Starting phenix.real_space_refine on Tue Mar 19 16:53:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/03_2024/8x84_38135_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/03_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_38135/03_2024/8x84_38135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/03_2024/8x84_38135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/03_2024/8x84_38135_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x84_38135/03_2024/8x84_38135_neut_trim_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.87, per 1000 atoms: 0.44 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: 19.42 Conformation dependent library (CDL) restraints added in 2.7 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... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 79.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 38 through 63 Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.551A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 160 Processing helix chain 'A' and resid 169 through 214 removed outlier: 3.784A pdb=" N TYR A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 263 through 320 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 325 through 356 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 372 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 402 through 425 removed outlier: 4.165A pdb=" N TYR A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 417 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 38 through 63 Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.551A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 118 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 160 Processing helix chain 'B' and resid 169 through 214 removed outlier: 3.784A pdb=" N TYR B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 263 through 320 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 325 through 356 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 372 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 402 through 425 removed outlier: 4.165A pdb=" N TYR B 415 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 416 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 417 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 38 through 63 Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.551A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 160 Processing helix chain 'C' and resid 169 through 214 removed outlier: 3.784A pdb=" N TYR C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Proline residue: C 177 - end of helix Processing helix chain 'C' and resid 263 through 320 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 325 through 356 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 372 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 402 through 425 removed outlier: 4.165A pdb=" N TYR C 415 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU C 416 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 38 through 63 Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.551A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 118 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 125 through 160 Processing helix chain 'D' and resid 169 through 214 removed outlier: 3.784A pdb=" N TYR D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 177 - end of helix Processing helix chain 'D' and resid 263 through 320 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 325 through 356 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 372 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 402 through 425 removed outlier: 4.165A pdb=" N TYR D 415 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU D 416 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 417 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 26 Processing sheet with id= B, first strand: chain 'B' and resid 22 through 26 Processing sheet with id= C, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= D, first strand: chain 'D' and resid 22 through 26 988 hydrogen bonds defined for protein. 2748 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: 20.14 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: 1372 2.20 - 2.80: 51428 2.80 - 3.40: 72464 3.40 - 4.00: 92006 4.00 - 4.60: 146723 Nonbonded interactions: 363993 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=" O SER A 73 " pdb=" H LYS A 77 " model vdw 1.648 1.850 ... (remaining 363988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.770 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: 0.360 Extract box with map and model: 4.370 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 77.450 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.340 ------------------------------------------------------------------------------- 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= 0.269 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 : 1.624 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: 0.6727 time to fit residues: 86.2224 Evaluate side-chains 84 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN B 421 GLN C 27 ASN C 421 GLN D 27 ASN D 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12316 Z= 0.296 Angle : 0.482 4.265 16712 Z= 0.263 Chirality : 0.035 0.131 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.583 15.838 1760 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.61 % Allowed : 8.84 % 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: 2.42 (0.22), residues: 1508 helix: 1.99 (0.14), residues: 1252 sheet: 0.29 (0.81), residues: 48 loop : -0.34 (0.51), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 328 HIS 0.004 0.001 HIS C 349 PHE 0.007 0.001 PHE C 338 TYR 0.011 0.001 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 141 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.964 Fit side-chains REVERT: A 75 THR cc_start: 0.7806 (m) cc_final: 0.7552 (t) REVERT: A 126 ARG cc_start: 0.7154 (ttt180) cc_final: 0.6604 (ttp-110) REVERT: A 370 HIS cc_start: 0.5742 (m-70) cc_final: 0.5539 (m170) REVERT: A 421 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.5583 (tm130) REVERT: B 75 THR cc_start: 0.7809 (m) cc_final: 0.7555 (t) REVERT: B 126 ARG cc_start: 0.7155 (ttt180) cc_final: 0.6608 (ttp-110) REVERT: B 370 HIS cc_start: 0.5746 (m-70) cc_final: 0.5540 (m170) REVERT: B 421 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5586 (tm130) REVERT: C 75 THR cc_start: 0.7811 (m) cc_final: 0.7559 (t) REVERT: C 126 ARG cc_start: 0.7154 (ttt180) cc_final: 0.6606 (ttp-110) REVERT: C 370 HIS cc_start: 0.5736 (m-70) cc_final: 0.5532 (m170) REVERT: C 421 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5579 (tm130) REVERT: D 75 THR cc_start: 0.7806 (m) cc_final: 0.7554 (t) REVERT: D 126 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6602 (ttp-110) REVERT: D 370 HIS cc_start: 0.5734 (m-70) cc_final: 0.5532 (m170) REVERT: D 421 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.5579 (tm130) outliers start: 8 outliers final: 0 residues processed: 141 average time/residue: 0.6272 time to fit residues: 123.3158 Evaluate side-chains 129 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain D residue 421 GLN 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: 4.9990 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: 0.0470 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12316 Z= 0.230 Angle : 0.448 6.850 16712 Z= 0.246 Chirality : 0.033 0.128 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.086 10.559 1756 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.22 % Allowed : 10.29 % 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: 2.70 (0.22), residues: 1508 helix: 2.19 (0.14), residues: 1252 sheet: 0.23 (0.83), residues: 48 loop : -0.34 (0.51), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 328 HIS 0.002 0.001 HIS B 337 PHE 0.009 0.001 PHE C 422 TYR 0.005 0.001 TYR B 179 ARG 0.001 0.000 ARG D 36 *********************** 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 144 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.883 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.7847 (m) cc_final: 0.7589 (t) REVERT: A 126 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6624 (ttp-110) REVERT: B 75 THR cc_start: 0.7852 (m) cc_final: 0.7594 (t) REVERT: B 126 ARG cc_start: 0.7221 (ttt180) cc_final: 0.6626 (ttp-110) REVERT: C 75 THR cc_start: 0.7851 (m) cc_final: 0.7594 (t) REVERT: C 126 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6628 (ttp-110) REVERT: D 75 THR cc_start: 0.7849 (m) cc_final: 0.7591 (t) REVERT: D 126 ARG cc_start: 0.7221 (ttt180) cc_final: 0.6625 (ttp-110) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.6291 time to fit residues: 115.8127 Evaluate side-chains 132 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 371 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7719 moved from start: 0.1856 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= 0.196 Angle : 0.411 4.221 16712 Z= 0.225 Chirality : 0.032 0.130 2008 Planarity : 0.003 0.027 2040 Dihedral : 3.058 10.764 1756 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.91 % Allowed : 10.37 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.68 (0.22), residues: 1508 helix: 2.18 (0.14), residues: 1252 sheet: 0.11 (0.83), residues: 48 loop : -0.29 (0.51), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 328 HIS 0.002 0.001 HIS B 337 PHE 0.006 0.001 PHE C 40 TYR 0.006 0.001 TYR A 56 ARG 0.002 0.000 ARG B 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 136 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 2.064 Fit side-chains REVERT: A 75 THR cc_start: 0.7843 (m) cc_final: 0.7613 (t) REVERT: A 110 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: A 126 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6432 (ttp80) REVERT: A 130 TRP cc_start: 0.6657 (m100) cc_final: 0.6118 (m100) REVERT: B 75 THR cc_start: 0.7847 (m) cc_final: 0.7617 (t) REVERT: B 110 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: B 126 ARG cc_start: 0.7242 (ttt180) cc_final: 0.6437 (ttp80) REVERT: B 130 TRP cc_start: 0.6657 (m100) cc_final: 0.6115 (m100) REVERT: C 75 THR cc_start: 0.7845 (m) cc_final: 0.7615 (t) REVERT: C 110 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: C 126 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6434 (ttp80) REVERT: C 130 TRP cc_start: 0.6655 (m100) cc_final: 0.6113 (m100) REVERT: D 75 THR cc_start: 0.7851 (m) cc_final: 0.7611 (t) REVERT: D 110 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: D 126 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6432 (ttp80) REVERT: D 130 TRP cc_start: 0.6655 (m100) cc_final: 0.6114 (m100) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.6324 time to fit residues: 112.4027 Evaluate side-chains 130 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 371 GLU 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: 4.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 37 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 370 HIS B 370 HIS D 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12316 Z= 0.347 Angle : 0.482 4.477 16712 Z= 0.267 Chirality : 0.035 0.134 2008 Planarity : 0.003 0.029 2040 Dihedral : 3.427 11.312 1756 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.52 % Allowed : 10.29 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.14 (0.22), residues: 1508 helix: 1.80 (0.14), residues: 1248 sheet: -0.06 (0.86), residues: 48 loop : -0.36 (0.51), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 328 HIS 0.003 0.001 HIS C 337 PHE 0.008 0.001 PHE A 315 TYR 0.009 0.002 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 172 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.812 Fit side-chains REVERT: A 75 THR cc_start: 0.7967 (m) cc_final: 0.7678 (t) REVERT: A 110 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: A 126 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6652 (ttp-110) REVERT: B 75 THR cc_start: 0.7971 (m) cc_final: 0.7681 (t) REVERT: B 110 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: B 126 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6637 (ttp-110) REVERT: C 75 THR cc_start: 0.7967 (m) cc_final: 0.7678 (t) REVERT: C 110 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: C 126 ARG cc_start: 0.7260 (ttt180) cc_final: 0.6641 (ttp-110) REVERT: D 75 THR cc_start: 0.7964 (m) cc_final: 0.7676 (t) REVERT: D 110 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: D 126 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6652 (ttp-110) outliers start: 20 outliers final: 16 residues processed: 160 average time/residue: 0.6408 time to fit residues: 142.0102 Evaluate side-chains 161 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain A residue 416 LEU 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 371 GLU Chi-restraints excluded: chain B residue 416 LEU 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 371 GLU Chi-restraints excluded: chain C residue 416 LEU 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 371 GLU Chi-restraints excluded: chain D residue 416 LEU 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: 2.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12316 Z= 0.131 Angle : 0.404 4.846 16712 Z= 0.220 Chirality : 0.032 0.128 2008 Planarity : 0.003 0.029 2040 Dihedral : 3.044 11.209 1756 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.22 % Allowed : 10.82 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.73 (0.22), residues: 1508 helix: 2.23 (0.14), residues: 1248 sheet: 0.03 (0.84), residues: 48 loop : -0.34 (0.50), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.002 0.001 HIS C 337 PHE 0.006 0.001 PHE D 40 TYR 0.005 0.001 TYR C 96 ARG 0.002 0.000 ARG C 156 *********************** 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 154 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.775 Fit side-chains REVERT: A 75 THR cc_start: 0.7936 (m) cc_final: 0.7692 (t) REVERT: A 110 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 126 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6360 (ttp80) REVERT: A 130 TRP cc_start: 0.6653 (m100) cc_final: 0.6071 (m100) REVERT: B 75 THR cc_start: 0.7939 (m) cc_final: 0.7695 (t) REVERT: B 110 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: B 126 ARG cc_start: 0.7253 (ttt180) cc_final: 0.6365 (ttp80) REVERT: B 130 TRP cc_start: 0.6652 (m100) cc_final: 0.6069 (m100) REVERT: C 75 THR cc_start: 0.7938 (m) cc_final: 0.7692 (t) REVERT: C 110 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: C 126 ARG cc_start: 0.7253 (ttt180) cc_final: 0.6365 (ttp80) REVERT: C 130 TRP cc_start: 0.6653 (m100) cc_final: 0.6070 (m100) REVERT: D 75 THR cc_start: 0.7938 (m) cc_final: 0.7692 (t) REVERT: D 110 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: D 126 ARG cc_start: 0.7252 (ttt180) cc_final: 0.6362 (ttp80) REVERT: D 130 TRP cc_start: 0.6654 (m100) cc_final: 0.6070 (m100) outliers start: 16 outliers final: 8 residues processed: 146 average time/residue: 0.6414 time to fit residues: 128.6190 Evaluate side-chains 146 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 371 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.2324 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= 0.210 Angle : 0.422 5.236 16712 Z= 0.230 Chirality : 0.033 0.131 2008 Planarity : 0.003 0.028 2040 Dihedral : 3.107 11.216 1756 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.91 % Allowed : 11.28 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.71 (0.22), residues: 1508 helix: 2.21 (0.14), residues: 1244 sheet: -0.03 (0.84), residues: 48 loop : -0.18 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.002 0.001 HIS C 337 PHE 0.006 0.001 PHE B 40 TYR 0.006 0.001 TYR D 56 ARG 0.001 0.000 ARG D 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 156 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 2.011 Fit side-chains REVERT: A 75 THR cc_start: 0.7956 (m) cc_final: 0.7721 (t) REVERT: A 110 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: A 126 ARG cc_start: 0.7238 (ttt180) cc_final: 0.6338 (ttp80) REVERT: A 130 TRP cc_start: 0.6632 (m100) cc_final: 0.6022 (m100) REVERT: B 75 THR cc_start: 0.7959 (m) cc_final: 0.7710 (t) REVERT: B 110 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: B 126 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6339 (ttp80) REVERT: B 130 TRP cc_start: 0.6630 (m100) cc_final: 0.6018 (m100) REVERT: C 75 THR cc_start: 0.7946 (m) cc_final: 0.7703 (t) REVERT: C 110 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: C 126 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6342 (ttp80) REVERT: C 130 TRP cc_start: 0.6630 (m100) cc_final: 0.6018 (m100) REVERT: D 75 THR cc_start: 0.7945 (m) cc_final: 0.7706 (t) REVERT: D 110 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: D 126 ARG cc_start: 0.7239 (ttt180) cc_final: 0.6339 (ttp80) REVERT: D 130 TRP cc_start: 0.6632 (m100) cc_final: 0.6020 (m100) outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 0.6797 time to fit residues: 138.8005 Evaluate side-chains 150 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 371 GLU 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 0.0060 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12316 Z= 0.240 Angle : 0.432 5.310 16712 Z= 0.237 Chirality : 0.033 0.132 2008 Planarity : 0.003 0.029 2040 Dihedral : 3.172 11.324 1756 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.91 % Allowed : 10.52 % Favored : 88.57 % 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: 2.61 (0.22), residues: 1508 helix: 2.13 (0.14), residues: 1244 sheet: -0.07 (0.84), residues: 48 loop : -0.13 (0.50), residues: 216 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 0.006 0.001 PHE C 40 TYR 0.006 0.001 TYR A 415 ARG 0.002 0.000 ARG C 36 *********************** 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 150 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.929 Fit side-chains REVERT: A 75 THR cc_start: 0.7958 (m) cc_final: 0.7715 (t) REVERT: A 110 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: A 126 ARG cc_start: 0.7254 (ttt180) cc_final: 0.6679 (ttt90) REVERT: A 130 TRP cc_start: 0.6636 (m100) cc_final: 0.5949 (m100) REVERT: B 75 THR cc_start: 0.7959 (m) cc_final: 0.7720 (t) REVERT: B 110 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: B 126 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6338 (ttp80) REVERT: B 130 TRP cc_start: 0.6635 (m100) cc_final: 0.5975 (m100) REVERT: C 75 THR cc_start: 0.7958 (m) cc_final: 0.7716 (t) REVERT: C 110 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: C 126 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6337 (ttp80) REVERT: C 130 TRP cc_start: 0.6637 (m100) cc_final: 0.5974 (m100) REVERT: D 75 THR cc_start: 0.7957 (m) cc_final: 0.7725 (t) REVERT: D 110 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: D 126 ARG cc_start: 0.7216 (ttt180) cc_final: 0.6332 (ttp80) REVERT: D 130 TRP cc_start: 0.6648 (m100) cc_final: 0.5991 (m100) outliers start: 12 outliers final: 8 residues processed: 142 average time/residue: 0.6923 time to fit residues: 135.0715 Evaluate side-chains 150 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 371 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7717 moved from start: 0.2508 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= 0.154 Angle : 0.403 6.233 16712 Z= 0.218 Chirality : 0.032 0.129 2008 Planarity : 0.003 0.029 2040 Dihedral : 2.991 11.324 1756 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.91 % Allowed : 10.37 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.94 (0.22), residues: 1508 helix: 2.37 (0.14), residues: 1244 sheet: 0.01 (0.84), residues: 48 loop : -0.09 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 328 HIS 0.002 0.001 HIS B 337 PHE 0.007 0.001 PHE C 40 TYR 0.004 0.001 TYR A 56 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 153 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.918 Fit side-chains REVERT: A 75 THR cc_start: 0.7840 (m) cc_final: 0.7633 (t) REVERT: A 110 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: A 126 ARG cc_start: 0.7209 (ttt180) cc_final: 0.6332 (ttp80) REVERT: A 130 TRP cc_start: 0.6637 (m100) cc_final: 0.5989 (m100) REVERT: B 75 THR cc_start: 0.7845 (m) cc_final: 0.7633 (t) REVERT: B 110 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: B 126 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6337 (ttp80) REVERT: B 130 TRP cc_start: 0.6631 (m100) cc_final: 0.5985 (m100) REVERT: C 75 THR cc_start: 0.7842 (m) cc_final: 0.7628 (t) REVERT: C 110 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: C 126 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6334 (ttp80) REVERT: C 130 TRP cc_start: 0.6631 (m100) cc_final: 0.5981 (m100) REVERT: D 75 THR cc_start: 0.7841 (m) cc_final: 0.7632 (t) REVERT: D 110 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: D 126 ARG cc_start: 0.7211 (ttt180) cc_final: 0.6334 (ttp80) REVERT: D 130 TRP cc_start: 0.6646 (m100) cc_final: 0.6000 (m100) outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 0.6632 time to fit residues: 132.4507 Evaluate side-chains 150 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 371 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 371 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.0020 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12316 Z= 0.118 Angle : 0.388 6.989 16712 Z= 0.207 Chirality : 0.032 0.125 2008 Planarity : 0.002 0.029 2040 Dihedral : 2.765 10.429 1756 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.30 % Allowed : 10.82 % Favored : 88.87 % 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: 3.48 (0.22), residues: 1508 helix: 2.74 (0.14), residues: 1240 sheet: 0.14 (0.82), residues: 48 loop : 0.10 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 154 HIS 0.002 0.001 HIS A 306 PHE 0.008 0.001 PHE B 40 TYR 0.006 0.001 TYR B 122 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 171 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.7195 (ttt180) cc_final: 0.6325 (ttp80) REVERT: A 130 TRP cc_start: 0.6555 (m100) cc_final: 0.5910 (m100) REVERT: B 126 ARG cc_start: 0.7199 (ttt180) cc_final: 0.6332 (ttp80) REVERT: B 130 TRP cc_start: 0.6561 (m100) cc_final: 0.5916 (m100) REVERT: C 126 ARG cc_start: 0.7195 (ttt180) cc_final: 0.6328 (ttp80) REVERT: C 130 TRP cc_start: 0.6555 (m100) cc_final: 0.5906 (m100) REVERT: D 126 ARG cc_start: 0.7194 (ttt180) cc_final: 0.6325 (ttp80) REVERT: D 130 TRP cc_start: 0.6559 (m100) cc_final: 0.5911 (m100) outliers start: 4 outliers final: 4 residues processed: 167 average time/residue: 0.6832 time to fit residues: 156.0728 Evaluate side-chains 167 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.132023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.107162 restraints weight = 39724.816| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.58 r_work: 0.3019 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2583 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= 0.130 Angle : 0.395 6.590 16712 Z= 0.209 Chirality : 0.032 0.127 2008 Planarity : 0.002 0.029 2040 Dihedral : 2.761 10.437 1756 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.30 % Allowed : 11.43 % Favored : 88.26 % 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: 3.56 (0.22), residues: 1508 helix: 2.79 (0.14), residues: 1240 sheet: 0.16 (0.82), residues: 48 loop : 0.20 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.002 0.001 HIS C 306 PHE 0.007 0.001 PHE B 40 TYR 0.005 0.001 TYR D 122 ARG 0.001 0.000 ARG C 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4943.47 seconds wall clock time: 88 minutes 23.40 seconds (5303.40 seconds total)