Starting phenix.real_space_refine on Thu Jul 2 07:35:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s05_24784/07_2026/7s05_24784.map" } 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 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. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.67, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 0.54 Conformation dependent library (CDL) restraints added in 390.0 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: 0.20 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: 1.00 Time building geometry restraints manager: 0.75 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: 0.00 - 1.40: 9845 1.40 - 2.80: 463 2.80 - 4.21: 70 4.21 - 5.61: 14 5.61 - 7.01: 6 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 - 16.85: 3987 16.85 - 33.70: 441 33.70 - 50.55: 81 50.55 - 67.39: 16 67.39 - 84.24: 6 Dihedral angle restraints: 4531 sinusoidal: 1925 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 4528 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 3.040 nonbonded pdb=" OH TYR A 79 " pdb=" OG SER A 332 " model vdw 2.213 3.040 nonbonded pdb=" O SER B 356 " pdb=" NH2 ARG B1186 " model vdw 2.304 3.120 nonbonded pdb=" O SER A 356 " pdb=" NH2 ARG A1186 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 937 " pdb=" OE1 GLU A 976 " model vdw 2.344 3.040 ... (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 Time spend for trying shortcut: 0.02 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: 2.730 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- 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 : 0.004 0.053 7703 Z= 0.181 Angle : 0.721 10.314 10442 Z= 0.381 Chirality : 0.052 0.465 1152 Planarity : 0.004 0.043 1326 Dihedral : 14.589 84.243 2824 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG A1127 TYR 0.016 0.001 TYR A 999 PHE 0.010 0.001 PHE B1176 TRP 0.007 0.001 TRP A1201 HIS 0.013 0.001 HIS A 987 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 7688) covalent geometry : angle 0.67856 / 0.37 (10398) SS BOND : bond 0.00430 / 0.23 ( 1) SS BOND : angle 2.44459 / 1.44 ( 2) hydrogen bonds : bond 0.16026 / 10.16 ( 313) hydrogen bonds : angle 6.74831 / 4.83 ( 921) link_BETA1-4 : bond 0.00799 / 0.40 ( 4) link_BETA1-4 : angle 1.63571 / 0.90 ( 12) link_NAG-ASN : bond 0.00890 / 0.43 ( 10) link_NAG-ASN : angle 4.45648 / 3.37 ( 30) *********************** 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 to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.221 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0689 time to fit residues: 11.4046 Evaluate side-chains 85 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 987 HIS B1012 GLN A 987 HIS A1012 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134123 restraints weight = 8125.779| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.18 r_work: 0.3302 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7703 Z= 0.143 Angle : 0.618 6.854 10442 Z= 0.311 Chirality : 0.049 0.338 1152 Planarity : 0.004 0.034 1326 Dihedral : 4.608 26.122 956 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.09 % Allowed : 7.16 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.29), residues: 858 helix: 1.61 (0.25), residues: 394 sheet: 0.33 (0.54), residues: 102 loop : -1.23 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1127 TYR 0.024 0.002 TYR B 999 PHE 0.008 0.001 PHE B 931 TRP 0.007 0.001 TRP B1201 HIS 0.003 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7688) covalent geometry : angle 0.59254 / 0.31 (10398) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 0.19123 / 0.11 ( 2) hydrogen bonds : bond 0.04229 / 2.75 ( 313) hydrogen bonds : angle 5.11842 / 3.66 ( 921) link_BETA1-4 : bond 0.00507 / 0.25 ( 4) link_BETA1-4 : angle 1.11908 / 0.64 ( 12) link_NAG-ASN : bond 0.00948 / 0.46 ( 10) link_NAG-ASN : angle 3.29957 / 2.36 ( 30) *********************** 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 113 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.198 Fit side-chains REVERT: B 1116 MET cc_start: 0.7868 (mpp) cc_final: 0.7408 (mpp) REVERT: A 975 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6612 (pm20) outliers start: 9 outliers final: 6 residues processed: 113 average time/residue: 0.0783 time to fit residues: 11.9782 Evaluate side-chains 96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 372 ASP Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 372 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 68 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 326 ASN B 987 HIS A 326 ASN A 987 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129315 restraints weight = 8134.067| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.16 r_work: 0.3280 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7703 Z= 0.161 Angle : 0.623 7.339 10442 Z= 0.311 Chirality : 0.049 0.319 1152 Planarity : 0.004 0.033 1326 Dihedral : 4.602 26.332 956 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.46 % Allowed : 9.95 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.29), residues: 858 helix: 1.72 (0.25), residues: 394 sheet: 0.12 (0.53), residues: 102 loop : -1.26 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1127 TYR 0.021 0.002 TYR B 999 PHE 0.010 0.001 PHE A 998 TRP 0.008 0.001 TRP B 357 HIS 0.003 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 7688) covalent geometry : angle 0.60098 / 0.31 (10398) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.04703 / 0.03 ( 2) hydrogen bonds : bond 0.03683 / 2.38 ( 313) hydrogen bonds : angle 4.69454 / 3.34 ( 921) link_BETA1-4 : bond 0.00528 / 0.26 ( 4) link_BETA1-4 : angle 1.06440 / 0.61 ( 12) link_NAG-ASN : bond 0.00897 / 0.44 ( 10) link_NAG-ASN : angle 3.07483 / 2.16 ( 30) *********************** 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 113 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.294 Fit side-chains REVERT: B 392 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8405 (mp) REVERT: B 975 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6768 (pm20) REVERT: A 392 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 1127 ARG cc_start: 0.8417 (mtt-85) cc_final: 0.8152 (mtt-85) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.0842 time to fit residues: 12.9497 Evaluate side-chains 102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 985 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 392 ILE 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 25 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.0060 chunk 26 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 987 HIS A 987 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130742 restraints weight = 8188.833| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.22 r_work: 0.3291 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7703 Z= 0.126 Angle : 0.575 6.946 10442 Z= 0.288 Chirality : 0.047 0.301 1152 Planarity : 0.004 0.040 1326 Dihedral : 4.456 25.731 956 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.06 % Allowed : 10.80 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.29), residues: 858 helix: 1.91 (0.25), residues: 394 sheet: 0.36 (0.54), residues: 98 loop : -1.16 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1127 TYR 0.020 0.002 TYR A 999 PHE 0.011 0.001 PHE A 993 TRP 0.006 0.001 TRP B1201 HIS 0.002 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7688) covalent geometry : angle 0.55403 / 0.28 (10398) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.19035 / 0.11 ( 2) hydrogen bonds : bond 0.03299 / 2.17 ( 313) hydrogen bonds : angle 4.57621 / 3.25 ( 921) link_BETA1-4 : bond 0.00455 / 0.23 ( 4) link_BETA1-4 : angle 1.07826 / 0.63 ( 12) link_NAG-ASN : bond 0.00840 / 0.41 ( 10) link_NAG-ASN : angle 2.87771 / 2.02 ( 30) *********************** 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 111 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.272 Fit side-chains REVERT: B 107 MET cc_start: 0.5147 (mmp) cc_final: 0.4659 (mtt) REVERT: B 975 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6752 (pm20) REVERT: A 107 MET cc_start: 0.5305 (mmp) cc_final: 0.4834 (mtt) REVERT: A 392 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 975 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6662 (pm20) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.0721 time to fit residues: 11.0815 Evaluate side-chains 99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 392 ILE Chi-restraints excluded: chain A residue 985 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 74 optimal weight: 0.0030 chunk 43 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 326 ASN B 987 HIS B1151 ASN A 326 ASN A 987 HIS A 992 GLN A1151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130707 restraints weight = 8117.469| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.21 r_work: 0.3279 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7703 Z= 0.129 Angle : 0.577 7.148 10442 Z= 0.289 Chirality : 0.047 0.298 1152 Planarity : 0.004 0.035 1326 Dihedral : 4.358 27.409 956 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.79 % Allowed : 10.68 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.29), residues: 858 helix: 2.01 (0.25), residues: 394 sheet: 0.41 (0.55), residues: 98 loop : -1.07 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1127 TYR 0.020 0.002 TYR B 999 PHE 0.011 0.001 PHE A 993 TRP 0.006 0.001 TRP B1201 HIS 0.006 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7688) covalent geometry : angle 0.55720 / 0.29 (10398) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.18092 / 0.10 ( 2) hydrogen bonds : bond 0.03211 / 2.07 ( 313) hydrogen bonds : angle 4.52320 / 3.25 ( 921) link_BETA1-4 : bond 0.00543 / 0.27 ( 4) link_BETA1-4 : angle 1.07084 / 0.61 ( 12) link_NAG-ASN : bond 0.00818 / 0.40 ( 10) link_NAG-ASN : angle 2.77370 / 1.94 ( 30) *********************** 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 114 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.188 Fit side-chains REVERT: B 107 MET cc_start: 0.5098 (mmp) cc_final: 0.4635 (mtt) REVERT: A 107 MET cc_start: 0.5349 (mmp) cc_final: 0.4811 (mtt) REVERT: A 975 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6639 (pm20) REVERT: A 1127 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.8018 (mtt-85) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 0.0751 time to fit residues: 11.3981 Evaluate side-chains 107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 418 ASP Chi-restraints excluded: chain B residue 985 VAL Chi-restraints excluded: chain B residue 1118 GLU 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 1116 MET Chi-restraints excluded: chain A residue 1118 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 987 HIS B 992 GLN ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.174381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122862 restraints weight = 8140.081| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.27 r_work: 0.3244 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7703 Z= 0.167 Angle : 0.619 8.275 10442 Z= 0.311 Chirality : 0.049 0.300 1152 Planarity : 0.004 0.039 1326 Dihedral : 4.432 27.018 956 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.06 % Allowed : 12.01 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 858 helix: 1.99 (0.25), residues: 394 sheet: 0.55 (0.62), residues: 74 loop : -0.96 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1127 TYR 0.018 0.002 TYR A 999 PHE 0.016 0.001 PHE A 998 TRP 0.008 0.001 TRP B 357 HIS 0.003 0.001 HIS B 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 7688) covalent geometry : angle 0.60008 / 0.31 (10398) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 0.07095 / 0.04 ( 2) hydrogen bonds : bond 0.03426 / 2.21 ( 313) hydrogen bonds : angle 4.50361 / 3.22 ( 921) link_BETA1-4 : bond 0.00555 / 0.28 ( 4) link_BETA1-4 : angle 1.11510 / 0.65 ( 12) link_NAG-ASN : bond 0.00788 / 0.38 ( 10) link_NAG-ASN : angle 2.80401 / 1.95 ( 30) *********************** 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 109 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.287 Fit side-chains REVERT: B 107 MET cc_start: 0.5076 (mmp) cc_final: 0.4608 (mtt) REVERT: B 1170 ASP cc_start: 0.8017 (t0) cc_final: 0.7799 (t70) REVERT: A 107 MET cc_start: 0.5219 (mmp) cc_final: 0.4691 (mtt) REVERT: A 337 GLU cc_start: 0.8120 (tt0) cc_final: 0.7920 (tt0) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.0753 time to fit residues: 11.1213 Evaluate side-chains 98 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 987 HIS ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS ** A1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128440 restraints weight = 8197.509| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.33 r_work: 0.3227 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7703 Z= 0.173 Angle : 0.638 8.934 10442 Z= 0.318 Chirality : 0.049 0.297 1152 Planarity : 0.004 0.039 1326 Dihedral : 4.541 30.319 956 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.82 % Allowed : 12.99 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 858 helix: 1.99 (0.25), residues: 392 sheet: 0.50 (0.62), residues: 74 loop : -0.93 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1127 TYR 0.020 0.002 TYR B 999 PHE 0.017 0.001 PHE B 998 TRP 0.008 0.001 TRP A 357 HIS 0.006 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 7688) covalent geometry : angle 0.62064 / 0.31 (10398) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 0.12905 / 0.07 ( 2) hydrogen bonds : bond 0.03434 / 2.21 ( 313) hydrogen bonds : angle 4.47368 / 3.18 ( 921) link_BETA1-4 : bond 0.00535 / 0.27 ( 4) link_BETA1-4 : angle 1.10388 / 0.63 ( 12) link_NAG-ASN : bond 0.00756 / 0.36 ( 10) link_NAG-ASN : angle 2.79960 / 1.94 ( 30) *********************** 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 107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.219 Fit side-chains REVERT: B 107 MET cc_start: 0.5092 (mmp) cc_final: 0.4628 (mtt) REVERT: A 107 MET cc_start: 0.5298 (mmp) cc_final: 0.4771 (mtt) REVERT: A 337 GLU cc_start: 0.8133 (tt0) cc_final: 0.7930 (tt0) outliers start: 15 outliers final: 13 residues processed: 105 average time/residue: 0.0810 time to fit residues: 11.5699 Evaluate side-chains 99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 987 HIS ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS A 992 GLN ** A1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130055 restraints weight = 8160.493| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.32 r_work: 0.3246 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7703 Z= 0.130 Angle : 0.607 8.836 10442 Z= 0.303 Chirality : 0.048 0.285 1152 Planarity : 0.004 0.087 1326 Dihedral : 4.476 32.073 956 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.82 % Allowed : 13.83 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.29), residues: 858 helix: 2.07 (0.26), residues: 394 sheet: 0.47 (0.63), residues: 74 loop : -0.82 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B1127 TYR 0.022 0.002 TYR A 999 PHE 0.010 0.001 PHE A 998 TRP 0.006 0.001 TRP B1201 HIS 0.010 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7688) covalent geometry : angle 0.59044 / 0.30 (10398) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.18239 / 0.10 ( 2) hydrogen bonds : bond 0.03271 / 2.08 ( 313) hydrogen bonds : angle 4.48568 / 3.23 ( 921) link_BETA1-4 : bond 0.00483 / 0.24 ( 4) link_BETA1-4 : angle 1.08535 / 0.62 ( 12) link_NAG-ASN : bond 0.00769 / 0.37 ( 10) link_NAG-ASN : angle 2.65914 / 1.84 ( 30) *********************** 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 102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.285 Fit side-chains REVERT: B 107 MET cc_start: 0.5151 (mmp) cc_final: 0.4682 (mtt) REVERT: A 107 MET cc_start: 0.5286 (mmp) cc_final: 0.4738 (mtt) REVERT: A 337 GLU cc_start: 0.8143 (tt0) cc_final: 0.7940 (tt0) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 0.0770 time to fit residues: 10.7181 Evaluate side-chains 98 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1178 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4019 r_free = 0.4019 target = 0.176375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129858 restraints weight = 8180.455| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.40 r_work: 0.3231 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7703 Z= 0.143 Angle : 0.610 7.937 10442 Z= 0.304 Chirality : 0.048 0.283 1152 Planarity : 0.004 0.085 1326 Dihedral : 4.474 32.734 956 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.94 % Allowed : 13.59 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.30), residues: 858 helix: 2.09 (0.26), residues: 394 sheet: 0.54 (0.63), residues: 74 loop : -0.76 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B1127 TYR 0.018 0.002 TYR B 999 PHE 0.012 0.001 PHE B 998 TRP 0.006 0.001 TRP B1201 HIS 0.012 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 7688) covalent geometry : angle 0.59387 / 0.30 (10398) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 0.13600 / 0.08 ( 2) hydrogen bonds : bond 0.03348 / 2.14 ( 313) hydrogen bonds : angle 4.45910 / 3.20 ( 921) link_BETA1-4 : bond 0.00567 / 0.28 ( 4) link_BETA1-4 : angle 1.12759 / 0.66 ( 12) link_NAG-ASN : bond 0.00739 / 0.35 ( 10) link_NAG-ASN : angle 2.62536 / 1.82 ( 30) *********************** 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 103 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.317 Fit side-chains REVERT: B 107 MET cc_start: 0.5018 (mmp) cc_final: 0.4612 (mtt) REVERT: B 1127 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7698 (mpt-90) REVERT: A 107 MET cc_start: 0.5280 (mmp) cc_final: 0.4818 (mtt) REVERT: A 337 GLU cc_start: 0.8160 (tt0) cc_final: 0.7956 (tt0) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.0867 time to fit residues: 11.9217 Evaluate side-chains 99 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1178 ILE Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 941 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 987 HIS ** B1158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 HIS A 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129547 restraints weight = 8132.369| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.38 r_work: 0.3231 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7703 Z= 0.133 Angle : 0.603 8.072 10442 Z= 0.301 Chirality : 0.047 0.278 1152 Planarity : 0.004 0.082 1326 Dihedral : 4.439 32.764 956 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.70 % Allowed : 13.96 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.30), residues: 858 helix: 2.19 (0.26), residues: 392 sheet: 0.57 (0.63), residues: 74 loop : -0.70 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B1127 TYR 0.021 0.002 TYR A 999 PHE 0.011 0.001 PHE A 998 TRP 0.006 0.001 TRP A1201 HIS 0.012 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7688) covalent geometry : angle 0.58741 / 0.30 (10398) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 0.16857 / 0.09 ( 2) hydrogen bonds : bond 0.03242 / 2.07 ( 313) hydrogen bonds : angle 4.41940 / 3.18 ( 921) link_BETA1-4 : bond 0.00517 / 0.26 ( 4) link_BETA1-4 : angle 1.07763 / 0.62 ( 12) link_NAG-ASN : bond 0.00740 / 0.35 ( 10) link_NAG-ASN : angle 2.56678 / 1.78 ( 30) ********************** 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 102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.293 Fit side-chains REVERT: B 92 GLU cc_start: 0.5930 (mt-10) cc_final: 0.5588 (mm-30) REVERT: B 107 MET cc_start: 0.4999 (mmp) cc_final: 0.4534 (mtt) REVERT: B 992 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7413 (mm-40) REVERT: B 1127 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7599 (mpt-90) REVERT: A 107 MET cc_start: 0.5237 (mmp) cc_final: 0.4815 (mtt) outliers start: 14 outliers final: 14 residues processed: 100 average time/residue: 0.0914 time to fit residues: 12.5318 Evaluate side-chains 100 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1116 MET Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 1054 LEU 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 49 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4000 r_free = 0.4000 target = 0.174786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128449 restraints weight = 8163.625| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.38 r_work: 0.3214 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7703 Z= 0.165 Angle : 0.632 8.212 10442 Z= 0.315 Chirality : 0.048 0.282 1152 Planarity : 0.005 0.083 1326 Dihedral : 4.543 32.955 956 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.94 % Allowed : 13.83 % Favored : 84.22 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 858 helix: 2.14 (0.26), residues: 392 sheet: 0.24 (0.62), residues: 78 loop : -0.68 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B1127 TYR 0.019 0.002 TYR B 999 PHE 0.016 0.001 PHE B 998 TRP 0.008 0.001 TRP A 357 HIS 0.013 0.001 HIS B1158 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 7688) covalent geometry : angle 0.61642 / 0.31 (10398) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.09693 / 0.05 ( 2) hydrogen bonds : bond 0.03468 / 2.21 ( 313) hydrogen bonds : angle 4.45166 / 3.20 ( 921) link_BETA1-4 : bond 0.00505 / 0.25 ( 4) link_BETA1-4 : angle 1.06602 / 0.61 ( 12) link_NAG-ASN : bond 0.00714 / 0.34 ( 10) link_NAG-ASN : angle 2.59819 / 1.81 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.05 seconds wall clock time: 31 minutes 56.40 seconds (1916.40 seconds total)