Starting phenix.real_space_refine (version: dev) on Sun Dec 11 21:08:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/12_2022/7s05_24784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/12_2022/7s05_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_24784/12_2022/7s05_24784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/12_2022/7s05_24784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/12_2022/7s05_24784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s05_24784/12_2022/7s05_24784.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 4.60, per 1000 atoms: 0.61 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: 3.17 Conformation dependent library (CDL) restraints added in 955.0 milliseconds 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: 0.43 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: 1.97 Time building geometry restraints manager: 3.40 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=" CG1 ILE A 392 " pdb=" CD1 ILE A 392 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG1 ILE B 392 " pdb=" CD1 ILE B 392 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " ideal model delta sigma weight residual 1.526 1.549 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C1 NAG C 1 " pdb=" C2 NAG C 1 " ideal model delta sigma weight residual 1.526 1.547 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C2 NAG C 1 " pdb=" C3 NAG C 1 " ideal model delta sigma weight residual 1.526 1.542 -0.016 1.50e-02 4.44e+03 1.09e+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 - 19.85: 4174 19.85 - 39.70: 389 39.70 - 59.55: 30 59.55 - 79.39: 16 79.39 - 99.24: 6 Dihedral angle restraints: 4615 sinusoidal: 2009 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=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " ideal model delta sinusoidal sigma weight residual -50.00 49.24 -99.24 1 2.00e+01 2.50e-03 2.79e+01 ... (remaining 4612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1080 0.093 - 0.186: 66 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 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. 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: 1.160 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: 7.650 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.070 Process input model: 22.570 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.003 0.053 7688 Z= 0.203 Angle : 0.643 7.010 10398 Z= 0.370 Chirality : 0.051 0.465 1152 Planarity : 0.004 0.043 1326 Dihedral : 14.905 99.242 2908 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1886 time to fit residues: 30.5308 Evaluate side-chains 85 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3666 ------------------------------------------------------------------------------- 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: 0.8200 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 7688 Z= 0.215 Angle : 0.570 6.327 10398 Z= 0.302 Chirality : 0.049 0.363 1152 Planarity : 0.004 0.034 1326 Dihedral : 7.985 100.873 1040 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.82 % 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: 1.62 (0.25), residues: 394 sheet: 0.47 (0.55), residues: 102 loop : -1.29 (0.34), residues: 362 *********************** 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 115 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.936 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.1962 time to fit residues: 30.8275 Evaluate side-chains 100 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0698 time to fit residues: 2.6011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.0030 chunk 84 optimal weight: 0.0020 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7688 Z= 0.183 Angle : 0.538 6.233 10398 Z= 0.281 Chirality : 0.047 0.324 1152 Planarity : 0.004 0.032 1326 Dihedral : 7.975 102.296 1040 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.12 % 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: 0.65 (0.29), residues: 858 helix: 1.85 (0.26), residues: 392 sheet: 0.68 (0.54), residues: 98 loop : -1.26 (0.33), residues: 368 *********************** 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 103 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.936 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2239 time to fit residues: 30.6010 Evaluate side-chains 92 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0677 time to fit residues: 1.4315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7688 Z= 0.245 Angle : 0.561 7.615 10398 Z= 0.293 Chirality : 0.048 0.321 1152 Planarity : 0.004 0.035 1326 Dihedral : 8.016 102.932 1040 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 0.85 % 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: 0.70 (0.54), residues: 98 loop : -1.25 (0.33), residues: 368 *********************** 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: 7 poor density : 101 time to evaluate : 0.987 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 0.2001 time to fit residues: 29.1751 Evaluate side-chains 93 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0793 time to fit residues: 1.9054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.0370 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 A 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7688 Z= 0.221 Angle : 0.556 8.514 10398 Z= 0.287 Chirality : 0.047 0.310 1152 Planarity : 0.004 0.039 1326 Dihedral : 8.039 103.226 1040 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.58 % 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: 0.81 (0.29), residues: 858 helix: 1.97 (0.25), residues: 392 sheet: 0.67 (0.55), residues: 98 loop : -1.13 (0.33), residues: 368 *********************** 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 107 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.941 Fit side-chains outliers start: 13 outliers final: 2 residues processed: 103 average time/residue: 0.2088 time to fit residues: 28.8237 Evaluate side-chains 88 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0821 time to fit residues: 1.5919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS A 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7688 Z= 0.225 Angle : 0.560 7.383 10398 Z= 0.292 Chirality : 0.046 0.303 1152 Planarity : 0.004 0.038 1326 Dihedral : 8.023 103.450 1040 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.85 % 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: 0.87 (0.29), residues: 858 helix: 1.99 (0.25), residues: 392 sheet: 0.58 (0.55), residues: 98 loop : -1.02 (0.34), residues: 368 *********************** 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 94 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.910 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.2120 time to fit residues: 26.6941 Evaluate side-chains 86 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0847 time to fit residues: 1.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 A1151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7688 Z= 0.167 Angle : 0.524 6.476 10398 Z= 0.272 Chirality : 0.045 0.292 1152 Planarity : 0.004 0.037 1326 Dihedral : 7.982 103.978 1040 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.61 % 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: 1.06 (0.30), residues: 858 helix: 2.13 (0.26), residues: 392 sheet: 0.65 (0.57), residues: 98 loop : -0.89 (0.34), residues: 368 *********************** 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 101 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.939 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 100 average time/residue: 0.2034 time to fit residues: 27.5990 Evaluate side-chains 93 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0695 time to fit residues: 1.5650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN A 987 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7688 Z= 0.202 Angle : 0.542 7.138 10398 Z= 0.281 Chirality : 0.045 0.290 1152 Planarity : 0.004 0.062 1326 Dihedral : 8.002 104.096 1040 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.73 % 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: 1.07 (0.30), residues: 858 helix: 2.16 (0.26), residues: 392 sheet: 0.54 (0.56), residues: 98 loop : -0.87 (0.34), residues: 368 *********************** 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 98 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.916 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 97 average time/residue: 0.2087 time to fit residues: 27.3246 Evaluate side-chains 92 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0708 time to fit residues: 1.7150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 987 HIS B1151 ASN ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS A1151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7688 Z= 0.250 Angle : 0.566 7.773 10398 Z= 0.294 Chirality : 0.046 0.294 1152 Planarity : 0.004 0.082 1326 Dihedral : 8.058 103.858 1040 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.73 % 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: 1.02 (0.30), residues: 858 helix: 2.11 (0.25), residues: 392 sheet: 0.48 (0.55), residues: 98 loop : -0.87 (0.34), residues: 368 *********************** 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 98 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.880 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 97 average time/residue: 0.2152 time to fit residues: 28.2440 Evaluate side-chains 91 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0693 time to fit residues: 1.6516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7688 Z= 0.190 Angle : 0.541 7.007 10398 Z= 0.280 Chirality : 0.045 0.283 1152 Planarity : 0.005 0.085 1326 Dihedral : 8.045 103.983 1040 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.49 % 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: 1.14 (0.30), residues: 858 helix: 2.21 (0.25), residues: 392 sheet: 0.50 (0.56), residues: 98 loop : -0.79 (0.35), residues: 368 ********************** 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 95 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.999 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 0.2069 time to fit residues: 26.7916 Evaluate side-chains 88 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0738 time to fit residues: 1.4150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 326 ASN A 987 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.176545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131086 restraints weight = 8123.329| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.30 r_work: 0.3267 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7688 Z= 0.201 Angle : 0.534 7.197 10398 Z= 0.277 Chirality : 0.045 0.282 1152 Planarity : 0.004 0.036 1326 Dihedral : 8.015 104.122 1040 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.36 % 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: 1.21 (0.30), residues: 858 helix: 2.24 (0.25), residues: 392 sheet: 0.54 (0.57), residues: 98 loop : -0.74 (0.35), residues: 368 =============================================================================== Job complete usr+sys time: 1698.10 seconds wall clock time: 31 minutes 32.94 seconds (1892.94 seconds total)