Starting phenix.real_space_refine on Fri Sep 11 05:22:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.map" model { file = "/net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s06_24785/09_2026/7s06_24785.cif" } resolution = 3.3 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= 0.005 sd= 0.085 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5002 2.51 5 N 1332 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7862 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3833 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 436} Chain breaks: 4 Chain: "B" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3833 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 436} Chain breaks: 4 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.65, per 1000 atoms: 0.21 Number of scatterers: 7862 At special positions: 0 Unit cell: (113.436, 113.436, 73.692, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1488 8.00 N 1332 7.00 C 5002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS B 70 " distance=2.03 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 A 83 " " NAG D 1 " - " ASN A1129 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B1129 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 297.8 milliseconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 53.3% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.908A pdb=" N TYR A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) 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: 3.643A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.972A pdb=" N LEU A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.621A pdb=" N ILE A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 919 through 923 removed outlier: 3.687A pdb=" N ASN A 922 " --> pdb=" O ASP A 919 " (cutoff:3.500A) 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 removed outlier: 3.502A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 980 " --> pdb=" O GLU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 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: 3.783A pdb=" N LEU A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1094 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 1194 through 1204 removed outlier: 3.854A pdb=" N LEU A1198 " --> pdb=" O HIS A1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.909A pdb=" N TYR B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) 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: 3.643A pdb=" N TYR B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.972A pdb=" N LEU B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.620A pdb=" N ILE B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 904 through 913 Processing helix chain 'B' and resid 919 through 923 removed outlier: 3.688A pdb=" N ASN B 922 " --> pdb=" O ASP B 919 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N LYS B 979 " --> pdb=" O GLU B 975 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 980 " --> pdb=" O GLU B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1004 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: 3.783A pdb=" N LEU B1047 " --> pdb=" O SER B1043 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B1059 " --> pdb=" O ILE B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1094 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 1194 through 1204 removed outlier: 3.853A pdb=" N LEU B1198 " --> pdb=" O HIS B1194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 369 removed outlier: 6.659A pdb=" N ILE A 346 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A 368 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 348 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP A 76 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU A 405 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL A 78 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.817A pdb=" N ASN A1151 " --> pdb=" O LYS A1124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 4.009A pdb=" N VAL A 953 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.515A pdb=" N LEU A 431 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1005 through 1006 removed outlier: 4.382A pdb=" N LYS A1108 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 369 removed outlier: 6.659A pdb=" N ILE B 346 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL B 368 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE B 348 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP B 76 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU B 405 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 78 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.817A pdb=" N ASN B1151 " --> pdb=" O LYS B1124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 421 through 422 removed outlier: 4.009A pdb=" N VAL B 953 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.515A pdb=" N LEU B 431 " --> pdb=" O MET B1116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1005 through 1006 removed outlier: 4.382A pdb=" N LYS B1108 " --> pdb=" O GLN B1006 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 981 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: 1.09 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2538 1.34 - 1.46: 1442 1.46 - 1.57: 3998 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8050 Sorted by residual: bond pdb=" N ARG B 923 " pdb=" CA ARG B 923 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.28e+00 bond pdb=" N ARG A 923 " pdb=" CA ARG A 923 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.15e+00 bond pdb=" N GLU A1016 " pdb=" CA GLU A1016 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.11e+00 bond pdb=" N GLU B1016 " pdb=" CA GLU B1016 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.06e+00 bond pdb=" N TRP B 357 " pdb=" CA TRP B 357 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.33e-02 5.65e+03 6.58e+00 ... (remaining 8045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 10514 1.61 - 3.22: 309 3.22 - 4.83: 31 4.83 - 6.44: 16 6.44 - 8.05: 12 Bond angle restraints: 10882 Sorted by residual: angle pdb=" N GLU A1197 " pdb=" CA GLU A1197 " pdb=" C GLU A1197 " ideal model delta sigma weight residual 111.07 107.04 4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N GLU B1197 " pdb=" CA GLU B1197 " pdb=" C GLU B1197 " ideal model delta sigma weight residual 111.07 107.07 4.00 1.07e+00 8.73e-01 1.40e+01 angle pdb=" C ALA A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 121.58 114.81 6.77 1.95e+00 2.63e-01 1.21e+01 angle pdb=" C ALA B 106 " pdb=" N MET B 107 " pdb=" CA MET B 107 " ideal model delta sigma weight residual 121.58 114.82 6.76 1.95e+00 2.63e-01 1.20e+01 angle pdb=" N THR A1128 " pdb=" CA THR A1128 " pdb=" CB THR A1128 " ideal model delta sigma weight residual 113.65 108.75 4.90 1.47e+00 4.63e-01 1.11e+01 ... (remaining 10877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4227 17.98 - 35.96: 428 35.96 - 53.93: 79 53.93 - 71.91: 11 71.91 - 89.89: 12 Dihedral angle restraints: 4757 sinusoidal: 2019 harmonic: 2738 Sorted by residual: dihedral pdb=" CA ARG B1127 " pdb=" C ARG B1127 " pdb=" N THR B1128 " pdb=" CA THR B1128 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG A1127 " pdb=" C ARG A1127 " pdb=" N THR A1128 " pdb=" CA THR A1128 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR B 918 " pdb=" C THR B 918 " pdb=" N ASP B 919 " pdb=" CA ASP B 919 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1078 0.072 - 0.145: 118 0.145 - 0.217: 7 0.217 - 0.289: 2 0.289 - 0.362: 3 Chirality restraints: 1208 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 -2.04 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.24e+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 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1205 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 922 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ASN A 922 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 922 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG A 923 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 922 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN B 922 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN B 922 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG B 923 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 995 " 0.014 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE B 995 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 995 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 995 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 995 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 995 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 995 " -0.006 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 555 2.74 - 3.28: 7900 3.28 - 3.82: 12910 3.82 - 4.36: 15027 4.36 - 4.90: 25810 Nonbonded interactions: 62202 Sorted by model distance: nonbonded pdb=" O LEU A1025 " pdb=" OH TYR A1078 " model vdw 2.199 3.040 nonbonded pdb=" O LEU B1025 " pdb=" OH TYR B1078 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN B 351 " pdb=" N GLY B 352 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASN A 351 " pdb=" N GLY A 352 " model vdw 2.215 3.120 nonbonded pdb=" OG SER B 934 " pdb=" O ASP B 990 " model vdw 2.287 3.040 ... (remaining 62197 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: 1.070 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.650 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 0.039 8065 Z= 0.192 Angle : 0.680 8.048 10926 Z= 0.352 Chirality : 0.049 0.362 1208 Planarity : 0.004 0.040 1388 Dihedral : 15.060 89.888 2962 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 0.97 (0.29), residues: 898 helix: 1.94 (0.25), residues: 406 sheet: 1.28 (0.61), residues: 88 loop : -0.89 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 394 TYR 0.009 0.001 TYR B 916 PHE 0.044 0.001 PHE B 995 TRP 0.009 0.001 TRP B1201 HIS 0.006 0.001 HIS A1196 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 8050) covalent geometry : angle 0.66497 / 0.35 (10882) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 0.26749 / 0.15 ( 2) hydrogen bonds : bond 0.18016 / 10.79 ( 335) hydrogen bonds : angle 6.54230 / 4.67 ( 981) link_BETA1-4 : bond 0.00512 / 0.25 ( 4) link_BETA1-4 : angle 1.04756 / 0.60 ( 12) link_NAG-ASN : bond 0.00803 / 0.38 ( 10) link_NAG-ASN : angle 2.73983 / 2.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.307 Fit side-chains REVERT: A 76 ASP cc_start: 0.8082 (m-30) cc_final: 0.7748 (m-30) REVERT: A 107 MET cc_start: 0.6524 (pmm) cc_final: 0.6226 (pmm) REVERT: A 354 ILE cc_start: 0.9069 (mp) cc_final: 0.8809 (mt) REVERT: A 1012 GLN cc_start: 0.7858 (tt0) cc_final: 0.7650 (tt0) REVERT: A 1028 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7803 (mtm180) REVERT: A 1053 MET cc_start: 0.8068 (mtp) cc_final: 0.7814 (mtt) REVERT: A 1195 MET cc_start: 0.7487 (pmm) cc_final: 0.7123 (pmm) REVERT: B 76 ASP cc_start: 0.7916 (m-30) cc_final: 0.7628 (m-30) REVERT: B 107 MET cc_start: 0.6434 (pmm) cc_final: 0.6019 (pmm) REVERT: B 354 ILE cc_start: 0.9092 (mp) cc_final: 0.8837 (mt) REVERT: B 1095 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7281 (tppt) REVERT: B 1125 MET cc_start: 0.5988 (mmt) cc_final: 0.5778 (mmt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0838 time to fit residues: 22.1608 Evaluate side-chains 111 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 GLN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS B1006 GLN B1156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118189 restraints weight = 9435.565| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.68 r_work: 0.3180 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 8065 Z= 0.395 Angle : 0.860 13.497 10926 Z= 0.442 Chirality : 0.057 0.346 1208 Planarity : 0.005 0.038 1388 Dihedral : 5.101 24.664 1002 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.05 % Allowed : 12.38 % Favored : 83.56 % 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: -0.06 (0.28), residues: 898 helix: 1.15 (0.25), residues: 414 sheet: -0.67 (0.47), residues: 102 loop : -1.17 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 364 TYR 0.026 0.003 TYR A 56 PHE 0.029 0.003 PHE A 973 TRP 0.023 0.004 TRP B 357 HIS 0.009 0.002 HIS B 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00962 / 0.39 ( 8050) covalent geometry : angle 0.84688 / 0.44 (10882) SS BOND : bond 0.00572 / 0.30 ( 1) SS BOND : angle 0.30670 / 0.17 ( 2) hydrogen bonds : bond 0.04836 / 3.14 ( 335) hydrogen bonds : angle 5.07703 / 3.67 ( 981) link_BETA1-4 : bond 0.00052 / 0.03 ( 4) link_BETA1-4 : angle 1.17593 / 0.67 ( 12) link_NAG-ASN : bond 0.00876 / 0.42 ( 10) link_NAG-ASN : angle 2.93782 / 2.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.205 Fit side-chains REVERT: A 923 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6737 (ttm-80) REVERT: A 935 LEU cc_start: 0.7707 (mt) cc_final: 0.6969 (mt) REVERT: A 1053 MET cc_start: 0.8337 (mtp) cc_final: 0.8018 (mtt) REVERT: B 935 LEU cc_start: 0.7712 (mt) cc_final: 0.6976 (mt) REVERT: B 978 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8018 (t0) REVERT: B 1027 ASP cc_start: 0.7973 (m-30) cc_final: 0.7636 (t0) REVERT: B 1103 LYS cc_start: 0.8774 (tppt) cc_final: 0.8568 (mtmm) outliers start: 35 outliers final: 21 residues processed: 143 average time/residue: 0.0750 time to fit residues: 15.3693 Evaluate side-chains 115 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.181666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133642 restraints weight = 9318.638| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.81 r_work: 0.3174 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8065 Z= 0.147 Angle : 0.644 8.457 10926 Z= 0.324 Chirality : 0.048 0.285 1208 Planarity : 0.004 0.046 1388 Dihedral : 4.662 23.053 1002 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.17 % Allowed : 14.58 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.28), residues: 898 helix: 1.41 (0.25), residues: 414 sheet: -1.17 (0.53), residues: 78 loop : -1.04 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1036 TYR 0.019 0.002 TYR A 999 PHE 0.016 0.001 PHE A 973 TRP 0.006 0.001 TRP B 357 HIS 0.001 0.000 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8050) covalent geometry : angle 0.62908 / 0.32 (10882) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.34868 / 0.20 ( 2) hydrogen bonds : bond 0.03879 / 2.48 ( 335) hydrogen bonds : angle 4.62877 / 3.34 ( 981) link_BETA1-4 : bond 0.00565 / 0.28 ( 4) link_BETA1-4 : angle 1.11493 / 0.63 ( 12) link_NAG-ASN : bond 0.00821 / 0.39 ( 10) link_NAG-ASN : angle 2.64815 / 1.91 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.275 Fit side-chains REVERT: A 107 MET cc_start: 0.6605 (pmm) cc_final: 0.6142 (pmm) REVERT: A 392 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8103 (mm) REVERT: A 1053 MET cc_start: 0.8342 (mtp) cc_final: 0.8110 (mtt) REVERT: A 1116 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7521 (mtm) REVERT: A 1125 MET cc_start: 0.7263 (mmt) cc_final: 0.7014 (tpp) REVERT: B 107 MET cc_start: 0.6674 (pmm) cc_final: 0.6167 (pmm) REVERT: B 392 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 978 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8071 (t70) REVERT: B 1116 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7522 (mtm) REVERT: B 1125 MET cc_start: 0.7211 (mmt) cc_final: 0.6944 (tpp) outliers start: 36 outliers final: 27 residues processed: 135 average time/residue: 0.0799 time to fit residues: 15.1698 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 49 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN A 406 ASN ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS B 371 GLN B 406 ASN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.183499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136124 restraints weight = 9594.196| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.72 r_work: 0.3236 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8065 Z= 0.122 Angle : 0.592 8.477 10926 Z= 0.294 Chirality : 0.047 0.273 1208 Planarity : 0.003 0.034 1388 Dihedral : 4.333 21.036 1002 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.94 % Allowed : 17.59 % Favored : 78.47 % 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: 0.37 (0.29), residues: 898 helix: 1.68 (0.26), residues: 414 sheet: -0.73 (0.48), residues: 96 loop : -1.09 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1036 TYR 0.015 0.001 TYR A 999 PHE 0.017 0.001 PHE A 973 TRP 0.005 0.001 TRP B 357 HIS 0.002 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8050) covalent geometry : angle 0.57783 / 0.29 (10882) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.14778 / 0.08 ( 2) hydrogen bonds : bond 0.03325 / 2.11 ( 335) hydrogen bonds : angle 4.33338 / 3.12 ( 981) link_BETA1-4 : bond 0.00259 / 0.13 ( 4) link_BETA1-4 : angle 1.02754 / 0.59 ( 12) link_NAG-ASN : bond 0.00771 / 0.37 ( 10) link_NAG-ASN : angle 2.42994 / 1.71 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.296 Fit side-chains REVERT: A 107 MET cc_start: 0.6530 (pmm) cc_final: 0.6099 (pmm) REVERT: A 354 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8839 (mt) REVERT: A 406 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7752 (t0) REVERT: A 935 LEU cc_start: 0.7441 (mt) cc_final: 0.6864 (mt) REVERT: A 1053 MET cc_start: 0.8291 (mtp) cc_final: 0.8021 (mtt) REVERT: A 1060 MET cc_start: 0.7851 (mtp) cc_final: 0.7596 (mmp) REVERT: A 1116 MET cc_start: 0.8456 (mtm) cc_final: 0.8078 (mtt) REVERT: A 1125 MET cc_start: 0.7166 (mmt) cc_final: 0.6941 (tpp) REVERT: B 93 LEU cc_start: 0.8575 (tp) cc_final: 0.8204 (pp) REVERT: B 107 MET cc_start: 0.6435 (pmm) cc_final: 0.5865 (pmm) REVERT: B 354 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8821 (mt) REVERT: B 406 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7719 (t0) REVERT: B 935 LEU cc_start: 0.7497 (mt) cc_final: 0.6700 (mt) REVERT: B 972 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7822 (ttt) REVERT: B 978 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7952 (t70) REVERT: B 1116 MET cc_start: 0.8481 (mtm) cc_final: 0.8060 (mtt) REVERT: B 1125 MET cc_start: 0.7235 (mmt) cc_final: 0.7035 (tpp) outliers start: 34 outliers final: 19 residues processed: 135 average time/residue: 0.0845 time to fit residues: 15.9784 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.184103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137602 restraints weight = 9553.235| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.89 r_work: 0.3218 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8065 Z= 0.117 Angle : 0.575 8.431 10926 Z= 0.285 Chirality : 0.046 0.271 1208 Planarity : 0.004 0.036 1388 Dihedral : 4.272 20.093 1002 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.82 % Allowed : 17.82 % Favored : 78.36 % 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: 0.39 (0.29), residues: 898 helix: 1.69 (0.25), residues: 426 sheet: -0.83 (0.49), residues: 98 loop : -1.13 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1127 TYR 0.024 0.001 TYR A 999 PHE 0.012 0.001 PHE A 973 TRP 0.005 0.001 TRP B 357 HIS 0.001 0.000 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8050) covalent geometry : angle 0.56097 / 0.28 (10882) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.20470 / 0.11 ( 2) hydrogen bonds : bond 0.03183 / 2.03 ( 335) hydrogen bonds : angle 4.25149 / 3.07 ( 981) link_BETA1-4 : bond 0.00414 / 0.21 ( 4) link_BETA1-4 : angle 1.06578 / 0.61 ( 12) link_NAG-ASN : bond 0.00783 / 0.38 ( 10) link_NAG-ASN : angle 2.41353 / 1.69 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.321 Fit side-chains REVERT: A 354 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8839 (mt) REVERT: A 923 ARG cc_start: 0.6751 (ttm170) cc_final: 0.6459 (mtm-85) REVERT: A 935 LEU cc_start: 0.7410 (mt) cc_final: 0.6610 (mt) REVERT: A 1026 SER cc_start: 0.8621 (t) cc_final: 0.8200 (m) REVERT: A 1027 ASP cc_start: 0.7828 (t0) cc_final: 0.7417 (t0) REVERT: A 1053 MET cc_start: 0.8318 (mtp) cc_final: 0.8058 (mtt) REVERT: A 1060 MET cc_start: 0.7854 (mtp) cc_final: 0.7599 (mmp) REVERT: A 1116 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7630 (mtm) REVERT: B 93 LEU cc_start: 0.8562 (tp) cc_final: 0.8203 (pp) REVERT: B 354 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8824 (mt) REVERT: B 935 LEU cc_start: 0.7527 (mt) cc_final: 0.6764 (mt) REVERT: B 972 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: B 978 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8005 (t70) REVERT: B 1116 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: B 1125 MET cc_start: 0.7237 (mmt) cc_final: 0.7031 (tpp) outliers start: 33 outliers final: 24 residues processed: 131 average time/residue: 0.0779 time to fit residues: 14.9654 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 972 MET Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN A 970 GLN A 992 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135118 restraints weight = 9521.279| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.89 r_work: 0.3187 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8065 Z= 0.150 Angle : 0.634 10.656 10926 Z= 0.311 Chirality : 0.047 0.274 1208 Planarity : 0.004 0.036 1388 Dihedral : 4.289 21.703 1002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.40 % Allowed : 18.63 % Favored : 76.97 % 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: 0.40 (0.29), residues: 898 helix: 1.74 (0.26), residues: 414 sheet: -1.13 (0.56), residues: 78 loop : -1.02 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1127 TYR 0.023 0.002 TYR A 999 PHE 0.010 0.001 PHE A 973 TRP 0.010 0.001 TRP B 357 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 8050) covalent geometry : angle 0.62104 / 0.31 (10882) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.05825 / 0.03 ( 2) hydrogen bonds : bond 0.03257 / 2.08 ( 335) hydrogen bonds : angle 4.27054 / 3.09 ( 981) link_BETA1-4 : bond 0.00400 / 0.20 ( 4) link_BETA1-4 : angle 1.07694 / 0.61 ( 12) link_NAG-ASN : bond 0.00767 / 0.37 ( 10) link_NAG-ASN : angle 2.41274 / 1.71 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.289 Fit side-chains REVERT: A 354 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8830 (mt) REVERT: A 406 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7608 (t0) REVERT: A 935 LEU cc_start: 0.7434 (mt) cc_final: 0.6676 (mt) REVERT: A 1053 MET cc_start: 0.8304 (mtp) cc_final: 0.8086 (mtt) REVERT: A 1060 MET cc_start: 0.7899 (mtp) cc_final: 0.7611 (mmp) REVERT: A 1116 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7580 (mtm) REVERT: B 93 LEU cc_start: 0.8549 (tp) cc_final: 0.8216 (pp) REVERT: B 107 MET cc_start: 0.6512 (pmm) cc_final: 0.6257 (pmm) REVERT: B 354 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8821 (mt) REVERT: B 935 LEU cc_start: 0.7523 (mt) cc_final: 0.6873 (mt) REVERT: B 978 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8008 (t70) REVERT: B 1116 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7605 (mtm) outliers start: 38 outliers final: 28 residues processed: 140 average time/residue: 0.0786 time to fit residues: 15.5747 Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1107 ASP Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.0670 chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132730 restraints weight = 9640.433| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.07 r_work: 0.3277 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8065 Z= 0.110 Angle : 0.604 9.846 10926 Z= 0.300 Chirality : 0.046 0.266 1208 Planarity : 0.003 0.037 1388 Dihedral : 4.188 21.255 1002 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.59 % Allowed : 19.68 % Favored : 76.74 % 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: 0.56 (0.29), residues: 898 helix: 1.86 (0.26), residues: 414 sheet: -0.94 (0.49), residues: 102 loop : -0.91 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1036 TYR 0.021 0.001 TYR A 999 PHE 0.016 0.001 PHE A 993 TRP 0.005 0.001 TRP B 357 HIS 0.010 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8050) covalent geometry : angle 0.59171 / 0.30 (10882) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.18270 / 0.10 ( 2) hydrogen bonds : bond 0.03027 / 1.91 ( 335) hydrogen bonds : angle 4.21606 / 3.04 ( 981) link_BETA1-4 : bond 0.00452 / 0.22 ( 4) link_BETA1-4 : angle 1.04449 / 0.60 ( 12) link_NAG-ASN : bond 0.00802 / 0.39 ( 10) link_NAG-ASN : angle 2.34363 / 1.65 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.302 Fit side-chains REVERT: A 935 LEU cc_start: 0.7356 (mt) cc_final: 0.6613 (mt) REVERT: A 1026 SER cc_start: 0.8634 (t) cc_final: 0.8198 (m) REVERT: A 1027 ASP cc_start: 0.7748 (t0) cc_final: 0.7366 (t0) REVERT: A 1053 MET cc_start: 0.8279 (mtp) cc_final: 0.8062 (mtt) REVERT: A 1060 MET cc_start: 0.7916 (mtp) cc_final: 0.7602 (mmp) REVERT: A 1116 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7658 (mtm) REVERT: A 1195 MET cc_start: 0.7046 (pmm) cc_final: 0.6763 (pmm) REVERT: B 93 LEU cc_start: 0.8544 (tp) cc_final: 0.8226 (pp) REVERT: B 107 MET cc_start: 0.6419 (pmm) cc_final: 0.6159 (pmm) REVERT: B 354 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 978 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7915 (t70) REVERT: B 1116 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8067 (mtt) REVERT: B 1195 MET cc_start: 0.7096 (pmm) cc_final: 0.6824 (pmm) REVERT: B 1197 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4563 (mm-30) outliers start: 31 outliers final: 24 residues processed: 132 average time/residue: 0.0820 time to fit residues: 15.3995 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 GLN B1156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128026 restraints weight = 9667.063| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.75 r_work: 0.3307 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8065 Z= 0.111 Angle : 0.594 9.893 10926 Z= 0.295 Chirality : 0.046 0.264 1208 Planarity : 0.003 0.037 1388 Dihedral : 4.077 20.894 1002 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.94 % Allowed : 19.21 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.29), residues: 898 helix: 2.17 (0.26), residues: 402 sheet: -0.82 (0.50), residues: 102 loop : -0.96 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.020 0.001 TYR B 999 PHE 0.015 0.001 PHE A 993 TRP 0.005 0.001 TRP A 357 HIS 0.002 0.000 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 8050) covalent geometry : angle 0.58162 / 0.29 (10882) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.19388 / 0.11 ( 2) hydrogen bonds : bond 0.02895 / 1.84 ( 335) hydrogen bonds : angle 4.12312 / 2.98 ( 981) link_BETA1-4 : bond 0.00435 / 0.22 ( 4) link_BETA1-4 : angle 1.03470 / 0.59 ( 12) link_NAG-ASN : bond 0.00773 / 0.37 ( 10) link_NAG-ASN : angle 2.29828 / 1.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.299 Fit side-chains REVERT: A 354 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8846 (mt) REVERT: A 432 THR cc_start: 0.8911 (m) cc_final: 0.8683 (p) REVERT: A 923 ARG cc_start: 0.6636 (ttm170) cc_final: 0.6297 (mtm180) REVERT: A 935 LEU cc_start: 0.7451 (mt) cc_final: 0.6712 (mt) REVERT: A 1053 MET cc_start: 0.8260 (mtp) cc_final: 0.8059 (mtt) REVERT: A 1116 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: A 1195 MET cc_start: 0.7068 (pmm) cc_final: 0.6841 (pmm) REVERT: A 1197 GLU cc_start: 0.4757 (OUTLIER) cc_final: 0.4451 (mm-30) REVERT: B 93 LEU cc_start: 0.8513 (tp) cc_final: 0.8221 (pp) REVERT: B 1195 MET cc_start: 0.7064 (pmm) cc_final: 0.6797 (pmm) REVERT: B 1197 GLU cc_start: 0.4728 (OUTLIER) cc_final: 0.4516 (mm-30) outliers start: 34 outliers final: 22 residues processed: 134 average time/residue: 0.0860 time to fit residues: 16.0109 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 0.0670 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.187000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127629 restraints weight = 9591.089| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.75 r_work: 0.3300 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8065 Z= 0.117 Angle : 0.611 10.277 10926 Z= 0.301 Chirality : 0.047 0.264 1208 Planarity : 0.003 0.039 1388 Dihedral : 4.046 20.746 1002 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.82 % Allowed : 19.10 % Favored : 77.08 % 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: 0.79 (0.29), residues: 898 helix: 2.24 (0.26), residues: 402 sheet: -0.81 (0.50), residues: 102 loop : -0.95 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1036 TYR 0.020 0.001 TYR B 999 PHE 0.012 0.001 PHE A 973 TRP 0.007 0.001 TRP B 357 HIS 0.003 0.000 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8050) covalent geometry : angle 0.59946 / 0.30 (10882) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.18108 / 0.10 ( 2) hydrogen bonds : bond 0.02869 / 1.83 ( 335) hydrogen bonds : angle 4.10466 / 2.95 ( 981) link_BETA1-4 : bond 0.00409 / 0.20 ( 4) link_BETA1-4 : angle 1.02150 / 0.58 ( 12) link_NAG-ASN : bond 0.00742 / 0.36 ( 10) link_NAG-ASN : angle 2.28359 / 1.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.284 Fit side-chains REVERT: A 354 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8840 (mt) REVERT: A 432 THR cc_start: 0.8909 (m) cc_final: 0.8637 (p) REVERT: A 935 LEU cc_start: 0.7491 (mt) cc_final: 0.6752 (mt) REVERT: A 1116 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: A 1195 MET cc_start: 0.7038 (pmm) cc_final: 0.6768 (pmm) REVERT: A 1197 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4463 (mm-30) REVERT: B 93 LEU cc_start: 0.8483 (tp) cc_final: 0.8204 (pp) REVERT: B 354 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8835 (mt) REVERT: B 978 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7900 (t70) REVERT: B 1195 MET cc_start: 0.7056 (pmm) cc_final: 0.6794 (pmm) REVERT: B 1197 GLU cc_start: 0.4730 (OUTLIER) cc_final: 0.4530 (mm-30) outliers start: 33 outliers final: 26 residues processed: 131 average time/residue: 0.0841 time to fit residues: 15.3755 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1156 HIS Chi-restraints excluded: chain B residue 1163 THR Chi-restraints excluded: chain B residue 1197 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126856 restraints weight = 9550.835| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.73 r_work: 0.3285 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8065 Z= 0.126 Angle : 0.628 10.621 10926 Z= 0.309 Chirality : 0.047 0.265 1208 Planarity : 0.004 0.066 1388 Dihedral : 4.061 20.887 1002 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.82 % Allowed : 19.56 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.29), residues: 898 helix: 2.25 (0.26), residues: 402 sheet: -0.81 (0.50), residues: 102 loop : -0.94 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1036 TYR 0.021 0.001 TYR B 79 PHE 0.011 0.001 PHE A 973 TRP 0.008 0.001 TRP A 357 HIS 0.008 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8050) covalent geometry : angle 0.61640 / 0.31 (10882) SS BOND : bond 0.00079 / 0.04 ( 1) SS BOND : angle 0.15494 / 0.09 ( 2) hydrogen bonds : bond 0.02852 / 1.83 ( 335) hydrogen bonds : angle 4.13706 / 2.98 ( 981) link_BETA1-4 : bond 0.00347 / 0.17 ( 4) link_BETA1-4 : angle 1.04182 / 0.60 ( 12) link_NAG-ASN : bond 0.00752 / 0.36 ( 10) link_NAG-ASN : angle 2.29259 / 1.61 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.324 Fit side-chains REVERT: A 354 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8847 (mt) REVERT: A 935 LEU cc_start: 0.7440 (mt) cc_final: 0.6704 (mt) REVERT: A 1116 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7565 (mtm) REVERT: A 1195 MET cc_start: 0.7054 (pmm) cc_final: 0.6790 (pmm) REVERT: A 1197 GLU cc_start: 0.4758 (OUTLIER) cc_final: 0.4496 (mm-30) REVERT: B 93 LEU cc_start: 0.8508 (tp) cc_final: 0.8211 (pp) REVERT: B 354 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8829 (mt) REVERT: B 978 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7924 (t70) REVERT: B 1195 MET cc_start: 0.7067 (pmm) cc_final: 0.6814 (pmm) outliers start: 33 outliers final: 25 residues processed: 127 average time/residue: 0.0804 time to fit residues: 14.3557 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129478 restraints weight = 9571.322| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.73 r_work: 0.3333 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8065 Z= 0.111 Angle : 0.608 10.111 10926 Z= 0.301 Chirality : 0.046 0.258 1208 Planarity : 0.003 0.038 1388 Dihedral : 3.933 20.302 1002 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.12 % Allowed : 20.25 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.92 (0.29), residues: 898 helix: 2.35 (0.26), residues: 402 sheet: -0.67 (0.51), residues: 102 loop : -0.89 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 923 TYR 0.019 0.001 TYR B 999 PHE 0.010 0.001 PHE A1176 TRP 0.005 0.001 TRP A 357 HIS 0.001 0.000 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8050) covalent geometry : angle 0.59722 / 0.30 (10882) SS BOND : bond 0.00062 / 0.03 ( 1) SS BOND : angle 0.30919 / 0.17 ( 2) hydrogen bonds : bond 0.02763 / 1.77 ( 335) hydrogen bonds : angle 4.05484 / 2.92 ( 981) link_BETA1-4 : bond 0.00406 / 0.20 ( 4) link_BETA1-4 : angle 0.99533 / 0.57 ( 12) link_NAG-ASN : bond 0.00758 / 0.36 ( 10) link_NAG-ASN : angle 2.22642 / 1.57 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.57 seconds wall clock time: 34 minutes 6.09 seconds (2046.09 seconds total)