Starting phenix.real_space_refine on Wed Mar 12 13:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s06_24785/03_2025/7s06_24785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s06_24785/03_2025/7s06_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_2025/7s06_24785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s06_24785/03_2025/7s06_24785.map" model { file = "/net/cci-nas-00/data/ceres_data/7s06_24785/03_2025/7s06_24785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s06_24785/03_2025/7s06_24785.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.84, per 1000 atoms: 0.62 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: 1.85 Conformation dependent library (CDL) restraints added in 927.1 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: 0.90 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: 2.06 Time building geometry restraints manager: 2.21 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: 0.04 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: 0.660 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- 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 8050 Z= 0.244 Angle : 0.665 8.048 10882 Z= 0.350 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (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 TRP 0.009 0.001 TRP B1201 HIS 0.006 0.001 HIS A1196 PHE 0.044 0.001 PHE B 995 TYR 0.009 0.001 TYR B 916 ARG 0.006 0.001 ARG A 394 *********************** 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 : 0.815 Fit side-chains REVERT: A 76 ASP cc_start: 0.8082 (m-30) cc_final: 0.7749 (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: 0.1815 time to fit residues: 47.2906 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 : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1006 GLN B1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.191106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132864 restraints weight = 9357.829| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.68 r_work: 0.3396 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8050 Z= 0.209 Angle : 0.617 8.458 10882 Z= 0.314 Chirality : 0.048 0.297 1208 Planarity : 0.003 0.036 1388 Dihedral : 11.353 89.280 1296 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.78 % Allowed : 11.81 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.29), residues: 898 helix: 1.81 (0.25), residues: 414 sheet: 0.62 (0.55), residues: 94 loop : -0.89 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 433 HIS 0.002 0.000 HIS A 393 PHE 0.021 0.001 PHE A 973 TYR 0.020 0.002 TYR A 56 ARG 0.003 0.000 ARG B 986 *********************** 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 148 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.881 Fit side-chains REVERT: A 76 ASP cc_start: 0.8314 (m-30) cc_final: 0.8100 (m-30) REVERT: A 354 ILE cc_start: 0.9129 (mp) cc_final: 0.8888 (mt) REVERT: A 432 THR cc_start: 0.8767 (m) cc_final: 0.8521 (p) REVERT: A 1053 MET cc_start: 0.8262 (mtp) cc_final: 0.7924 (mtt) REVERT: B 354 ILE cc_start: 0.9120 (mp) cc_final: 0.8865 (mt) REVERT: B 433 TRP cc_start: 0.8387 (p-90) cc_final: 0.8169 (p-90) REVERT: B 978 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 1012 GLN cc_start: 0.7919 (tt0) cc_final: 0.7665 (tt0) REVERT: B 1095 LYS cc_start: 0.7974 (mtpp) cc_final: 0.7487 (tppt) REVERT: B 1195 MET cc_start: 0.7156 (pmm) cc_final: 0.6941 (pmm) outliers start: 24 outliers final: 19 residues processed: 140 average time/residue: 0.1776 time to fit residues: 35.0012 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 ASN 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 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 67 ASN 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.187976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139831 restraints weight = 9400.158| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.70 r_work: 0.3284 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8050 Z= 0.221 Angle : 0.623 9.335 10882 Z= 0.309 Chirality : 0.048 0.286 1208 Planarity : 0.004 0.034 1388 Dihedral : 9.672 77.571 1296 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.47 % Allowed : 13.08 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 898 helix: 1.85 (0.25), residues: 414 sheet: 0.20 (0.52), residues: 98 loop : -0.94 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 342 HIS 0.003 0.001 HIS A 393 PHE 0.015 0.001 PHE A 973 TYR 0.016 0.002 TYR A 56 ARG 0.003 0.000 ARG A1036 *********************** 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 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.900 Fit side-chains REVERT: A 107 MET cc_start: 0.6505 (pmm) cc_final: 0.5963 (pmm) REVERT: A 354 ILE cc_start: 0.9124 (mp) cc_final: 0.8857 (mt) REVERT: A 432 THR cc_start: 0.8868 (m) cc_final: 0.8551 (p) REVERT: A 1053 MET cc_start: 0.8309 (mtp) cc_final: 0.7986 (mtt) REVERT: B 107 MET cc_start: 0.6421 (pmm) cc_final: 0.5793 (pmm) REVERT: B 354 ILE cc_start: 0.9113 (mp) cc_final: 0.8845 (mt) REVERT: B 978 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8016 (t70) REVERT: B 1012 GLN cc_start: 0.8014 (tt0) cc_final: 0.7791 (tt0) REVERT: B 1026 SER cc_start: 0.8776 (t) cc_final: 0.8260 (m) REVERT: B 1095 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7697 (tppt) outliers start: 30 outliers final: 22 residues processed: 126 average time/residue: 0.1770 time to fit residues: 31.3310 Evaluate side-chains 118 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 410 MET 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 1132 HIS Chi-restraints excluded: chain A residue 1163 THR 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 373 VAL Chi-restraints excluded: chain B residue 377 LEU 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 1156 HIS 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 67 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 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 371 GLN ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS B1156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.187407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128855 restraints weight = 9352.313| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.64 r_work: 0.3321 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8050 Z= 0.183 Angle : 0.586 8.311 10882 Z= 0.288 Chirality : 0.048 0.275 1208 Planarity : 0.003 0.035 1388 Dihedral : 8.777 69.584 1296 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.82 % Allowed : 14.47 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 898 helix: 1.92 (0.25), residues: 414 sheet: 0.04 (0.52), residues: 98 loop : -0.92 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 433 HIS 0.007 0.001 HIS B1156 PHE 0.010 0.001 PHE A 973 TYR 0.023 0.001 TYR A 999 ARG 0.003 0.000 ARG A1036 *********************** 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 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.842 Fit side-chains REVERT: A 107 MET cc_start: 0.6518 (pmm) cc_final: 0.6056 (pmm) REVERT: A 432 THR cc_start: 0.8890 (m) cc_final: 0.8551 (p) REVERT: A 1053 MET cc_start: 0.8248 (mtp) cc_final: 0.7946 (mtt) REVERT: B 93 LEU cc_start: 0.8592 (tp) cc_final: 0.8179 (pp) REVERT: B 107 MET cc_start: 0.6433 (pmm) cc_final: 0.5821 (pmm) REVERT: B 354 ILE cc_start: 0.9084 (mp) cc_final: 0.8833 (mt) REVERT: B 425 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8220 (mttm) REVERT: B 978 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7884 (t70) REVERT: B 1026 SER cc_start: 0.8743 (t) cc_final: 0.8196 (m) outliers start: 33 outliers final: 27 residues processed: 126 average time/residue: 0.1733 time to fit residues: 30.8235 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 373 VAL Chi-restraints excluded: chain A residue 410 MET 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 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR 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 373 VAL Chi-restraints excluded: chain B residue 377 LEU 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 1107 ASP 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 33 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.186266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138269 restraints weight = 9348.690| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.59 r_work: 0.3266 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8050 Z= 0.188 Angle : 0.578 8.196 10882 Z= 0.284 Chirality : 0.047 0.270 1208 Planarity : 0.003 0.035 1388 Dihedral : 7.340 55.868 1296 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.28 % Allowed : 15.51 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 898 helix: 1.97 (0.25), residues: 414 sheet: -0.16 (0.52), residues: 98 loop : -0.94 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 433 HIS 0.004 0.001 HIS B1156 PHE 0.013 0.001 PHE A 973 TYR 0.021 0.001 TYR A 999 ARG 0.002 0.000 ARG A 394 *********************** 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 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.971 Fit side-chains REVERT: A 1026 SER cc_start: 0.8839 (t) cc_final: 0.8266 (m) REVERT: A 1053 MET cc_start: 0.8295 (mtp) cc_final: 0.8036 (mtt) REVERT: A 1125 MET cc_start: 0.7177 (mmt) cc_final: 0.6934 (tpp) REVERT: B 93 LEU cc_start: 0.8547 (tp) cc_final: 0.8211 (pp) REVERT: B 425 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8338 (mtpt) REVERT: B 935 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7409 (mp) REVERT: B 978 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8014 (t70) REVERT: B 1026 SER cc_start: 0.8899 (t) cc_final: 0.8338 (m) outliers start: 37 outliers final: 23 residues processed: 137 average time/residue: 0.1767 time to fit residues: 34.3083 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 : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 LEU 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 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 64 SER 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 410 MET Chi-restraints excluded: chain B residue 935 LEU 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 1107 ASP 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 9 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.187704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140284 restraints weight = 9377.183| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.63 r_work: 0.3299 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8050 Z= 0.167 Angle : 0.625 12.170 10882 Z= 0.303 Chirality : 0.047 0.266 1208 Planarity : 0.003 0.035 1388 Dihedral : 6.654 48.706 1296 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.70 % Allowed : 16.09 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.29), residues: 898 helix: 2.06 (0.25), residues: 414 sheet: -0.03 (0.52), residues: 96 loop : -0.90 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 433 HIS 0.002 0.000 HIS B1194 PHE 0.011 0.001 PHE A 973 TYR 0.020 0.001 TYR A 999 ARG 0.004 0.000 ARG B1036 *********************** 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 : 0.886 Fit side-chains REVERT: A 425 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8274 (mttm) REVERT: A 1026 SER cc_start: 0.8745 (t) cc_final: 0.8217 (m) REVERT: A 1053 MET cc_start: 0.8262 (mtp) cc_final: 0.8030 (mtt) REVERT: A 1116 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8030 (mtt) REVERT: A 1125 MET cc_start: 0.7213 (mmt) cc_final: 0.6976 (tpp) REVERT: B 93 LEU cc_start: 0.8519 (tp) cc_final: 0.8226 (pp) REVERT: B 107 MET cc_start: 0.6532 (pmm) cc_final: 0.6290 (pmm) REVERT: B 425 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8310 (mtpt) REVERT: B 972 MET cc_start: 0.8253 (tpp) cc_final: 0.7885 (ttt) REVERT: B 978 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8002 (t70) REVERT: B 1116 MET cc_start: 0.8425 (mtm) cc_final: 0.8074 (mtt) REVERT: B 1125 MET cc_start: 0.7204 (mmt) cc_final: 0.6995 (tpp) REVERT: B 1197 GLU cc_start: 0.5005 (OUTLIER) cc_final: 0.4636 (mm-30) outliers start: 32 outliers final: 23 residues processed: 132 average time/residue: 0.1783 time to fit residues: 33.2468 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 : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 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 1132 HIS Chi-restraints excluded: chain A residue 1163 THR 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 373 VAL Chi-restraints excluded: chain B residue 377 LEU 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 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 83 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141112 restraints weight = 9500.536| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.96 r_work: 0.3262 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8050 Z= 0.168 Angle : 0.608 9.832 10882 Z= 0.295 Chirality : 0.047 0.260 1208 Planarity : 0.003 0.036 1388 Dihedral : 6.011 40.661 1296 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.70 % Allowed : 16.09 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 898 helix: 2.14 (0.25), residues: 414 sheet: 0.01 (0.52), residues: 96 loop : -0.88 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 433 HIS 0.002 0.000 HIS A1194 PHE 0.009 0.001 PHE A 973 TYR 0.018 0.001 TYR A 999 ARG 0.003 0.000 ARG B1036 *********************** 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: 32 poor density : 109 time to evaluate : 0.926 Fit side-chains REVERT: A 425 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8294 (mttm) REVERT: A 1026 SER cc_start: 0.8817 (t) cc_final: 0.8275 (m) REVERT: A 1053 MET cc_start: 0.8232 (mtp) cc_final: 0.8028 (mtt) REVERT: A 1116 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: A 1125 MET cc_start: 0.7240 (mmt) cc_final: 0.7039 (tpp) REVERT: A 1197 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4569 (mm-30) REVERT: B 93 LEU cc_start: 0.8526 (tp) cc_final: 0.8240 (pp) REVERT: B 107 MET cc_start: 0.6433 (pmm) cc_final: 0.6180 (pmm) REVERT: B 425 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8337 (mtpt) REVERT: B 972 MET cc_start: 0.8349 (tpp) cc_final: 0.8061 (ttt) REVERT: B 978 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7988 (t70) REVERT: B 1116 MET cc_start: 0.8410 (mtm) cc_final: 0.8136 (mtt) REVERT: B 1197 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.4589 (mm-30) outliers start: 32 outliers final: 23 residues processed: 134 average time/residue: 0.1876 time to fit residues: 34.7855 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 373 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 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 360 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 373 VAL 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 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 48 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 62 optimal weight: 0.0000 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 50 optimal weight: 7.9990 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 HIS A1196 HIS B 970 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.187119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127993 restraints weight = 9596.369| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.73 r_work: 0.3301 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8050 Z= 0.221 Angle : 0.626 9.936 10882 Z= 0.307 Chirality : 0.047 0.266 1208 Planarity : 0.003 0.038 1388 Dihedral : 5.560 33.103 1296 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.36 % Allowed : 17.36 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 898 helix: 2.10 (0.25), residues: 414 sheet: -0.12 (0.52), residues: 96 loop : -0.92 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 433 HIS 0.003 0.001 HIS B1194 PHE 0.012 0.001 PHE B 995 TYR 0.017 0.001 TYR A 999 ARG 0.004 0.000 ARG B1036 *********************** 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 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 1.103 Fit side-chains REVERT: A 425 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8215 (mttm) REVERT: A 1093 ASN cc_start: 0.8761 (m110) cc_final: 0.8253 (m110) REVERT: A 1116 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7520 (mtm) REVERT: B 93 LEU cc_start: 0.8531 (tp) cc_final: 0.8251 (pp) REVERT: B 392 ILE cc_start: 0.8302 (mp) cc_final: 0.8046 (mm) REVERT: B 425 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8269 (mtpt) REVERT: B 978 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7936 (t70) REVERT: B 1197 GLU cc_start: 0.4767 (OUTLIER) cc_final: 0.4556 (mm-30) outliers start: 29 outliers final: 23 residues processed: 126 average time/residue: 0.1944 time to fit residues: 34.7607 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 : 0.876 ------------------------------------------------------------------------------- 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 377 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 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 377 LEU 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 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 77 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 6 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.187350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128760 restraints weight = 9618.683| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.71 r_work: 0.3336 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8050 Z= 0.170 Angle : 0.629 10.303 10882 Z= 0.309 Chirality : 0.046 0.258 1208 Planarity : 0.003 0.039 1388 Dihedral : 5.214 28.938 1296 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.66 % Allowed : 18.52 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 898 helix: 2.18 (0.25), residues: 414 sheet: 0.01 (0.61), residues: 72 loop : -0.82 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 433 HIS 0.002 0.000 HIS A 379 PHE 0.010 0.001 PHE B 383 TYR 0.016 0.001 TYR A 999 ARG 0.004 0.000 ARG B1036 *********************** 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 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.909 Fit side-chains REVERT: A 425 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8217 (mttm) REVERT: A 1054 LEU cc_start: 0.8682 (mm) cc_final: 0.8465 (mp) REVERT: A 1093 ASN cc_start: 0.8755 (m110) cc_final: 0.8258 (m110) REVERT: A 1116 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: B 93 LEU cc_start: 0.8515 (tp) cc_final: 0.8245 (pp) REVERT: B 425 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8234 (mtpt) REVERT: B 978 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7863 (t70) REVERT: B 1116 MET cc_start: 0.8393 (mtm) cc_final: 0.8122 (mtt) REVERT: B 1195 MET cc_start: 0.7147 (pmm) cc_final: 0.6916 (pmm) outliers start: 23 outliers final: 20 residues processed: 126 average time/residue: 0.1979 time to fit residues: 34.2455 Evaluate side-chains 123 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 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 377 LEU 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 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.187496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139717 restraints weight = 9581.877| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.43 r_work: 0.3305 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8050 Z= 0.177 Angle : 0.630 10.686 10882 Z= 0.311 Chirality : 0.047 0.260 1208 Planarity : 0.003 0.039 1388 Dihedral : 4.915 28.808 1296 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.55 % Allowed : 18.40 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 898 helix: 2.24 (0.25), residues: 414 sheet: 0.04 (0.61), residues: 72 loop : -0.80 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 433 HIS 0.002 0.000 HIS A 379 PHE 0.012 0.001 PHE B 995 TYR 0.015 0.001 TYR A 999 ARG 0.002 0.000 ARG B1036 ********************** 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 121 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.860 Fit side-chains REVERT: A 425 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8276 (mttm) REVERT: A 1116 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8086 (mtt) REVERT: B 425 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8309 (mtpt) REVERT: B 978 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7969 (t70) REVERT: B 1116 MET cc_start: 0.8387 (mtm) cc_final: 0.8072 (mtt) REVERT: B 1195 MET cc_start: 0.7152 (pmm) cc_final: 0.6930 (pmm) outliers start: 22 outliers final: 20 residues processed: 117 average time/residue: 0.2034 time to fit residues: 32.4376 Evaluate side-chains 120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 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 377 LEU 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 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.185350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137724 restraints weight = 9593.389| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.89 r_work: 0.3230 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8050 Z= 0.226 Angle : 0.649 10.221 10882 Z= 0.321 Chirality : 0.047 0.265 1208 Planarity : 0.003 0.039 1388 Dihedral : 4.805 28.887 1296 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.89 % Allowed : 18.52 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 898 helix: 2.22 (0.25), residues: 402 sheet: -0.39 (0.60), residues: 76 loop : -0.69 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 433 HIS 0.002 0.001 HIS B 370 PHE 0.012 0.001 PHE B 995 TYR 0.018 0.001 TYR A 999 ARG 0.002 0.000 ARG B1145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.96 seconds wall clock time: 70 minutes 23.80 seconds (4223.80 seconds total)