Starting phenix.real_space_refine on Mon Sep 30 03:12:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/09_2024/8x84_38135_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/09_2024/8x84_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/09_2024/8x84_38135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/09_2024/8x84_38135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/09_2024/8x84_38135_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/09_2024/8x84_38135_neut_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 S 72 5.16 5 C 7836 2.51 5 N 2056 2.21 5 O 2124 1.98 5 H 12444 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24534 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 15.20, per 1000 atoms: 0.62 Number of scatterers: 24534 At special positions: 0 Unit cell: (110.67, 110.67, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 72 16.00 O 2124 8.00 N 2056 7.00 C 7836 6.00 H 12444 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 2.0 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: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.551A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.571A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.328A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 368 removed outlier: 3.687A pdb=" N ILE D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.980A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 removed outlier: 4.309A pdb=" N LEU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.608A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.28 Time building geometry restraints manager: 7.36 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.390 Extract box with map and model: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 53.370 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.040 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.920 ------------------------------------------------------------------------------- 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= 0.265 Angle : 0.527 5.753 16712 Z= 0.316 Chirality : 0.033 0.126 2008 Planarity : 0.002 0.022 2040 Dihedral : 14.451 89.610 4464 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.30 % Allowed : 7.93 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.22), residues: 1508 helix: 2.52 (0.14), residues: 1248 sheet: 0.73 (0.81), residues: 48 loop : -0.01 (0.51), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.001 0.000 HIS C 349 PHE 0.007 0.001 PHE C 315 TYR 0.005 0.001 TYR B 96 ARG 0.001 0.000 ARG D 31 *********************** 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 fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.708 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: 0.6735 time to fit residues: 85.7760 Evaluate side-chains 84 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain D residue 25 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12316 Z= 0.343 Angle : 0.517 4.444 16712 Z= 0.286 Chirality : 0.036 0.132 2008 Planarity : 0.003 0.029 2040 Dihedral : 3.726 23.100 1760 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.30 % Allowed : 9.15 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.21), residues: 1508 helix: 2.26 (0.14), residues: 1264 sheet: 0.23 (0.86), residues: 48 loop : -0.62 (0.51), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 328 HIS 0.004 0.001 HIS D 349 PHE 0.008 0.001 PHE D 338 TYR 0.010 0.002 TYR B 182 ARG 0.003 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 1.873 Fit side-chains REVERT: A 75 THR cc_start: 0.7876 (m) cc_final: 0.7568 (t) REVERT: A 126 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6616 (ttp-110) REVERT: A 420 ILE cc_start: 0.8588 (mm) cc_final: 0.8382 (mt) REVERT: B 75 THR cc_start: 0.7878 (m) cc_final: 0.7571 (t) REVERT: B 126 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6618 (ttp-110) REVERT: B 420 ILE cc_start: 0.8589 (mm) cc_final: 0.8379 (mt) REVERT: C 75 THR cc_start: 0.7874 (m) cc_final: 0.7570 (t) REVERT: C 126 ARG cc_start: 0.7161 (ttt180) cc_final: 0.6615 (ttp-110) REVERT: C 420 ILE cc_start: 0.8589 (mm) cc_final: 0.8379 (mt) REVERT: D 75 THR cc_start: 0.7874 (m) cc_final: 0.7568 (t) REVERT: D 126 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6326 (ttp-110) REVERT: D 130 TRP cc_start: 0.6655 (m100) cc_final: 0.6219 (m100) REVERT: D 420 ILE cc_start: 0.8590 (mm) cc_final: 0.8381 (mt) outliers start: 4 outliers final: 0 residues processed: 144 average time/residue: 0.6077 time to fit residues: 122.7628 Evaluate side-chains 128 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN B 370 HIS B 421 GLN C 370 HIS C 421 GLN D 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12316 Z= 0.268 Angle : 0.462 4.181 16712 Z= 0.254 Chirality : 0.035 0.136 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.401 12.441 1756 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.21), residues: 1508 helix: 2.44 (0.14), residues: 1268 sheet: -0.05 (0.87), residues: 48 loop : -0.61 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE B 11 TYR 0.007 0.001 TYR D 179 ARG 0.003 0.000 ARG B 402 *********************** 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 150 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.791 Fit side-chains REVERT: A 75 THR cc_start: 0.7907 (m) cc_final: 0.7602 (t) REVERT: A 110 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: A 126 ARG cc_start: 0.7242 (ttt180) cc_final: 0.6630 (ttp-110) REVERT: A 420 ILE cc_start: 0.8605 (mm) cc_final: 0.8386 (mt) REVERT: B 75 THR cc_start: 0.7911 (m) cc_final: 0.7605 (t) REVERT: B 110 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: B 126 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6716 (ttp80) REVERT: B 420 ILE cc_start: 0.8606 (mm) cc_final: 0.8400 (mt) REVERT: C 75 THR cc_start: 0.7908 (m) cc_final: 0.7603 (t) REVERT: C 110 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: C 126 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6714 (ttp80) REVERT: C 420 ILE cc_start: 0.8605 (mm) cc_final: 0.8399 (mt) REVERT: D 75 THR cc_start: 0.7903 (m) cc_final: 0.7599 (t) REVERT: D 110 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: D 126 ARG cc_start: 0.7173 (ttt180) cc_final: 0.6346 (ttp80) REVERT: D 130 TRP cc_start: 0.6645 (m100) cc_final: 0.6190 (m100) REVERT: D 420 ILE cc_start: 0.8606 (mm) cc_final: 0.8386 (mt) outliers start: 20 outliers final: 12 residues processed: 146 average time/residue: 0.6420 time to fit residues: 128.8586 Evaluate side-chains 146 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2153 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= 0.203 Angle : 0.430 4.080 16712 Z= 0.236 Chirality : 0.033 0.132 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.331 13.916 1756 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.52 % Allowed : 9.98 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.22), residues: 1508 helix: 2.63 (0.14), residues: 1268 sheet: -0.09 (0.88), residues: 48 loop : -0.52 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS B 337 PHE 0.007 0.001 PHE C 40 TYR 0.007 0.001 TYR A 96 ARG 0.002 0.000 ARG D 402 *********************** 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 168 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.768 Fit side-chains REVERT: A 75 THR cc_start: 0.7937 (m) cc_final: 0.7635 (t) REVERT: A 83 ASP cc_start: 0.8234 (t0) cc_final: 0.7497 (m-30) REVERT: A 110 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: A 126 ARG cc_start: 0.7222 (ttt180) cc_final: 0.6717 (ttp80) REVERT: A 420 ILE cc_start: 0.8635 (mm) cc_final: 0.8431 (mt) REVERT: B 75 THR cc_start: 0.7939 (m) cc_final: 0.7638 (t) REVERT: B 83 ASP cc_start: 0.8225 (t0) cc_final: 0.7496 (m-30) REVERT: B 110 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: B 126 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6717 (ttp80) REVERT: B 420 ILE cc_start: 0.8619 (mm) cc_final: 0.8418 (mt) REVERT: C 75 THR cc_start: 0.7935 (m) cc_final: 0.7635 (t) REVERT: C 83 ASP cc_start: 0.8236 (t0) cc_final: 0.7498 (m-30) REVERT: C 110 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: C 126 ARG cc_start: 0.7225 (ttt180) cc_final: 0.6719 (ttp80) REVERT: C 420 ILE cc_start: 0.8608 (mm) cc_final: 0.8406 (mt) REVERT: D 75 THR cc_start: 0.7933 (m) cc_final: 0.7633 (t) REVERT: D 83 ASP cc_start: 0.8233 (t0) cc_final: 0.7493 (m-30) REVERT: D 110 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 126 ARG cc_start: 0.7170 (ttt180) cc_final: 0.6380 (ttp80) REVERT: D 130 TRP cc_start: 0.6615 (m100) cc_final: 0.6106 (m100) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.6801 time to fit residues: 146.9937 Evaluate side-chains 159 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12316 Z= 0.301 Angle : 0.470 4.296 16712 Z= 0.261 Chirality : 0.035 0.137 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.521 17.305 1756 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.60 % Allowed : 10.37 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.21), residues: 1508 helix: 2.44 (0.14), residues: 1268 sheet: -0.25 (0.89), residues: 48 loop : -0.57 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 328 HIS 0.003 0.001 HIS C 337 PHE 0.009 0.001 PHE D 315 TYR 0.010 0.001 TYR A 182 ARG 0.003 0.000 ARG C 402 *********************** 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 164 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.900 Fit side-chains REVERT: A 75 THR cc_start: 0.8072 (m) cc_final: 0.7731 (t) REVERT: A 110 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: A 126 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6705 (ttp80) REVERT: A 420 ILE cc_start: 0.8599 (mm) cc_final: 0.8368 (mt) REVERT: B 75 THR cc_start: 0.8075 (m) cc_final: 0.7734 (t) REVERT: B 110 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: B 126 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6705 (ttp80) REVERT: B 420 ILE cc_start: 0.8625 (mm) cc_final: 0.8398 (mt) REVERT: C 75 THR cc_start: 0.8065 (m) cc_final: 0.7732 (t) REVERT: C 110 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: C 126 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6706 (ttp80) REVERT: C 420 ILE cc_start: 0.8628 (mm) cc_final: 0.8404 (mt) REVERT: D 75 THR cc_start: 0.8068 (m) cc_final: 0.7733 (t) REVERT: D 110 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: D 126 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6377 (ttp80) REVERT: D 130 TRP cc_start: 0.6654 (m100) cc_final: 0.6120 (m100) outliers start: 21 outliers final: 12 residues processed: 160 average time/residue: 0.6245 time to fit residues: 138.6740 Evaluate side-chains 159 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2439 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= 0.206 Angle : 0.432 4.067 16712 Z= 0.238 Chirality : 0.033 0.133 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.375 13.205 1756 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 11.36 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.21), residues: 1508 helix: 2.59 (0.14), residues: 1268 sheet: -0.20 (0.90), residues: 48 loop : -0.60 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE C 40 TYR 0.006 0.001 TYR D 96 ARG 0.001 0.000 ARG C 367 *********************** 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 158 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.673 Fit side-chains REVERT: A 75 THR cc_start: 0.8068 (m) cc_final: 0.7743 (t) REVERT: A 110 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: A 126 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6355 (ttp80) REVERT: A 130 TRP cc_start: 0.6640 (m100) cc_final: 0.6035 (m100) REVERT: A 420 ILE cc_start: 0.8597 (mm) cc_final: 0.8385 (mt) REVERT: B 75 THR cc_start: 0.8071 (m) cc_final: 0.7745 (t) REVERT: B 110 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: B 126 ARG cc_start: 0.7253 (ttt180) cc_final: 0.6357 (ttp80) REVERT: B 130 TRP cc_start: 0.6639 (m100) cc_final: 0.6032 (m100) REVERT: B 420 ILE cc_start: 0.8635 (mm) cc_final: 0.8421 (mt) REVERT: C 75 THR cc_start: 0.8060 (m) cc_final: 0.7743 (t) REVERT: C 110 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: C 126 ARG cc_start: 0.7257 (ttt180) cc_final: 0.6359 (ttp80) REVERT: C 130 TRP cc_start: 0.6642 (m100) cc_final: 0.6033 (m100) REVERT: C 420 ILE cc_start: 0.8612 (mm) cc_final: 0.8403 (mt) REVERT: D 75 THR cc_start: 0.8061 (m) cc_final: 0.7743 (t) REVERT: D 110 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 126 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6393 (ttp80) REVERT: D 127 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6989 (ttt180) REVERT: D 130 TRP cc_start: 0.6619 (m100) cc_final: 0.6082 (m100) outliers start: 16 outliers final: 12 residues processed: 153 average time/residue: 0.6528 time to fit residues: 137.2287 Evaluate side-chains 154 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12316 Z= 0.198 Angle : 0.436 5.674 16712 Z= 0.237 Chirality : 0.033 0.135 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.339 13.209 1756 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.22 % Allowed : 11.66 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.22), residues: 1508 helix: 2.65 (0.14), residues: 1268 sheet: -0.23 (0.89), residues: 48 loop : -0.61 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE B 40 TYR 0.007 0.001 TYR C 182 ARG 0.001 0.000 ARG B 31 *********************** 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 fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.788 Fit side-chains REVERT: A 75 THR cc_start: 0.7977 (m) cc_final: 0.7668 (t) REVERT: A 110 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: A 126 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6356 (ttp80) REVERT: A 127 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6983 (ttt180) REVERT: A 130 TRP cc_start: 0.6638 (m100) cc_final: 0.6028 (m100) REVERT: A 420 ILE cc_start: 0.8630 (mm) cc_final: 0.8411 (mt) REVERT: B 75 THR cc_start: 0.7978 (m) cc_final: 0.7671 (t) REVERT: B 110 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: B 126 ARG cc_start: 0.7224 (ttt180) cc_final: 0.6357 (ttp80) REVERT: B 127 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6985 (ttt180) REVERT: B 130 TRP cc_start: 0.6634 (m100) cc_final: 0.6026 (m100) REVERT: B 420 ILE cc_start: 0.8635 (mm) cc_final: 0.8419 (mt) REVERT: C 75 THR cc_start: 0.7964 (m) cc_final: 0.7664 (t) REVERT: C 110 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: C 126 ARG cc_start: 0.7225 (ttt180) cc_final: 0.6357 (ttp80) REVERT: C 127 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6984 (ttt180) REVERT: C 130 TRP cc_start: 0.6637 (m100) cc_final: 0.6028 (m100) REVERT: C 420 ILE cc_start: 0.8637 (mm) cc_final: 0.8423 (mt) REVERT: D 75 THR cc_start: 0.7967 (m) cc_final: 0.7662 (t) REVERT: D 110 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: D 126 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6378 (ttp80) REVERT: D 127 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6987 (ttt180) REVERT: D 130 TRP cc_start: 0.6605 (m100) cc_final: 0.6063 (m100) outliers start: 16 outliers final: 12 residues processed: 163 average time/residue: 0.6698 time to fit residues: 148.1797 Evaluate side-chains 159 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12316 Z= 0.363 Angle : 0.502 5.399 16712 Z= 0.276 Chirality : 0.036 0.141 2008 Planarity : 0.003 0.023 2040 Dihedral : 3.628 17.557 1756 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.52 % Allowed : 11.05 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.21), residues: 1508 helix: 2.28 (0.14), residues: 1268 sheet: -0.22 (0.89), residues: 48 loop : -0.74 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 328 HIS 0.004 0.001 HIS C 337 PHE 0.007 0.001 PHE C 392 TYR 0.012 0.002 TYR C 182 ARG 0.002 0.000 ARG D 402 *********************** 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 155 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.954 Fit side-chains REVERT: A 110 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: A 126 ARG cc_start: 0.7229 (ttt180) cc_final: 0.6703 (ttp80) REVERT: A 420 ILE cc_start: 0.8630 (mm) cc_final: 0.8403 (mt) REVERT: B 110 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: B 126 ARG cc_start: 0.7222 (ttt180) cc_final: 0.6694 (ttp80) REVERT: B 420 ILE cc_start: 0.8641 (mm) cc_final: 0.8418 (mt) REVERT: C 110 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: C 126 ARG cc_start: 0.7208 (ttt180) cc_final: 0.6699 (ttp80) REVERT: C 420 ILE cc_start: 0.8605 (mm) cc_final: 0.8393 (mt) REVERT: D 110 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: D 126 ARG cc_start: 0.7229 (ttt180) cc_final: 0.6437 (ttp80) REVERT: D 130 TRP cc_start: 0.6662 (m100) cc_final: 0.6107 (m100) outliers start: 20 outliers final: 16 residues processed: 151 average time/residue: 0.6437 time to fit residues: 133.5666 Evaluate side-chains 155 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.0870 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12316 Z= 0.156 Angle : 0.430 6.139 16712 Z= 0.232 Chirality : 0.033 0.131 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.337 11.897 1756 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.22 % Allowed : 11.36 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.22), residues: 1508 helix: 2.66 (0.14), residues: 1268 sheet: -0.21 (0.90), residues: 48 loop : -0.67 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.003 0.001 HIS B 337 PHE 0.008 0.001 PHE A 40 TYR 0.007 0.001 TYR A 96 ARG 0.002 0.000 ARG C 367 *********************** 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 155 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.714 Fit side-chains REVERT: A 75 THR cc_start: 0.8057 (m) cc_final: 0.7734 (t) REVERT: A 110 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: A 126 ARG cc_start: 0.7235 (ttt180) cc_final: 0.6346 (ttp80) REVERT: A 127 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6966 (ttt180) REVERT: A 130 TRP cc_start: 0.6664 (m100) cc_final: 0.6053 (m100) REVERT: A 420 ILE cc_start: 0.8623 (mm) cc_final: 0.8403 (mt) REVERT: B 75 THR cc_start: 0.8059 (m) cc_final: 0.7736 (t) REVERT: B 110 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: B 126 ARG cc_start: 0.7238 (ttt180) cc_final: 0.6351 (ttp80) REVERT: B 127 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6977 (ttt180) REVERT: B 130 TRP cc_start: 0.6662 (m100) cc_final: 0.6053 (m100) REVERT: C 75 THR cc_start: 0.8046 (m) cc_final: 0.7733 (t) REVERT: C 110 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: C 126 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6345 (ttp80) REVERT: C 127 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6974 (ttt180) REVERT: C 130 TRP cc_start: 0.6662 (m100) cc_final: 0.6049 (m100) REVERT: D 75 THR cc_start: 0.7959 (m) cc_final: 0.7659 (t) REVERT: D 110 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: D 126 ARG cc_start: 0.7165 (ttt180) cc_final: 0.6364 (ttp80) REVERT: D 127 ARG cc_start: 0.7202 (ttt180) cc_final: 0.6984 (ttt180) REVERT: D 130 TRP cc_start: 0.6599 (m100) cc_final: 0.6058 (m100) outliers start: 16 outliers final: 12 residues processed: 151 average time/residue: 0.6930 time to fit residues: 140.9548 Evaluate side-chains 153 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2696 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= 0.202 Angle : 0.438 6.308 16712 Z= 0.237 Chirality : 0.033 0.132 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.330 13.228 1756 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 11.51 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.22), residues: 1508 helix: 2.68 (0.14), residues: 1268 sheet: -0.34 (0.89), residues: 48 loop : -0.69 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE A 40 TYR 0.008 0.001 TYR D 96 ARG 0.002 0.000 ARG C 367 ********************** 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 169 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.865 Fit side-chains REVERT: A 75 THR cc_start: 0.7977 (m) cc_final: 0.7674 (t) REVERT: A 110 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: A 126 ARG cc_start: 0.7225 (ttt180) cc_final: 0.6342 (ttp80) REVERT: A 127 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6968 (ttt180) REVERT: A 130 TRP cc_start: 0.6662 (m100) cc_final: 0.6045 (m100) REVERT: A 420 ILE cc_start: 0.8629 (mm) cc_final: 0.8400 (mt) REVERT: B 75 THR cc_start: 0.7977 (m) cc_final: 0.7678 (t) REVERT: B 110 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: B 126 ARG cc_start: 0.7195 (ttt180) cc_final: 0.6324 (ttp80) REVERT: B 127 ARG cc_start: 0.7193 (ttt180) cc_final: 0.6977 (ttt180) REVERT: B 130 TRP cc_start: 0.6658 (m100) cc_final: 0.6041 (m100) REVERT: C 75 THR cc_start: 0.7974 (m) cc_final: 0.7675 (t) REVERT: C 110 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: C 126 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6330 (ttp80) REVERT: C 127 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6977 (ttt180) REVERT: C 130 TRP cc_start: 0.6658 (m100) cc_final: 0.6040 (m100) REVERT: D 75 THR cc_start: 0.7974 (m) cc_final: 0.7666 (t) REVERT: D 110 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: D 126 ARG cc_start: 0.7168 (ttt180) cc_final: 0.6386 (ttp80) REVERT: D 127 ARG cc_start: 0.7196 (ttt180) cc_final: 0.6984 (ttt180) REVERT: D 130 TRP cc_start: 0.6611 (m100) cc_final: 0.6059 (m100) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.6899 time to fit residues: 150.9678 Evaluate side-chains 170 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS C 370 HIS D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105679 restraints weight = 39632.314| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.60 r_work: 0.2993 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2661 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= 0.136 Angle : 0.416 6.478 16712 Z= 0.223 Chirality : 0.032 0.128 2008 Planarity : 0.002 0.026 2040 Dihedral : 3.186 11.156 1756 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.91 % Allowed : 12.04 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.22), residues: 1508 helix: 2.90 (0.14), residues: 1268 sheet: -0.30 (0.88), residues: 48 loop : -0.62 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 154 HIS 0.003 0.001 HIS C 337 PHE 0.009 0.001 PHE A 40 TYR 0.008 0.001 TYR D 96 ARG 0.002 0.000 ARG B 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.82 seconds wall clock time: 85 minutes 29.51 seconds (5129.51 seconds total)