Starting phenix.real_space_refine on Mon Mar 11 07:09:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/03_2024/7s05_24784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/03_2024/7s05_24784.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/7s05_24784/03_2024/7s05_24784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/03_2024/7s05_24784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/03_2024/7s05_24784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/03_2024/7s05_24784.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= 0.004 sd= 0.077 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 40 5.16 5 C 4778 2.51 5 N 1274 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 975": "OE1" <-> "OE2" Residue "B GLU 1016": "OE1" <-> "OE2" Residue "B TYR 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1119": "OE1" <-> "OE2" Residue "B GLU 1173": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A TYR 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1119": "OE1" <-> "OE2" Residue "A GLU 1173": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7504 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3653 Classifications: {'peptide': 437} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3653 Classifications: {'peptide': 437} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 414} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.50, per 1000 atoms: 0.60 Number of scatterers: 7504 At special positions: 0 Unit cell: (116.748, 123.372, 72.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 40 16.00 O 1410 8.00 N 1274 7.00 C 4778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS A 70 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A1009 " " NAG A1302 " - " ASN A1056 " " NAG A1303 " - " ASN A 376 " " NAG B1301 " - " ASN B1009 " " NAG B1302 " - " ASN B1056 " " NAG B1303 " - " ASN B 376 " " NAG C 1 " - " ASN B 83 " " NAG D 1 " - " ASN B1129 " " NAG E 1 " - " ASN A 83 " " NAG F 1 " - " ASN A1129 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 52.3% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'B' and resid 49 through 55 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 85 through 111 Processing helix chain 'B' and resid 327 through 340 removed outlier: 3.589A pdb=" N TYR B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.606A pdb=" N VAL B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 removed outlier: 4.216A pdb=" N HIS B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 931 through 947 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 983 Processing helix chain 'B' and resid 993 through 1003 Processing helix chain 'B' and resid 1009 through 1018 Processing helix chain 'B' and resid 1026 through 1038 Processing helix chain 'B' and resid 1043 through 1061 removed outlier: 3.642A pdb=" N LEU B1047 " --> pdb=" O SER B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1094 removed outlier: 3.634A pdb=" N VAL B1091 " --> pdb=" O THR B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1105 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1161 through 1176 Processing helix chain 'B' and resid 1195 through 1204 Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 85 through 111 Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.591A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.605A pdb=" N VAL A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 removed outlier: 4.216A pdb=" N HIS A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 931 through 947 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 973 through 983 Processing helix chain 'A' and resid 993 through 1003 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1026 through 1038 Processing helix chain 'A' and resid 1043 through 1061 removed outlier: 3.641A pdb=" N LEU A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1094 removed outlier: 3.634A pdb=" N VAL A1091 " --> pdb=" O THR A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1105 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1161 through 1176 Processing helix chain 'A' and resid 1195 through 1204 Processing sheet with id=AA1, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.607A pdb=" N ILE B 346 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 368 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE B 348 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE B 347 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 77 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 349 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR B 79 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 76 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 405 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL B 78 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.533A pdb=" N VAL B1148 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA B1122 " --> pdb=" O CYS B1149 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN B1151 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS B1124 " --> pdb=" O ASN B1151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 421 through 422 removed outlier: 4.142A pdb=" N VAL B 953 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.632A pdb=" N LEU B 431 " --> pdb=" O MET B1116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1005 through 1006 removed outlier: 3.774A pdb=" N GLN B1006 " --> pdb=" O LYS B1108 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B1108 " --> pdb=" O GLN B1006 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.606A pdb=" N ILE A 346 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 368 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A 348 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N PHE A 347 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 77 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 349 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 79 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 76 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 405 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 78 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.533A pdb=" N VAL A1148 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA A1122 " --> pdb=" O CYS A1149 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN A1151 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS A1124 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 421 through 422 removed outlier: 4.143A pdb=" N VAL A 953 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.633A pdb=" N LEU A 431 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1005 through 1006 removed outlier: 3.774A pdb=" N GLN A1006 " --> pdb=" O LYS A1108 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A1108 " --> pdb=" O GLN A1006 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 317 hydrogen bonds defined for protein. 921 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: 2.17 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2421 1.34 - 1.46: 1682 1.46 - 1.58: 3513 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 7688 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 ... (remaining 7683 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.61: 190 105.61 - 112.70: 4055 112.70 - 119.80: 2511 119.80 - 126.89: 3528 126.89 - 133.99: 114 Bond angle restraints: 10398 Sorted by residual: angle pdb=" C GLU A1118 " pdb=" CA GLU A1118 " pdb=" CB GLU A1118 " ideal model delta sigma weight residual 111.22 106.92 4.30 1.24e+00 6.50e-01 1.21e+01 angle pdb=" C GLU B1118 " pdb=" CA GLU B1118 " pdb=" CB GLU B1118 " ideal model delta sigma weight residual 111.22 106.96 4.26 1.24e+00 6.50e-01 1.18e+01 angle pdb=" N THR B1128 " pdb=" CA THR B1128 " pdb=" CB THR B1128 " ideal model delta sigma weight residual 112.28 107.19 5.09 1.49e+00 4.50e-01 1.17e+01 angle pdb=" N THR A1128 " pdb=" CA THR A1128 " pdb=" CB THR A1128 " ideal model delta sigma weight residual 112.28 107.24 5.04 1.49e+00 4.50e-01 1.14e+01 angle pdb=" N LEU B 380 " pdb=" CA LEU B 380 " pdb=" C LEU B 380 " ideal model delta sigma weight residual 109.81 115.90 -6.09 2.21e+00 2.05e-01 7.58e+00 ... (remaining 10393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.33: 4336 20.33 - 40.65: 419 40.65 - 60.98: 40 60.98 - 81.31: 20 81.31 - 101.63: 10 Dihedral angle restraints: 4825 sinusoidal: 2219 harmonic: 2606 Sorted by residual: dihedral pdb=" CA ARG A1127 " pdb=" C ARG A1127 " pdb=" N THR A1128 " pdb=" CA THR A1128 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG B1127 " pdb=" C ARG B1127 " pdb=" N THR B1128 " pdb=" CA THR B1128 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PRO B 381 " pdb=" C PRO B 381 " pdb=" N THR B 382 " pdb=" CA THR B 382 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1078 0.093 - 0.186: 68 0.186 - 0.279: 0 0.279 - 0.372: 2 0.372 - 0.465: 4 Chirality restraints: 1152 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 376 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 376 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1056 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 1149 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 376 " -0.027 2.00e-02 2.50e+03 2.58e-02 8.33e+00 pdb=" CG ASN B 376 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 376 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 376 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 376 " 0.027 2.00e-02 2.50e+03 2.58e-02 8.32e+00 pdb=" CG ASN A 376 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 376 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 376 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B1178 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B1179 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B1179 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1179 " 0.024 5.00e-02 4.00e+02 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 797 2.75 - 3.29: 7235 3.29 - 3.82: 12351 3.82 - 4.36: 14719 4.36 - 4.90: 25433 Nonbonded interactions: 60535 Sorted by model distance: nonbonded pdb=" OH TYR B 79 " pdb=" OG SER B 332 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 79 " pdb=" OG SER A 332 " model vdw 2.213 2.440 nonbonded pdb=" O SER B 356 " pdb=" NH2 ARG B1186 " model vdw 2.304 2.520 nonbonded pdb=" O SER A 356 " pdb=" NH2 ARG A1186 " model vdw 2.304 2.520 nonbonded pdb=" OH TYR A 937 " pdb=" OE1 GLU A 976 " model vdw 2.344 2.440 ... (remaining 60530 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.010 Extract box with map and model: 7.200 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 23.420 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 0.053 7688 Z= 0.241 Angle : 0.679 7.010 10398 Z= 0.372 Chirality : 0.052 0.465 1152 Planarity : 0.004 0.043 1326 Dihedral : 16.047 101.632 3118 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.10 (0.29), residues: 858 helix: 1.27 (0.26), residues: 394 sheet: 0.37 (0.55), residues: 98 loop : -1.39 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1201 HIS 0.013 0.001 HIS A 987 PHE 0.010 0.001 PHE B1176 TYR 0.016 0.001 TYR A 999 ARG 0.006 0.000 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.907 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1904 time to fit residues: 30.6194 Evaluate side-chains 85 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS B1012 GLN A 987 HIS A1012 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7688 Z= 0.213 Angle : 0.599 6.308 10398 Z= 0.303 Chirality : 0.049 0.358 1152 Planarity : 0.004 0.035 1326 Dihedral : 10.606 78.501 1250 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.82 % Allowed : 6.80 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.44 (0.29), residues: 858 helix: 1.61 (0.25), residues: 394 sheet: 0.48 (0.55), residues: 102 loop : -1.29 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1201 HIS 0.003 0.001 HIS B 423 PHE 0.008 0.001 PHE B 411 TYR 0.020 0.002 TYR B 999 ARG 0.005 0.000 ARG A1127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.764 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 0.1999 time to fit residues: 31.9697 Evaluate side-chains 103 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN B 987 HIS A 326 ASN A 987 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7688 Z= 0.228 Angle : 0.599 7.252 10398 Z= 0.299 Chirality : 0.049 0.326 1152 Planarity : 0.004 0.033 1326 Dihedral : 9.281 67.491 1250 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.21 % Allowed : 10.07 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.56 (0.29), residues: 858 helix: 1.80 (0.26), residues: 392 sheet: 0.37 (0.53), residues: 102 loop : -1.27 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 357 HIS 0.003 0.001 HIS A 983 PHE 0.010 0.001 PHE A 998 TYR 0.018 0.002 TYR B 999 ARG 0.005 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.801 Fit side-chains REVERT: B 410 MET cc_start: 0.8475 (mtm) cc_final: 0.8273 (mtm) REVERT: B 1116 MET cc_start: 0.7913 (mpp) cc_final: 0.7685 (mpp) outliers start: 10 outliers final: 10 residues processed: 111 average time/residue: 0.2212 time to fit residues: 32.4305 Evaluate side-chains 103 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 1178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 22 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN B 987 HIS A 326 ASN A 987 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7688 Z= 0.195 Angle : 0.575 7.357 10398 Z= 0.285 Chirality : 0.048 0.312 1152 Planarity : 0.004 0.042 1326 Dihedral : 8.285 59.408 1250 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.46 % Allowed : 10.92 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.74 (0.29), residues: 858 helix: 1.93 (0.25), residues: 392 sheet: 0.63 (0.54), residues: 98 loop : -1.20 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1201 HIS 0.002 0.001 HIS B 983 PHE 0.011 0.001 PHE A 993 TYR 0.018 0.001 TYR B 999 ARG 0.008 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.876 Fit side-chains REVERT: B 388 ILE cc_start: 0.8145 (mp) cc_final: 0.7935 (mp) REVERT: A 107 MET cc_start: 0.5175 (mmp) cc_final: 0.4749 (mtt) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.2354 time to fit residues: 34.2547 Evaluate side-chains 99 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 1178 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS B 992 GLN B1151 ASN A 987 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7688 Z= 0.284 Angle : 0.620 8.321 10398 Z= 0.307 Chirality : 0.049 0.320 1152 Planarity : 0.004 0.039 1326 Dihedral : 7.237 48.151 1250 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.16 % Allowed : 11.77 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.71 (0.29), residues: 858 helix: 1.91 (0.25), residues: 392 sheet: 0.53 (0.60), residues: 78 loop : -1.10 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 357 HIS 0.004 0.001 HIS B 423 PHE 0.018 0.001 PHE A 998 TYR 0.018 0.002 TYR B1105 ARG 0.006 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.858 Fit side-chains REVERT: B 107 MET cc_start: 0.4904 (mmp) cc_final: 0.4504 (mtt) REVERT: B 337 GLU cc_start: 0.7546 (tt0) cc_final: 0.7341 (tt0) REVERT: A 107 MET cc_start: 0.5250 (mmp) cc_final: 0.4775 (mtt) REVERT: A 1127 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7721 (mtt-85) outliers start: 26 outliers final: 11 residues processed: 116 average time/residue: 0.2075 time to fit residues: 32.4382 Evaluate side-chains 98 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1178 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS B 992 GLN A 987 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7688 Z= 0.292 Angle : 0.645 9.420 10398 Z= 0.319 Chirality : 0.049 0.313 1152 Planarity : 0.004 0.040 1326 Dihedral : 6.847 44.752 1250 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.43 % Allowed : 13.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.67 (0.29), residues: 858 helix: 1.86 (0.25), residues: 392 sheet: 0.48 (0.60), residues: 78 loop : -1.09 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 357 HIS 0.003 0.001 HIS B 423 PHE 0.018 0.001 PHE B 998 TYR 0.018 0.002 TYR B1105 ARG 0.005 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.806 Fit side-chains REVERT: B 107 MET cc_start: 0.4984 (mmp) cc_final: 0.4556 (mtt) REVERT: B 337 GLU cc_start: 0.7568 (tt0) cc_final: 0.7352 (tt0) REVERT: B 1170 ASP cc_start: 0.7734 (t0) cc_final: 0.7530 (t70) REVERT: A 107 MET cc_start: 0.5098 (mmp) cc_final: 0.4620 (mtt) REVERT: A 1116 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7567 (mtm) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 0.2067 time to fit residues: 28.9544 Evaluate side-chains 101 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.0000 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS A 987 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7688 Z= 0.193 Angle : 0.582 7.200 10398 Z= 0.288 Chirality : 0.047 0.298 1152 Planarity : 0.004 0.034 1326 Dihedral : 6.374 43.911 1250 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.31 % Allowed : 14.44 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.91 (0.29), residues: 858 helix: 2.04 (0.26), residues: 392 sheet: 0.90 (0.61), residues: 74 loop : -0.99 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 357 HIS 0.002 0.001 HIS A1194 PHE 0.010 0.001 PHE A 998 TYR 0.017 0.001 TYR B1105 ARG 0.006 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.877 Fit side-chains REVERT: B 107 MET cc_start: 0.5018 (mmp) cc_final: 0.4601 (mtt) REVERT: B 337 GLU cc_start: 0.7530 (tt0) cc_final: 0.7313 (tt0) REVERT: A 107 MET cc_start: 0.5165 (mmp) cc_final: 0.4686 (mtt) REVERT: A 1116 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7688 (mtm) outliers start: 19 outliers final: 14 residues processed: 106 average time/residue: 0.2123 time to fit residues: 30.2995 Evaluate side-chains 102 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS A 987 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7688 Z= 0.200 Angle : 0.575 7.269 10398 Z= 0.286 Chirality : 0.047 0.293 1152 Planarity : 0.004 0.072 1326 Dihedral : 6.128 42.632 1250 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.18 % Allowed : 14.20 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.02 (0.30), residues: 858 helix: 2.11 (0.26), residues: 392 sheet: 0.92 (0.63), residues: 74 loop : -0.90 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 357 HIS 0.002 0.001 HIS A 423 PHE 0.011 0.001 PHE A 998 TYR 0.017 0.001 TYR A 999 ARG 0.017 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.874 Fit side-chains REVERT: B 107 MET cc_start: 0.4927 (mmp) cc_final: 0.4560 (mtt) REVERT: B 337 GLU cc_start: 0.7526 (tt0) cc_final: 0.7308 (tt0) REVERT: A 107 MET cc_start: 0.5130 (mmp) cc_final: 0.4629 (mtt) REVERT: A 1116 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7672 (mtm) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.2037 time to fit residues: 28.5743 Evaluate side-chains 103 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS A 987 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7688 Z= 0.208 Angle : 0.571 7.373 10398 Z= 0.285 Chirality : 0.047 0.289 1152 Planarity : 0.004 0.084 1326 Dihedral : 5.850 41.004 1250 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.31 % Allowed : 13.59 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.10 (0.30), residues: 858 helix: 2.15 (0.26), residues: 392 sheet: 0.89 (0.63), residues: 74 loop : -0.81 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 357 HIS 0.003 0.001 HIS A 423 PHE 0.011 0.001 PHE B 998 TYR 0.016 0.001 TYR A1105 ARG 0.018 0.000 ARG B1127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.885 Fit side-chains REVERT: B 107 MET cc_start: 0.4841 (mmp) cc_final: 0.4486 (mtt) REVERT: B 337 GLU cc_start: 0.7541 (tt0) cc_final: 0.7319 (tt0) REVERT: A 107 MET cc_start: 0.5105 (mmp) cc_final: 0.4696 (mtt) REVERT: A 1116 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7678 (mtm) REVERT: A 1125 MET cc_start: 0.6334 (tpt) cc_final: 0.6070 (tpt) outliers start: 19 outliers final: 16 residues processed: 107 average time/residue: 0.1963 time to fit residues: 28.6286 Evaluate side-chains 104 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 52 optimal weight: 0.0060 chunk 41 optimal weight: 0.0570 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS B1151 ASN A 987 HIS A 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7688 Z= 0.173 Angle : 0.559 6.895 10398 Z= 0.281 Chirality : 0.046 0.282 1152 Planarity : 0.004 0.086 1326 Dihedral : 5.680 39.959 1250 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.18 % Allowed : 13.83 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.21 (0.30), residues: 858 helix: 2.23 (0.26), residues: 392 sheet: 0.80 (0.65), residues: 74 loop : -0.71 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 357 HIS 0.002 0.001 HIS A1194 PHE 0.009 0.001 PHE A 993 TYR 0.016 0.001 TYR A1105 ARG 0.018 0.000 ARG B1127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.921 Fit side-chains REVERT: B 107 MET cc_start: 0.4805 (mmp) cc_final: 0.4429 (mtt) REVERT: B 337 GLU cc_start: 0.7524 (tt0) cc_final: 0.7308 (tt0) REVERT: A 107 MET cc_start: 0.5080 (mmp) cc_final: 0.4715 (mtt) REVERT: A 1116 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7695 (mtm) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.1922 time to fit residues: 28.8755 Evaluate side-chains 107 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.170873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127019 restraints weight = 8079.549| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.10 r_work: 0.3257 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7688 Z= 0.234 Angle : 0.576 7.795 10398 Z= 0.291 Chirality : 0.047 0.285 1152 Planarity : 0.004 0.053 1326 Dihedral : 5.638 38.641 1250 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.18 % Allowed : 14.08 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.20 (0.30), residues: 858 helix: 2.19 (0.26), residues: 392 sheet: 0.84 (0.65), residues: 74 loop : -0.68 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 357 HIS 0.003 0.001 HIS B 423 PHE 0.015 0.001 PHE B 998 TYR 0.016 0.002 TYR B1105 ARG 0.012 0.000 ARG A1127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.49 seconds wall clock time: 36 minutes 34.65 seconds (2194.65 seconds total)