine on Mon Aug 25 01:08:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x84_38135/08_2025/8x84_38135_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x84_38135/08_2025/8x84_38135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x84_38135/08_2025/8x84_38135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x84_38135/08_2025/8x84_38135.map" model { file = "/net/cci-nas-00/data/ceres_data/8x84_38135/08_2025/8x84_38135_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x84_38135/08_2025/8x84_38135_neut_trim.cif" } 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24534 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.93, 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: 2.06 Conformation dependent library (CDL) restraints added in 563.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.53 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: 4.53 Time building geometry restraints manager: 2.79 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: 1.240 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.120 Find NCS groups from input model: 0.400 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- 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 aren 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 : 0.684 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: 0.3334 time to fit residues: 42.1985 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 : 0.616 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108840 restraints weight = 38667.253| |-----------------------------------------------------------------------------| 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: 3.63 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 aren 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 : 0.649 Fit side-chains REVERT: A 209 MET cc_start: 0.8168 (ttt) cc_final: 0.7902 (ttm) REVERT: B 209 MET cc_start: 0.8144 (ttt) cc_final: 0.7861 (ttm) REVERT: C 209 MET cc_start: 0.8157 (ttt) cc_final: 0.7867 (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: 0.2440 time to fit residues: 46.9171 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 : 0.597 ------------------------------------------------------------------------------- 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: 2.9990 chunk 77 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN C 421 GLN D 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109537 restraints weight = 38839.392| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.59 r_work: 0.3052 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12316 Z= 0.112 Angle : 0.408 3.929 16712 Z= 0.222 Chirality : 0.032 0.132 2008 Planarity : 0.002 0.028 2040 Dihedral : 3.162 10.382 1756 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.30 % Allowed : 9.45 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.64 (0.21), residues: 1508 helix: 2.92 (0.13), residues: 1264 sheet: 0.19 (0.85), residues: 48 loop : -0.73 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 367 TYR 0.009 0.001 TYR A 96 PHE 0.007 0.001 PHE B 11 TRP 0.004 0.001 TRP D 328 HIS 0.002 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00223 (12316) covalent geometry : angle 0.40758 (16712) hydrogen bonds : bond 0.03843 ( 1064) hydrogen bonds : angle 3.76324 ( 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 112 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.573 Fit side-chains REVERT: A 126 ARG cc_start: 0.7463 (ttt180) cc_final: 0.6683 (ttp-110) REVERT: A 209 MET cc_start: 0.8210 (ttt) cc_final: 0.7924 (ttm) REVERT: B 126 ARG cc_start: 0.7442 (ttt180) cc_final: 0.6666 (ttp-110) REVERT: B 209 MET cc_start: 0.8194 (ttt) cc_final: 0.7900 (ttm) REVERT: C 126 ARG cc_start: 0.7460 (ttt180) cc_final: 0.6677 (ttp-110) REVERT: C 209 MET cc_start: 0.8205 (ttt) cc_final: 0.7911 (ttm) REVERT: D 126 ARG cc_start: 0.7452 (ttt180) cc_final: 0.6663 (ttp-110) REVERT: D 209 MET cc_start: 0.8175 (ttt) cc_final: 0.7895 (ttm) outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.3274 time to fit residues: 50.0319 Evaluate side-chains 104 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 0.6980 chunk 106 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 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: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.132169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106564 restraints weight = 39235.938| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.60 r_work: 0.3010 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1776 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 : 0.417 4.640 16712 Z= 0.229 Chirality : 0.032 0.130 2008 Planarity : 0.002 0.029 2040 Dihedral : 3.229 14.114 1756 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.09 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 aren not related in a simple way. whole: 3.68 (0.21), residues: 1508 helix: 2.94 (0.13), residues: 1264 sheet: 0.08 (0.85), residues: 48 loop : -0.63 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.006 0.001 TYR D 96 PHE 0.007 0.001 PHE C 11 TRP 0.006 0.001 TRP C 328 HIS 0.002 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00284 (12316) covalent geometry : angle 0.41729 (16712) hydrogen bonds : bond 0.03891 ( 1064) hydrogen bonds : angle 3.73325 ( 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 133 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.482 Fit side-chains REVERT: A 126 ARG cc_start: 0.7485 (ttt180) cc_final: 0.7018 (ttt90) REVERT: A 130 TRP cc_start: 0.6926 (m100) cc_final: 0.6244 (m100) REVERT: A 209 MET cc_start: 0.8213 (ttt) cc_final: 0.7919 (ttm) REVERT: B 126 ARG cc_start: 0.7462 (ttt180) cc_final: 0.6997 (ttt90) REVERT: B 130 TRP cc_start: 0.6918 (m100) cc_final: 0.6238 (m100) REVERT: B 209 MET cc_start: 0.8173 (ttt) cc_final: 0.7863 (ttm) REVERT: C 126 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7002 (ttt90) REVERT: C 130 TRP cc_start: 0.6906 (m100) cc_final: 0.6219 (m100) REVERT: C 209 MET cc_start: 0.8176 (ttt) cc_final: 0.7861 (ttm) REVERT: D 126 ARG cc_start: 0.7462 (ttt180) cc_final: 0.6993 (ttt90) REVERT: D 130 TRP cc_start: 0.6918 (m100) cc_final: 0.6234 (m100) REVERT: D 209 MET cc_start: 0.8161 (ttt) cc_final: 0.7846 (ttm) outliers start: 8 outliers final: 8 residues processed: 133 average time/residue: 0.2965 time to fit residues: 55.0184 Evaluate side-chains 121 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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: 0.9980 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.129119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103240 restraints weight = 39674.413| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.61 r_work: 0.2965 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2164 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= 0.173 Angle : 0.438 4.233 16712 Z= 0.244 Chirality : 0.034 0.133 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.411 17.428 1756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.60 % Allowed : 8.92 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.44 (0.21), residues: 1508 helix: 2.76 (0.14), residues: 1268 sheet: -0.15 (0.88), residues: 48 loop : -0.57 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 402 TYR 0.007 0.001 TYR A 96 PHE 0.010 0.001 PHE A 315 TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00377 (12316) covalent geometry : angle 0.43801 (16712) hydrogen bonds : bond 0.04191 ( 1064) hydrogen bonds : angle 3.82376 ( 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 153 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.758 Fit side-chains REVERT: A 75 THR cc_start: 0.8090 (m) cc_final: 0.7796 (t) REVERT: A 110 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 126 ARG cc_start: 0.7533 (ttt180) cc_final: 0.6590 (ttp80) REVERT: A 130 TRP cc_start: 0.6963 (m100) cc_final: 0.6452 (m100) REVERT: B 75 THR cc_start: 0.8082 (m) cc_final: 0.7790 (t) REVERT: B 110 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: B 126 ARG cc_start: 0.7520 (ttt180) cc_final: 0.6567 (ttp80) REVERT: B 130 TRP cc_start: 0.6937 (m100) cc_final: 0.6420 (m100) REVERT: C 75 THR cc_start: 0.8091 (m) cc_final: 0.7804 (t) REVERT: C 110 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: C 126 ARG cc_start: 0.7557 (ttt180) cc_final: 0.6614 (ttp80) REVERT: C 130 TRP cc_start: 0.6930 (m100) cc_final: 0.6414 (m100) REVERT: D 75 THR cc_start: 0.8074 (m) cc_final: 0.7784 (t) REVERT: D 110 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: D 126 ARG cc_start: 0.7538 (ttt180) cc_final: 0.6588 (ttp80) REVERT: D 130 TRP cc_start: 0.6948 (m100) cc_final: 0.6436 (m100) outliers start: 21 outliers final: 9 residues processed: 152 average time/residue: 0.3278 time to fit residues: 68.4658 Evaluate side-chains 145 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.128810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103351 restraints weight = 40058.561| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.61 r_work: 0.2962 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2341 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= 0.161 Angle : 0.427 4.131 16712 Z= 0.237 Chirality : 0.033 0.134 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.343 15.293 1756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.83 % Allowed : 9.45 % 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 aren not related in a simple way. whole: 3.41 (0.21), residues: 1508 helix: 2.74 (0.14), residues: 1268 sheet: -0.22 (0.88), residues: 48 loop : -0.56 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.006 0.001 TYR D 96 PHE 0.006 0.001 PHE B 11 TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00348 (12316) covalent geometry : angle 0.42652 (16712) hydrogen bonds : bond 0.04111 ( 1064) hydrogen bonds : angle 3.78836 ( 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 172 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.620 Fit side-chains REVERT: A 75 THR cc_start: 0.8098 (m) cc_final: 0.7810 (t) REVERT: A 110 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: A 126 ARG cc_start: 0.7529 (ttt180) cc_final: 0.6542 (ttp80) REVERT: A 130 TRP cc_start: 0.6957 (m100) cc_final: 0.6441 (m100) REVERT: B 75 THR cc_start: 0.8091 (m) cc_final: 0.7804 (t) REVERT: B 110 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: B 126 ARG cc_start: 0.7526 (ttt180) cc_final: 0.6540 (ttp80) REVERT: B 130 TRP cc_start: 0.6909 (m100) cc_final: 0.6382 (m100) REVERT: C 75 THR cc_start: 0.8096 (m) cc_final: 0.7815 (t) REVERT: C 110 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: C 126 ARG cc_start: 0.7535 (ttt180) cc_final: 0.6539 (ttp80) REVERT: C 130 TRP cc_start: 0.6926 (m100) cc_final: 0.6404 (m100) REVERT: D 75 THR cc_start: 0.8078 (m) cc_final: 0.7797 (t) REVERT: D 110 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: D 126 ARG cc_start: 0.7541 (ttt180) cc_final: 0.6541 (ttp80) REVERT: D 130 TRP cc_start: 0.6950 (m100) cc_final: 0.6436 (m100) outliers start: 24 outliers final: 16 residues processed: 156 average time/residue: 0.3300 time to fit residues: 71.3326 Evaluate side-chains 164 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.126823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101425 restraints weight = 40336.763| |-----------------------------------------------------------------------------| r_work (start): 0.3072 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: 3.63 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12316 Z= 0.202 Angle : 0.460 4.310 16712 Z= 0.256 Chirality : 0.035 0.136 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.515 17.747 1756 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 aren not related in a simple way. whole: 3.14 (0.21), residues: 1508 helix: 2.54 (0.14), residues: 1268 sheet: -0.27 (0.88), residues: 48 loop : -0.61 (0.50), 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 182 PHE 0.007 0.001 PHE D 315 TRP 0.007 0.001 TRP A 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00452 (12316) covalent geometry : angle 0.46025 (16712) hydrogen bonds : bond 0.04409 ( 1064) hydrogen bonds : angle 3.91911 ( 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 176 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.607 Fit side-chains REVERT: A 110 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: A 126 ARG cc_start: 0.7520 (ttt180) cc_final: 0.6583 (ttp80) REVERT: A 130 TRP cc_start: 0.7006 (m100) cc_final: 0.6489 (m100) REVERT: B 110 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: B 126 ARG cc_start: 0.7519 (ttt180) cc_final: 0.6586 (ttp80) REVERT: B 130 TRP cc_start: 0.6992 (m100) cc_final: 0.6461 (m100) REVERT: C 110 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: C 126 ARG cc_start: 0.7525 (ttt180) cc_final: 0.6587 (ttp80) REVERT: C 130 TRP cc_start: 0.6987 (m100) cc_final: 0.6466 (m100) REVERT: D 110 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: D 126 ARG cc_start: 0.7522 (ttt180) cc_final: 0.6584 (ttp80) REVERT: D 130 TRP cc_start: 0.7002 (m100) cc_final: 0.6485 (m100) outliers start: 24 outliers final: 17 residues processed: 160 average time/residue: 0.3284 time to fit residues: 72.4497 Evaluate side-chains 172 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 12 optimal weight: 0.1980 chunk 140 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.127703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102366 restraints weight = 40235.336| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.59 r_work: 0.2950 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12316 Z= 0.168 Angle : 0.434 4.138 16712 Z= 0.242 Chirality : 0.034 0.134 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.416 14.157 1756 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 10.06 % 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 aren not related in a simple way. whole: 3.21 (0.21), residues: 1508 helix: 2.60 (0.14), residues: 1268 sheet: -0.23 (0.89), residues: 48 loop : -0.65 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.006 0.001 TYR D 96 PHE 0.006 0.001 PHE B 11 TRP 0.007 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00364 (12316) covalent geometry : angle 0.43392 (16712) hydrogen bonds : bond 0.04196 ( 1064) hydrogen bonds : angle 3.83480 ( 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 171 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.693 Fit side-chains REVERT: A 75 THR cc_start: 0.8218 (m) cc_final: 0.7891 (t) REVERT: A 110 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: A 126 ARG cc_start: 0.7527 (ttt180) cc_final: 0.6552 (ttp80) REVERT: A 127 ARG cc_start: 0.7556 (ttt180) cc_final: 0.7321 (ttt180) REVERT: A 130 TRP cc_start: 0.7001 (m100) cc_final: 0.6485 (m100) REVERT: B 75 THR cc_start: 0.8210 (m) cc_final: 0.7886 (t) REVERT: B 110 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 126 ARG cc_start: 0.7530 (ttt180) cc_final: 0.6547 (ttp80) REVERT: B 127 ARG cc_start: 0.7562 (ttt180) cc_final: 0.7329 (ttt180) REVERT: B 130 TRP cc_start: 0.6955 (m100) cc_final: 0.6423 (m100) REVERT: C 75 THR cc_start: 0.8217 (m) cc_final: 0.7897 (t) REVERT: C 110 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7943 (m-30) REVERT: C 126 ARG cc_start: 0.7527 (ttt180) cc_final: 0.6544 (ttp80) REVERT: C 127 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7321 (ttt180) REVERT: C 130 TRP cc_start: 0.6981 (m100) cc_final: 0.6461 (m100) REVERT: D 75 THR cc_start: 0.8202 (m) cc_final: 0.7883 (t) REVERT: D 110 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: D 126 ARG cc_start: 0.7524 (ttt180) cc_final: 0.6550 (ttp80) REVERT: D 127 ARG cc_start: 0.7548 (ttt180) cc_final: 0.7315 (ttt180) REVERT: D 130 TRP cc_start: 0.6993 (m100) cc_final: 0.6476 (m100) outliers start: 20 outliers final: 16 residues processed: 163 average time/residue: 0.3272 time to fit residues: 72.7249 Evaluate side-chains 168 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103043 restraints weight = 40022.839| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.59 r_work: 0.2956 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2628 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 : 0.439 6.607 16712 Z= 0.239 Chirality : 0.033 0.137 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.380 13.933 1756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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 aren not related in a simple way. whole: 3.30 (0.21), residues: 1508 helix: 2.66 (0.14), residues: 1268 sheet: -0.28 (0.88), residues: 48 loop : -0.63 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 367 TYR 0.006 0.001 TYR B 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 0.00329 (12316) covalent geometry : angle 0.43857 (16712) hydrogen bonds : bond 0.04113 ( 1064) hydrogen bonds : angle 3.78270 ( 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 165 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.404 Fit side-chains REVERT: A 75 THR cc_start: 0.8212 (m) cc_final: 0.7895 (t) REVERT: A 110 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: A 126 ARG cc_start: 0.7549 (ttt180) cc_final: 0.6589 (ttp80) REVERT: A 127 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7323 (ttt180) REVERT: A 130 TRP cc_start: 0.6993 (m100) cc_final: 0.6466 (m100) REVERT: B 75 THR cc_start: 0.8199 (m) cc_final: 0.7884 (t) REVERT: B 110 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: B 126 ARG cc_start: 0.7533 (ttt180) cc_final: 0.6541 (ttp80) REVERT: B 127 ARG cc_start: 0.7538 (ttt180) cc_final: 0.7324 (ttt180) REVERT: B 130 TRP cc_start: 0.6955 (m100) cc_final: 0.6417 (m100) REVERT: C 75 THR cc_start: 0.8210 (m) cc_final: 0.7897 (t) REVERT: C 110 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: C 126 ARG cc_start: 0.7514 (ttt180) cc_final: 0.6536 (ttp80) REVERT: C 127 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7314 (ttt180) REVERT: C 130 TRP cc_start: 0.6956 (m100) cc_final: 0.6428 (m100) REVERT: D 75 THR cc_start: 0.8202 (m) cc_final: 0.7890 (t) REVERT: D 110 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: D 126 ARG cc_start: 0.7544 (ttt180) cc_final: 0.6587 (ttp80) REVERT: D 127 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7319 (ttt180) REVERT: D 130 TRP cc_start: 0.6988 (m100) cc_final: 0.6458 (m100) outliers start: 16 outliers final: 12 residues processed: 159 average time/residue: 0.3060 time to fit residues: 65.3926 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 : 0.680 ------------------------------------------------------------------------------- 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: 0.1980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.127155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101607 restraints weight = 40284.662| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.61 r_work: 0.2942 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12316 Z= 0.191 Angle : 0.459 5.987 16712 Z= 0.253 Chirality : 0.034 0.138 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.476 15.716 1756 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.52 % Allowed : 10.06 % 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 aren not related in a simple way. whole: 3.12 (0.21), residues: 1508 helix: 2.53 (0.14), residues: 1268 sheet: -0.30 (0.87), residues: 48 loop : -0.64 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.008 0.001 TYR B 182 PHE 0.006 0.001 PHE A 11 TRP 0.008 0.001 TRP A 328 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00422 (12316) covalent geometry : angle 0.45921 (16712) hydrogen bonds : bond 0.04311 ( 1064) hydrogen bonds : angle 3.86703 ( 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 170 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.636 Fit side-chains REVERT: A 110 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: A 126 ARG cc_start: 0.7531 (ttt180) cc_final: 0.6562 (ttp80) REVERT: A 127 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7305 (ttt180) REVERT: A 130 TRP cc_start: 0.6994 (m100) cc_final: 0.6452 (m100) REVERT: B 110 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: B 126 ARG cc_start: 0.7539 (ttt180) cc_final: 0.6564 (ttp80) REVERT: B 127 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7317 (ttt180) REVERT: B 130 TRP cc_start: 0.6978 (m100) cc_final: 0.6418 (m100) REVERT: C 110 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: C 126 ARG cc_start: 0.7527 (ttt180) cc_final: 0.6558 (ttp80) REVERT: C 127 ARG cc_start: 0.7538 (ttt180) cc_final: 0.7327 (ttt180) REVERT: C 130 TRP cc_start: 0.6986 (m100) cc_final: 0.6440 (m100) REVERT: D 110 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: D 126 ARG cc_start: 0.7516 (ttt180) cc_final: 0.6557 (ttp80) REVERT: D 127 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7306 (ttt180) REVERT: D 130 TRP cc_start: 0.6989 (m100) cc_final: 0.6447 (m100) outliers start: 20 outliers final: 12 residues processed: 166 average time/residue: 0.3344 time to fit residues: 75.3290 Evaluate side-chains 163 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 148 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.129095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.103505 restraints weight = 39953.155| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.61 r_work: 0.2965 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12316 Z= 0.134 Angle : 0.431 6.522 16712 Z= 0.234 Chirality : 0.033 0.135 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.327 12.792 1756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.91 % Allowed : 11.13 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.21), residues: 1508 helix: 2.75 (0.14), residues: 1268 sheet: -0.33 (0.87), residues: 48 loop : -0.58 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.007 0.001 TYR A 96 PHE 0.007 0.001 PHE D 40 TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00279 (12316) covalent geometry : angle 0.43134 (16712) hydrogen bonds : bond 0.04010 ( 1064) hydrogen bonds : angle 3.73145 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5086.08 seconds wall clock time: 87 minutes 24.70 seconds (5244.70 seconds total)