Starting phenix.real_space_refine on Tue Mar 3 18:19:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s06_24785/03_2026/7s06_24785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s06_24785/03_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_24785/03_2026/7s06_24785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s06_24785/03_2026/7s06_24785.map" model { file = "/net/cci-nas-00/data/ceres_data/7s06_24785/03_2026/7s06_24785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s06_24785/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.88, per 1000 atoms: 0.24 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: 0.84 Conformation dependent library (CDL) restraints added in 285.7 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: 0.28 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: 0.98 Time building geometry restraints manager: 1.08 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 - 21.72: 4595 21.72 - 43.43: 390 43.43 - 65.14: 32 65.14 - 86.86: 16 86.86 - 108.57: 18 Dihedral angle restraints: 5051 sinusoidal: 2313 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 5048 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: 0.01 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.860 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 16.630 108.573 3256 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 covalent geometry : bond 0.00382 ( 8050) covalent geometry : angle 0.66497 (10882) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.26749 ( 2) hydrogen bonds : bond 0.18016 ( 335) hydrogen bonds : angle 6.54230 ( 981) link_BETA1-4 : bond 0.00512 ( 4) link_BETA1-4 : angle 1.04756 ( 12) link_NAG-ASN : bond 0.00803 ( 10) link_NAG-ASN : angle 2.73983 ( 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 : 0.278 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: 0.0846 time to fit residues: 22.3459 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 : 0.193 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4041 r_free = 0.4041 target = 0.176250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120268 restraints weight = 9397.365| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.98 r_work: 0.3053 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.077 8065 Z= 0.393 Angle : 0.869 13.898 10926 Z= 0.442 Chirality : 0.057 0.350 1208 Planarity : 0.005 0.037 1388 Dihedral : 10.612 77.832 1296 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.05 % Allowed : 12.62 % Favored : 83.33 % 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: -0.65 (0.47), residues: 102 loop : -1.18 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 364 TYR 0.029 0.003 TYR A 56 PHE 0.029 0.003 PHE A 973 TRP 0.026 0.004 TRP B 357 HIS 0.009 0.002 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00964 ( 8050) covalent geometry : angle 0.85346 (10882) SS BOND : bond 0.00349 ( 1) SS BOND : angle 0.36562 ( 2) hydrogen bonds : bond 0.05082 ( 335) hydrogen bonds : angle 5.06847 ( 981) link_BETA1-4 : bond 0.00322 ( 4) link_BETA1-4 : angle 1.70435 ( 12) link_NAG-ASN : bond 0.00925 ( 10) link_NAG-ASN : angle 3.13384 ( 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 152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.355 Fit side-chains REVERT: A 923 ARG cc_start: 0.6908 (ttm170) cc_final: 0.6652 (ttm-80) REVERT: A 935 LEU cc_start: 0.7671 (mt) cc_final: 0.6928 (mt) REVERT: A 1053 MET cc_start: 0.8349 (mtp) cc_final: 0.8028 (mtt) REVERT: B 406 ASN cc_start: 0.8189 (t0) cc_final: 0.7965 (t0) REVERT: B 935 LEU cc_start: 0.7689 (mt) cc_final: 0.6959 (mt) REVERT: B 978 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7966 (t0) REVERT: B 1027 ASP cc_start: 0.7972 (m-30) cc_final: 0.7598 (t0) REVERT: B 1103 LYS cc_start: 0.8791 (tppt) cc_final: 0.8549 (mtmm) REVERT: B 1128 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8212 (t) outliers start: 35 outliers final: 21 residues processed: 144 average time/residue: 0.0769 time to fit residues: 15.7781 Evaluate side-chains 120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 1128 THR 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: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4110 r_free = 0.4110 target = 0.182851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128817 restraints weight = 9298.184| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.04 r_work: 0.3275 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2931 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= 0.130 Angle : 0.656 8.693 10926 Z= 0.325 Chirality : 0.048 0.291 1208 Planarity : 0.004 0.043 1388 Dihedral : 9.382 70.203 1296 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.36 % Allowed : 14.70 % Favored : 81.94 % 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: 0.22 (0.28), residues: 898 helix: 1.63 (0.25), residues: 402 sheet: -1.07 (0.54), residues: 78 loop : -1.10 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1036 TYR 0.018 0.002 TYR A 999 PHE 0.016 0.001 PHE A 973 TRP 0.008 0.001 TRP B 357 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8050) covalent geometry : angle 0.63917 (10882) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.42767 ( 2) hydrogen bonds : bond 0.03833 ( 335) hydrogen bonds : angle 4.58619 ( 981) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 1.65562 ( 12) link_NAG-ASN : bond 0.00876 ( 10) link_NAG-ASN : angle 2.72027 ( 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 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.275 Fit side-chains REVERT: A 107 MET cc_start: 0.6647 (pmm) cc_final: 0.6201 (pmm) REVERT: A 923 ARG cc_start: 0.6920 (ttm170) cc_final: 0.6514 (mtm180) REVERT: A 1053 MET cc_start: 0.8303 (mtp) cc_final: 0.8063 (mtt) REVERT: A 1060 MET cc_start: 0.7830 (mtp) cc_final: 0.7596 (mmp) REVERT: A 1125 MET cc_start: 0.7142 (mmt) cc_final: 0.6921 (tpp) REVERT: B 107 MET cc_start: 0.6624 (pmm) cc_final: 0.6132 (pmm) REVERT: B 392 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8035 (mm) REVERT: B 978 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7929 (t70) REVERT: B 1016 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 1103 LYS cc_start: 0.8793 (tppt) cc_final: 0.8590 (mtmm) REVERT: B 1125 MET cc_start: 0.7125 (mmt) cc_final: 0.6904 (tpp) outliers start: 29 outliers final: 22 residues processed: 131 average time/residue: 0.0759 time to fit residues: 14.3268 Evaluate side-chains 117 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 941 ILE 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 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 978 ASP Chi-restraints excluded: chain B residue 1040 LEU 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: 5.9990 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 406 ASN ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS B 371 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.183994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124924 restraints weight = 9579.653| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.67 r_work: 0.3293 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8065 Z= 0.124 Angle : 0.610 8.424 10926 Z= 0.296 Chirality : 0.047 0.280 1208 Planarity : 0.003 0.034 1388 Dihedral : 7.865 57.482 1296 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.63 % Allowed : 15.28 % Favored : 80.09 % 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: 0.42 (0.28), residues: 898 helix: 1.85 (0.26), residues: 402 sheet: -0.87 (0.55), residues: 74 loop : -1.09 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1036 TYR 0.022 0.001 TYR A 999 PHE 0.013 0.001 PHE A 973 TRP 0.006 0.001 TRP A 357 HIS 0.002 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8050) covalent geometry : angle 0.59354 (10882) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.09495 ( 2) hydrogen bonds : bond 0.03358 ( 335) hydrogen bonds : angle 4.33035 ( 981) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 1.85938 ( 12) link_NAG-ASN : bond 0.00809 ( 10) link_NAG-ASN : angle 2.53556 ( 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 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.265 Fit side-chains REVERT: A 107 MET cc_start: 0.6483 (pmm) cc_final: 0.6063 (pmm) REVERT: A 354 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8821 (mt) REVERT: A 923 ARG cc_start: 0.6875 (ttm170) cc_final: 0.6582 (mtm180) REVERT: A 935 LEU cc_start: 0.7432 (mt) cc_final: 0.6856 (mt) REVERT: A 1060 MET cc_start: 0.7854 (mtp) cc_final: 0.7598 (mmp) REVERT: A 1116 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7573 (mtm) REVERT: B 93 LEU cc_start: 0.8577 (tp) cc_final: 0.8203 (pp) REVERT: B 107 MET cc_start: 0.6430 (pmm) cc_final: 0.5870 (pmm) REVERT: B 354 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8808 (mt) REVERT: B 935 LEU cc_start: 0.7484 (mt) cc_final: 0.6692 (mt) REVERT: B 972 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7860 (ttt) REVERT: B 978 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7911 (t70) REVERT: B 1103 LYS cc_start: 0.8764 (tppt) cc_final: 0.8563 (mtmm) REVERT: B 1116 MET cc_start: 0.8437 (mtm) cc_final: 0.8167 (mtt) outliers start: 40 outliers final: 21 residues processed: 137 average time/residue: 0.0748 time to fit residues: 14.7363 Evaluate side-chains 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.9980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.183460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129306 restraints weight = 9566.878| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.01 r_work: 0.3263 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8065 Z= 0.131 Angle : 0.600 8.329 10926 Z= 0.291 Chirality : 0.047 0.278 1208 Planarity : 0.004 0.035 1388 Dihedral : 7.079 50.735 1296 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.47 % Allowed : 18.40 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.28), residues: 898 helix: 1.91 (0.26), residues: 402 sheet: -1.11 (0.55), residues: 78 loop : -1.06 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.021 0.001 TYR A 999 PHE 0.015 0.001 PHE A 973 TRP 0.008 0.001 TRP B 357 HIS 0.002 0.000 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8050) covalent geometry : angle 0.58380 (10882) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.15970 ( 2) hydrogen bonds : bond 0.03244 ( 335) hydrogen bonds : angle 4.24119 ( 981) link_BETA1-4 : bond 0.00365 ( 4) link_BETA1-4 : angle 1.87586 ( 12) link_NAG-ASN : bond 0.00815 ( 10) link_NAG-ASN : angle 2.47941 ( 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 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.312 Fit side-chains REVERT: A 923 ARG cc_start: 0.6920 (ttm170) cc_final: 0.6646 (mtm180) REVERT: A 935 LEU cc_start: 0.7397 (mt) cc_final: 0.6598 (mt) REVERT: A 1026 SER cc_start: 0.8608 (t) cc_final: 0.8217 (m) REVERT: A 1027 ASP cc_start: 0.7815 (t0) cc_final: 0.7383 (t0) REVERT: A 1060 MET cc_start: 0.7876 (mtp) cc_final: 0.7589 (mmp) REVERT: A 1116 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7588 (mtm) REVERT: B 93 LEU cc_start: 0.8562 (tp) cc_final: 0.8215 (pp) REVERT: B 935 LEU cc_start: 0.7520 (mt) cc_final: 0.6751 (mt) REVERT: B 978 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7956 (t70) outliers start: 30 outliers final: 24 residues processed: 129 average time/residue: 0.0727 time to fit residues: 13.5239 Evaluate side-chains 125 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 1017 VAL Chi-restraints excluded: chain A residue 1040 LEU 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 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 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 1156 HIS 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: 3.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 970 GLN A 992 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 = 0.4130 r_free = 0.4130 target = 0.185422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125827 restraints weight = 9603.634| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.72 r_work: 0.3265 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8065 Z= 0.136 Angle : 0.643 10.807 10926 Z= 0.309 Chirality : 0.047 0.276 1208 Planarity : 0.004 0.036 1388 Dihedral : 6.606 45.726 1296 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.70 % Allowed : 18.87 % Favored : 77.43 % 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: 0.50 (0.29), residues: 898 helix: 1.97 (0.26), residues: 402 sheet: -1.04 (0.57), residues: 78 loop : -1.06 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.021 0.001 TYR A 999 PHE 0.012 0.001 PHE A 973 TRP 0.010 0.001 TRP B 357 HIS 0.010 0.001 HIS B1156 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8050) covalent geometry : angle 0.62797 (10882) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.12133 ( 2) hydrogen bonds : bond 0.03164 ( 335) hydrogen bonds : angle 4.29177 ( 981) link_BETA1-4 : bond 0.00310 ( 4) link_BETA1-4 : angle 1.90396 ( 12) link_NAG-ASN : bond 0.00793 ( 10) link_NAG-ASN : angle 2.46277 ( 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 138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.289 Fit side-chains REVERT: A 354 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8830 (mt) REVERT: A 935 LEU cc_start: 0.7381 (mt) cc_final: 0.6617 (mt) REVERT: A 1026 SER cc_start: 0.8582 (t) cc_final: 0.8169 (m) REVERT: A 1027 ASP cc_start: 0.7769 (t0) cc_final: 0.7316 (t0) REVERT: A 1060 MET cc_start: 0.7917 (mtp) cc_final: 0.7589 (mmp) REVERT: A 1116 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7574 (mtm) REVERT: B 93 LEU cc_start: 0.8550 (tp) cc_final: 0.8217 (pp) REVERT: B 107 MET cc_start: 0.6526 (pmm) cc_final: 0.6275 (pmm) REVERT: B 354 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8818 (mt) REVERT: B 935 LEU cc_start: 0.7513 (mt) cc_final: 0.6804 (mt) REVERT: B 978 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7916 (t70) outliers start: 32 outliers final: 25 residues processed: 134 average time/residue: 0.0776 time to fit residues: 14.5670 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4120 r_free = 0.4120 target = 0.184402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125822 restraints weight = 9561.051| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.65 r_work: 0.3279 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8065 Z= 0.128 Angle : 0.632 9.767 10926 Z= 0.308 Chirality : 0.047 0.272 1208 Planarity : 0.003 0.036 1388 Dihedral : 5.855 36.141 1296 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.82 % Allowed : 18.40 % Favored : 77.78 % 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: 0.58 (0.29), residues: 898 helix: 2.04 (0.26), residues: 402 sheet: -1.00 (0.58), residues: 78 loop : -1.03 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.020 0.001 TYR A 999 PHE 0.009 0.001 PHE A 973 TRP 0.013 0.001 TRP B 357 HIS 0.002 0.000 HIS A1194 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8050) covalent geometry : angle 0.61676 (10882) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.12173 ( 2) hydrogen bonds : bond 0.03100 ( 335) hydrogen bonds : angle 4.18072 ( 981) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.88809 ( 12) link_NAG-ASN : bond 0.00787 ( 10) link_NAG-ASN : angle 2.42689 ( 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 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 354 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8829 (mt) REVERT: A 935 LEU cc_start: 0.7415 (mt) cc_final: 0.6671 (mt) REVERT: A 1116 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7597 (mtm) REVERT: B 93 LEU cc_start: 0.8551 (tp) cc_final: 0.8249 (pp) REVERT: B 107 MET cc_start: 0.6447 (pmm) cc_final: 0.6201 (pmm) REVERT: B 354 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8823 (mt) REVERT: B 978 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7972 (t70) REVERT: B 1195 MET cc_start: 0.7051 (pmm) cc_final: 0.6806 (pmm) REVERT: B 1197 GLU cc_start: 0.4799 (OUTLIER) cc_final: 0.4536 (mm-30) outliers start: 33 outliers final: 26 residues processed: 136 average time/residue: 0.0896 time to fit residues: 16.8450 Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 1107 ASP 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 1156 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 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 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: 0.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** 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 = 0.4126 r_free = 0.4126 target = 0.185214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126156 restraints weight = 9661.888| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.71 r_work: 0.3289 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8065 Z= 0.122 Angle : 0.611 9.962 10926 Z= 0.299 Chirality : 0.046 0.269 1208 Planarity : 0.004 0.052 1388 Dihedral : 5.360 29.982 1296 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.70 % Allowed : 18.98 % Favored : 77.31 % 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: 0.65 (0.29), residues: 898 helix: 2.10 (0.26), residues: 402 sheet: -0.84 (0.57), residues: 76 loop : -1.02 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.019 0.001 TYR A 999 PHE 0.011 0.001 PHE A 973 TRP 0.013 0.001 TRP A 357 HIS 0.002 0.000 HIS B1158 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8050) covalent geometry : angle 0.59579 (10882) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.14020 ( 2) hydrogen bonds : bond 0.03024 ( 335) hydrogen bonds : angle 4.15469 ( 981) link_BETA1-4 : bond 0.00358 ( 4) link_BETA1-4 : angle 1.88569 ( 12) link_NAG-ASN : bond 0.00790 ( 10) link_NAG-ASN : angle 2.39117 ( 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 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.299 Fit side-chains REVERT: A 354 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 923 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6652 (mtm-85) REVERT: A 935 LEU cc_start: 0.7398 (mt) cc_final: 0.6652 (mt) REVERT: A 1116 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7562 (mtm) REVERT: A 1127 ARG cc_start: 0.8206 (ptp-110) cc_final: 0.7306 (mtt-85) REVERT: A 1195 MET cc_start: 0.6978 (pmm) cc_final: 0.6770 (pmm) REVERT: A 1197 GLU cc_start: 0.4768 (OUTLIER) cc_final: 0.4439 (mm-30) REVERT: B 93 LEU cc_start: 0.8510 (tp) cc_final: 0.8231 (pp) REVERT: B 354 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8820 (mt) REVERT: B 935 LEU cc_start: 0.7550 (mt) cc_final: 0.6916 (mt) REVERT: B 978 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7962 (t70) REVERT: B 1195 MET cc_start: 0.7115 (pmm) cc_final: 0.6808 (pmm) REVERT: B 1197 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4542 (mm-30) outliers start: 32 outliers final: 19 residues processed: 133 average time/residue: 0.0859 time to fit residues: 15.8213 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 1116 MET 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 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 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 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: 4.9990 chunk 25 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** 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 = 0.4095 r_free = 0.4095 target = 0.182158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122325 restraints weight = 9645.502| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.71 r_work: 0.3227 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8065 Z= 0.174 Angle : 0.652 10.148 10926 Z= 0.323 Chirality : 0.048 0.276 1208 Planarity : 0.004 0.044 1388 Dihedral : 5.225 29.950 1296 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % 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: 0.50 (0.29), residues: 898 helix: 1.82 (0.26), residues: 414 sheet: -0.96 (0.57), residues: 76 loop : -1.00 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1127 TYR 0.021 0.002 TYR A 999 PHE 0.012 0.001 PHE B 995 TRP 0.016 0.002 TRP A 357 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8050) covalent geometry : angle 0.63777 (10882) SS BOND : bond 0.00255 ( 1) SS BOND : angle 0.04939 ( 2) hydrogen bonds : bond 0.03251 ( 335) hydrogen bonds : angle 4.21828 ( 981) link_BETA1-4 : bond 0.00359 ( 4) link_BETA1-4 : angle 1.86544 ( 12) link_NAG-ASN : bond 0.00739 ( 10) link_NAG-ASN : angle 2.46082 ( 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 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.358 Fit side-chains REVERT: A 354 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8755 (mt) REVERT: A 923 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6703 (mtm-85) REVERT: A 935 LEU cc_start: 0.7452 (mt) cc_final: 0.6807 (mt) REVERT: A 1116 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: A 1195 MET cc_start: 0.7057 (pmm) cc_final: 0.6782 (pmm) REVERT: A 1197 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.4424 (mm-30) REVERT: B 93 LEU cc_start: 0.8541 (tp) cc_final: 0.8275 (pp) REVERT: B 354 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8759 (mt) REVERT: B 935 LEU cc_start: 0.7613 (mt) cc_final: 0.7110 (mt) REVERT: B 978 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8005 (t70) REVERT: B 1195 MET cc_start: 0.7141 (pmm) cc_final: 0.6853 (pmm) REVERT: B 1197 GLU cc_start: 0.4769 (OUTLIER) cc_final: 0.4532 (mm-30) outliers start: 33 outliers final: 24 residues processed: 137 average time/residue: 0.0927 time to fit residues: 17.5005 Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR 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 1017 VAL Chi-restraints excluded: chain A residue 1040 LEU 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 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 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 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 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: 0.9980 chunk 44 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 86 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.184138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124647 restraints weight = 9605.438| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.72 r_work: 0.3260 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8065 Z= 0.125 Angle : 0.633 10.496 10926 Z= 0.312 Chirality : 0.047 0.265 1208 Planarity : 0.004 0.057 1388 Dihedral : 4.971 29.890 1296 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.47 % Allowed : 19.68 % 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: 0.66 (0.29), residues: 898 helix: 2.14 (0.26), residues: 402 sheet: -0.84 (0.58), residues: 76 loop : -1.05 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1127 TYR 0.025 0.001 TYR A 999 PHE 0.016 0.001 PHE A 993 TRP 0.010 0.001 TRP A 357 HIS 0.001 0.000 HIS B1194 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8050) covalent geometry : angle 0.61994 (10882) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.20631 ( 2) hydrogen bonds : bond 0.03020 ( 335) hydrogen bonds : angle 4.14176 ( 981) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 1.72766 ( 12) link_NAG-ASN : bond 0.00788 ( 10) link_NAG-ASN : angle 2.34048 ( 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 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.359 Fit side-chains REVERT: A 354 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8777 (mt) REVERT: A 923 ARG cc_start: 0.6974 (mtm-85) cc_final: 0.6708 (mtm-85) REVERT: A 935 LEU cc_start: 0.7604 (mt) cc_final: 0.6903 (mt) REVERT: A 1116 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7517 (mtm) REVERT: A 1120 GLU cc_start: 0.7797 (tp30) cc_final: 0.7555 (tp30) REVERT: A 1195 MET cc_start: 0.7041 (pmm) cc_final: 0.6800 (pmm) REVERT: A 1197 GLU cc_start: 0.4730 (OUTLIER) cc_final: 0.4431 (mm-30) REVERT: B 93 LEU cc_start: 0.8507 (tp) cc_final: 0.8265 (pp) REVERT: B 354 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8756 (mt) REVERT: B 978 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7987 (t70) REVERT: B 1195 MET cc_start: 0.7126 (pmm) cc_final: 0.6828 (pmm) outliers start: 30 outliers final: 23 residues processed: 133 average time/residue: 0.0868 time to fit residues: 16.0111 Evaluate side-chains 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR 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 86 ASP 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 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 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4129 r_free = 0.4129 target = 0.184897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125805 restraints weight = 9648.028| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.69 r_work: 0.3195 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8065 Z= 0.120 Angle : 0.624 10.299 10926 Z= 0.309 Chirality : 0.046 0.266 1208 Planarity : 0.004 0.042 1388 Dihedral : 4.793 29.730 1296 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.47 % Allowed : 19.33 % Favored : 77.20 % 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: 2.20 (0.26), residues: 402 sheet: -0.72 (0.59), residues: 76 loop : -1.04 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1127 TYR 0.025 0.001 TYR A 999 PHE 0.010 0.001 PHE B 982 TRP 0.010 0.001 TRP A 357 HIS 0.002 0.000 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8050) covalent geometry : angle 0.61081 (10882) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.13875 ( 2) hydrogen bonds : bond 0.02936 ( 335) hydrogen bonds : angle 4.09952 ( 981) link_BETA1-4 : bond 0.00422 ( 4) link_BETA1-4 : angle 1.66582 ( 12) link_NAG-ASN : bond 0.00772 ( 10) link_NAG-ASN : angle 2.30268 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.58 seconds wall clock time: 32 minutes 57.22 seconds (1977.22 seconds total)