Starting phenix.real_space_refine on Thu Aug 8 22:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/08_2024/8x84_38135_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/08_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_38135/08_2024/8x84_38135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/08_2024/8x84_38135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/08_2024/8x84_38135_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/08_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 Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24534 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6120 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' CA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.19, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 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: 20.23 Conformation dependent library (CDL) restraints added in 2.4 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: 1.53 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: 9.21 Time building geometry restraints manager: 21.17 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: 100.12 - 106.90: 308 106.90 - 113.67: 29413 113.67 - 120.45: 8584 120.45 - 127.22: 6303 127.22 - 134.00: 104 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: 0.690 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: 0.340 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 78.110 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.770 ------------------------------------------------------------------------------- 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 : 1.606 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: 0.6855 time to fit residues: 88.9469 Evaluate side-chains 84 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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 : 1.835 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: 0.8589 (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: 0.5937 time to fit residues: 119.9811 Evaluate side-chains 128 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12316 Z= 0.299 Angle : 0.476 4.240 16712 Z= 0.264 Chirality : 0.035 0.137 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.476 14.591 1756 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.09 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: 2.88 (0.21), residues: 1508 helix: 2.34 (0.14), residues: 1268 sheet: -0.10 (0.87), residues: 48 loop : -0.62 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.004 0.001 HIS C 337 PHE 0.007 0.001 PHE A 11 TYR 0.008 0.001 TYR B 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 156 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.795 Fit side-chains REVERT: A 75 THR cc_start: 0.7936 (m) cc_final: 0.7634 (t) REVERT: A 110 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: A 126 ARG cc_start: 0.7247 (ttt180) cc_final: 0.6715 (ttp80) REVERT: A 420 ILE cc_start: 0.8606 (mm) cc_final: 0.8385 (mt) REVERT: B 75 THR cc_start: 0.7941 (m) cc_final: 0.7637 (t) REVERT: B 110 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7643 (m-30) REVERT: B 126 ARG cc_start: 0.7251 (ttt180) cc_final: 0.6717 (ttp80) REVERT: B 420 ILE cc_start: 0.8607 (mm) cc_final: 0.8385 (mt) REVERT: C 75 THR cc_start: 0.7936 (m) cc_final: 0.7635 (t) REVERT: C 110 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: C 126 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6715 (ttp80) REVERT: C 420 ILE cc_start: 0.8606 (mm) cc_final: 0.8384 (mt) REVERT: D 75 THR cc_start: 0.7934 (m) cc_final: 0.7634 (t) REVERT: D 110 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 126 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6346 (ttp80) REVERT: D 130 TRP cc_start: 0.6666 (m100) cc_final: 0.6212 (m100) REVERT: D 420 ILE cc_start: 0.8606 (mm) cc_final: 0.8385 (mt) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.6408 time to fit residues: 134.1856 Evaluate side-chains 148 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.7721 moved from start: 0.2141 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= 0.176 Angle : 0.424 3.989 16712 Z= 0.233 Chirality : 0.033 0.131 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.328 13.142 1756 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.68 % Allowed : 10.21 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.22), residues: 1508 helix: 2.63 (0.14), residues: 1268 sheet: -0.05 (0.88), residues: 48 loop : -0.53 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 328 HIS 0.003 0.001 HIS C 337 PHE 0.008 0.001 PHE D 40 TYR 0.007 0.001 TYR C 96 ARG 0.002 0.000 ARG A 367 *********************** 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 166 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.800 Fit side-chains REVERT: A 75 THR cc_start: 0.7931 (m) cc_final: 0.7634 (t) REVERT: A 110 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: A 126 ARG cc_start: 0.7221 (ttt180) cc_final: 0.6720 (ttp80) REVERT: B 75 THR cc_start: 0.7937 (m) cc_final: 0.7640 (t) REVERT: B 110 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 126 ARG cc_start: 0.7222 (ttt180) cc_final: 0.6720 (ttp80) REVERT: C 75 THR cc_start: 0.7932 (m) cc_final: 0.7636 (t) REVERT: C 110 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: C 126 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6722 (ttp80) REVERT: D 75 THR cc_start: 0.7930 (m) cc_final: 0.7634 (t) REVERT: D 110 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: D 126 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6387 (ttp80) REVERT: D 130 TRP cc_start: 0.6614 (m100) cc_final: 0.6111 (m100) outliers start: 22 outliers final: 12 residues processed: 154 average time/residue: 0.6205 time to fit residues: 131.8937 Evaluate side-chains 152 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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: 4.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12316 Z= 0.333 Angle : 0.482 4.332 16712 Z= 0.268 Chirality : 0.035 0.137 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.590 17.641 1756 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.44 % Allowed : 9.83 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.84 (0.21), residues: 1508 helix: 2.33 (0.14), residues: 1268 sheet: -0.25 (0.89), residues: 48 loop : -0.62 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 328 HIS 0.004 0.001 HIS B 337 PHE 0.009 0.001 PHE A 315 TYR 0.011 0.001 TYR A 182 ARG 0.002 0.000 ARG A 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 172 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.780 Fit side-chains REVERT: A 75 THR cc_start: 0.8065 (m) cc_final: 0.7734 (t) REVERT: A 110 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: A 126 ARG cc_start: 0.7251 (ttt180) cc_final: 0.6708 (ttp80) REVERT: B 75 THR cc_start: 0.8069 (m) cc_final: 0.7738 (t) REVERT: B 110 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: B 126 ARG cc_start: 0.7251 (ttt180) cc_final: 0.6707 (ttp80) REVERT: C 75 THR cc_start: 0.8065 (m) cc_final: 0.7735 (t) REVERT: C 110 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: C 126 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6707 (ttp80) REVERT: D 75 THR cc_start: 0.8063 (m) cc_final: 0.7735 (t) REVERT: D 110 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: D 126 ARG cc_start: 0.7184 (ttt180) cc_final: 0.6427 (ttp80) REVERT: D 130 TRP cc_start: 0.6669 (m100) cc_final: 0.6136 (m100) outliers start: 32 outliers final: 20 residues processed: 160 average time/residue: 0.6300 time to fit residues: 139.6120 Evaluate side-chains 157 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER 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: 2.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.7743 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12316 Z= 0.220 Angle : 0.439 4.077 16712 Z= 0.241 Chirality : 0.033 0.135 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.439 13.297 1756 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.37 % Allowed : 11.43 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.22), residues: 1508 helix: 2.51 (0.14), residues: 1268 sheet: -0.20 (0.90), residues: 48 loop : -0.65 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 328 HIS 0.004 0.001 HIS C 337 PHE 0.007 0.001 PHE A 11 TYR 0.006 0.001 TYR A 96 ARG 0.002 0.000 ARG D 402 *********************** 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 153 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.777 Fit side-chains REVERT: A 75 THR cc_start: 0.8064 (m) cc_final: 0.7748 (t) REVERT: A 110 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: A 126 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6364 (ttp80) REVERT: A 130 TRP cc_start: 0.6659 (m100) cc_final: 0.6055 (m100) REVERT: B 75 THR cc_start: 0.8069 (m) cc_final: 0.7752 (t) REVERT: B 110 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: B 126 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6365 (ttp80) REVERT: B 130 TRP cc_start: 0.6662 (m100) cc_final: 0.6059 (m100) REVERT: C 75 THR cc_start: 0.8064 (m) cc_final: 0.7749 (t) REVERT: C 110 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: C 126 ARG cc_start: 0.7266 (ttt180) cc_final: 0.6366 (ttp80) REVERT: C 130 TRP cc_start: 0.6662 (m100) cc_final: 0.6058 (m100) REVERT: D 75 THR cc_start: 0.8062 (m) cc_final: 0.7747 (t) REVERT: D 110 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: D 126 ARG cc_start: 0.7212 (ttt180) cc_final: 0.6395 (ttp80) REVERT: D 130 TRP cc_start: 0.6630 (m100) cc_final: 0.6101 (m100) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.6647 time to fit residues: 134.1132 Evaluate side-chains 147 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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: 0.8980 chunk 82 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.2556 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= 0.265 Angle : 0.461 5.523 16712 Z= 0.251 Chirality : 0.034 0.137 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.489 15.030 1756 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.22 % Allowed : 11.74 % 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: 2.99 (0.21), residues: 1508 helix: 2.45 (0.14), residues: 1268 sheet: -0.29 (0.89), residues: 48 loop : -0.71 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 328 HIS 0.004 0.001 HIS C 337 PHE 0.007 0.001 PHE C 40 TYR 0.008 0.001 TYR A 182 ARG 0.001 0.000 ARG D 402 *********************** 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 148 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.831 Fit side-chains REVERT: A 75 THR cc_start: 0.8078 (m) cc_final: 0.7751 (t) REVERT: A 110 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: A 126 ARG cc_start: 0.7235 (ttt180) cc_final: 0.6705 (ttp80) REVERT: B 75 THR cc_start: 0.8081 (m) cc_final: 0.7753 (t) REVERT: B 110 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: B 126 ARG cc_start: 0.7270 (ttt180) cc_final: 0.6364 (ttp80) REVERT: B 130 TRP cc_start: 0.6666 (m100) cc_final: 0.6053 (m100) REVERT: C 75 THR cc_start: 0.8079 (m) cc_final: 0.7752 (t) REVERT: C 110 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: C 126 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6362 (ttp80) REVERT: C 130 TRP cc_start: 0.6671 (m100) cc_final: 0.6054 (m100) REVERT: D 75 THR cc_start: 0.8077 (m) cc_final: 0.7750 (t) REVERT: D 110 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: D 126 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6392 (ttp80) REVERT: D 130 TRP cc_start: 0.6630 (m100) cc_final: 0.6088 (m100) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.6711 time to fit residues: 133.1418 Evaluate side-chains 148 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.7757 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 : 0.004 0.033 12316 Z= 0.278 Angle : 0.469 5.874 16712 Z= 0.256 Chirality : 0.034 0.143 2008 Planarity : 0.003 0.024 2040 Dihedral : 3.501 14.483 1756 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 11.89 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.21), residues: 1508 helix: 2.40 (0.14), residues: 1268 sheet: -0.21 (0.89), residues: 48 loop : -0.80 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 328 HIS 0.004 0.001 HIS C 337 PHE 0.007 0.001 PHE B 40 TYR 0.008 0.001 TYR A 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 152 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 2.314 Fit side-chains REVERT: A 110 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: A 126 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6677 (ttp80) REVERT: B 110 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: B 126 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6676 (ttp80) REVERT: C 110 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: C 126 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6675 (ttp80) REVERT: D 110 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: D 126 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6395 (ttp80) REVERT: D 130 TRP cc_start: 0.6638 (m100) cc_final: 0.6102 (m100) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.6665 time to fit residues: 136.8403 Evaluate side-chains 148 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.2633 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= 0.164 Angle : 0.431 6.093 16712 Z= 0.232 Chirality : 0.033 0.132 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.335 11.668 1756 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.22 % Allowed : 11.89 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.22), residues: 1508 helix: 2.70 (0.14), residues: 1268 sheet: -0.24 (0.89), residues: 48 loop : -0.71 (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 0.008 0.001 PHE A 40 TYR 0.006 0.001 TYR D 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 152 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.846 Fit side-chains REVERT: A 75 THR cc_start: 0.7961 (m) cc_final: 0.7663 (t) REVERT: A 110 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: A 126 ARG cc_start: 0.7231 (ttt180) cc_final: 0.6347 (ttp80) REVERT: A 127 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6965 (ttt180) REVERT: A 130 TRP cc_start: 0.6665 (m100) cc_final: 0.6063 (m100) REVERT: B 75 THR cc_start: 0.7966 (m) cc_final: 0.7668 (t) REVERT: B 110 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: B 126 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6350 (ttp80) REVERT: B 127 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6977 (ttt180) REVERT: B 130 TRP cc_start: 0.6664 (m100) cc_final: 0.6062 (m100) REVERT: C 75 THR cc_start: 0.7962 (m) cc_final: 0.7665 (t) REVERT: C 110 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: C 126 ARG cc_start: 0.7231 (ttt180) cc_final: 0.6346 (ttp80) REVERT: C 127 ARG cc_start: 0.7195 (ttt180) cc_final: 0.6976 (ttt180) REVERT: C 130 TRP cc_start: 0.6665 (m100) cc_final: 0.6058 (m100) REVERT: D 75 THR cc_start: 0.7960 (m) cc_final: 0.7662 (t) REVERT: D 110 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: D 126 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6356 (ttp80) REVERT: D 127 ARG cc_start: 0.7196 (ttt180) cc_final: 0.6978 (ttt180) REVERT: D 130 TRP cc_start: 0.6594 (m100) cc_final: 0.6061 (m100) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.6991 time to fit residues: 139.6745 Evaluate side-chains 148 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.7741 moved from start: 0.2683 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= 0.221 Angle : 0.444 6.257 16712 Z= 0.241 Chirality : 0.033 0.133 2008 Planarity : 0.003 0.025 2040 Dihedral : 3.375 13.863 1756 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.22 % Allowed : 11.89 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.22), residues: 1508 helix: 2.64 (0.14), residues: 1268 sheet: -0.31 (0.89), residues: 48 loop : -0.72 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 328 HIS 0.003 0.001 HIS C 337 PHE 0.007 0.001 PHE A 40 TYR 0.007 0.001 TYR B 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 163 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.7980 (m) cc_final: 0.7681 (t) REVERT: A 110 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: A 126 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6326 (ttp80) REVERT: A 127 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6965 (ttt180) REVERT: A 130 TRP cc_start: 0.6667 (m100) cc_final: 0.6058 (m100) REVERT: B 75 THR cc_start: 0.7987 (m) cc_final: 0.7684 (t) REVERT: B 110 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: B 126 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6326 (ttp80) REVERT: B 130 TRP cc_start: 0.6665 (m100) cc_final: 0.6056 (m100) REVERT: C 75 THR cc_start: 0.7983 (m) cc_final: 0.7684 (t) REVERT: C 110 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: C 126 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6325 (ttp80) REVERT: C 127 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6967 (ttt180) REVERT: C 130 TRP cc_start: 0.6667 (m100) cc_final: 0.6053 (m100) REVERT: D 75 THR cc_start: 0.7979 (m) cc_final: 0.7680 (t) REVERT: D 110 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: D 126 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6397 (ttp80) REVERT: D 127 ARG cc_start: 0.7176 (ttt180) cc_final: 0.6974 (ttt180) REVERT: D 130 TRP cc_start: 0.6602 (m100) cc_final: 0.6057 (m100) outliers start: 16 outliers final: 12 residues processed: 158 average time/residue: 0.6840 time to fit residues: 145.8373 Evaluate side-chains 163 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain 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: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.129686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.104252 restraints weight = 39813.627| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.59 r_work: 0.2974 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2732 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= 0.171 Angle : 0.429 6.457 16712 Z= 0.230 Chirality : 0.033 0.131 2008 Planarity : 0.003 0.026 2040 Dihedral : 3.274 11.985 1756 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.91 % Allowed : 12.50 % Favored : 86.59 % 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: 3.46 (0.22), residues: 1508 helix: 2.79 (0.14), residues: 1268 sheet: -0.31 (0.89), residues: 48 loop : -0.68 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 328 HIS 0.003 0.001 HIS B 337 PHE 0.008 0.001 PHE A 40 TYR 0.008 0.001 TYR C 96 ARG 0.002 0.000 ARG C 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4816.95 seconds wall clock time: 85 minutes 29.46 seconds (5129.46 seconds total)