Starting phenix.real_space_refine on Tue Feb 13 22:01:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/02_2024/7s06_24785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/02_2024/7s06_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/02_2024/7s06_24785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/02_2024/7s06_24785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/02_2024/7s06_24785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/02_2024/7s06_24785.pdb" } 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 Residue "A ASP 58": "OD1" <-> "OD2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 962": "OD1" <-> "OD2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A ASP 1170": "OD1" <-> "OD2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B ASP 962": "OD1" <-> "OD2" Residue "B GLU 975": "OE1" <-> "OE2" Residue "B PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1120": "OE1" <-> "OE2" Residue "B ASP 1170": "OD1" <-> "OD2" Residue "B GLU 1187": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.59, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A1009 " " NAG A1302 " - " ASN A1056 " " NAG A1303 " - " ASN A 376 " " NAG B1301 " - " ASN B1009 " " NAG B1302 " - " ASN B1056 " " NAG B1303 " - " ASN B 376 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A1129 " " NAG E 1 " - " ASN B 83 " " NAG F 1 " - " ASN B1129 " Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 2.49 Time building geometry restraints manager: 3.38 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: 99.14 - 106.19: 237 106.19 - 113.24: 4363 113.24 - 120.29: 2913 120.29 - 127.34: 3275 127.34 - 134.39: 94 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 2.440 nonbonded pdb=" O LEU B1025 " pdb=" OH TYR B1078 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASN B 351 " pdb=" N GLY B 352 " model vdw 2.215 2.520 nonbonded pdb=" OD1 ASN A 351 " pdb=" N GLY A 352 " model vdw 2.215 2.520 nonbonded pdb=" OG SER B 934 " pdb=" O ASP B 990 " model vdw 2.287 2.440 ... (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 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: 0.780 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: 3.920 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.050 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.950 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.906 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: 0.1929 time to fit residues: 50.0516 Evaluate side-chains 111 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 0.7980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** B1006 GLN B1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1750 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= 0.202 Angle : 0.605 8.345 10882 Z= 0.305 Chirality : 0.048 0.300 1208 Planarity : 0.003 0.036 1388 Dihedral : 11.096 87.184 1296 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.01 % Allowed : 12.27 % Favored : 84.72 % 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: 0.93 (0.29), residues: 898 helix: 1.89 (0.25), residues: 414 sheet: 0.93 (0.55), residues: 92 loop : -0.88 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 433 HIS 0.002 0.000 HIS A 393 PHE 0.021 0.001 PHE A 973 TYR 0.020 0.001 TYR A 56 ARG 0.003 0.000 ARG A 394 *********************** 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 fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.979 Fit side-chains REVERT: A 76 ASP cc_start: 0.8114 (m-30) cc_final: 0.7707 (m-30) REVERT: A 354 ILE cc_start: 0.9069 (mp) cc_final: 0.8833 (mt) REVERT: B 73 MET cc_start: 0.8078 (mmp) cc_final: 0.7693 (mmm) REVERT: B 76 ASP cc_start: 0.8082 (m-30) cc_final: 0.7724 (m-30) REVERT: B 354 ILE cc_start: 0.9065 (mp) cc_final: 0.8827 (mt) REVERT: B 433 TRP cc_start: 0.8412 (p-90) cc_final: 0.8191 (p-90) REVERT: B 978 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7734 (t0) REVERT: B 1012 GLN cc_start: 0.7837 (tt0) cc_final: 0.7572 (tt0) REVERT: B 1027 ASP cc_start: 0.7546 (m-30) cc_final: 0.7341 (m-30) REVERT: B 1095 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7329 (tppt) REVERT: B 1125 MET cc_start: 0.6450 (mmt) cc_final: 0.6150 (mmt) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.1774 time to fit residues: 35.8031 Evaluate side-chains 126 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 59 ASN 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 45 optimal weight: 7.9990 chunk 25 optimal weight: 0.0670 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8050 Z= 0.287 Angle : 0.639 9.026 10882 Z= 0.319 Chirality : 0.049 0.293 1208 Planarity : 0.004 0.037 1388 Dihedral : 9.774 77.118 1296 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.28 % Allowed : 13.08 % Favored : 82.64 % 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: 1.96 (0.26), residues: 402 sheet: 0.19 (0.52), residues: 98 loop : -0.86 (0.34), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 357 HIS 0.003 0.001 HIS B 393 PHE 0.017 0.001 PHE A 973 TYR 0.016 0.002 TYR B 999 ARG 0.002 0.000 ARG A 986 *********************** 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 142 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 0.927 Fit side-chains REVERT: A 76 ASP cc_start: 0.8101 (m-30) cc_final: 0.7692 (m-30) REVERT: A 107 MET cc_start: 0.6531 (pmm) cc_final: 0.5814 (pmm) REVERT: B 76 ASP cc_start: 0.8108 (m-30) cc_final: 0.7709 (m-30) REVERT: B 107 MET cc_start: 0.6741 (pmm) cc_final: 0.6009 (pmm) REVERT: B 354 ILE cc_start: 0.9059 (mp) cc_final: 0.8831 (mt) REVERT: B 978 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7810 (t70) REVERT: B 1012 GLN cc_start: 0.7914 (tt0) cc_final: 0.7652 (tt0) outliers start: 37 outliers final: 27 residues processed: 132 average time/residue: 0.1694 time to fit residues: 31.9239 Evaluate side-chains 123 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 59 ASN 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 432 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8050 Z= 0.217 Angle : 0.603 8.074 10882 Z= 0.298 Chirality : 0.048 0.279 1208 Planarity : 0.003 0.035 1388 Dihedral : 8.667 67.423 1296 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.82 % Allowed : 15.39 % Favored : 80.79 % 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: 0.81 (0.29), residues: 898 helix: 2.02 (0.26), residues: 402 sheet: -0.04 (0.52), residues: 98 loop : -0.88 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 433 HIS 0.015 0.001 HIS B1156 PHE 0.013 0.001 PHE A 973 TYR 0.014 0.001 TYR B 999 ARG 0.003 0.000 ARG A 986 *********************** 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 fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 0.937 Fit side-chains REVERT: A 76 ASP cc_start: 0.8092 (m-30) cc_final: 0.7832 (m-30) REVERT: A 107 MET cc_start: 0.6484 (pmm) cc_final: 0.6084 (pmm) REVERT: A 392 ILE cc_start: 0.8089 (mp) cc_final: 0.7849 (mm) REVERT: B 76 ASP cc_start: 0.8089 (m-30) cc_final: 0.7791 (m-30) REVERT: B 107 MET cc_start: 0.6377 (pmm) cc_final: 0.5832 (pmm) REVERT: B 978 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7756 (t70) REVERT: B 1012 GLN cc_start: 0.7938 (tt0) cc_final: 0.7713 (tt0) outliers start: 33 outliers final: 25 residues processed: 127 average time/residue: 0.1698 time to fit residues: 30.6834 Evaluate side-chains 124 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 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 59 ASN 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 432 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 1 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8050 Z= 0.214 Angle : 0.583 7.978 10882 Z= 0.286 Chirality : 0.047 0.274 1208 Planarity : 0.003 0.036 1388 Dihedral : 7.447 55.808 1296 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.09 % Allowed : 15.39 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.26), residues: 402 sheet: -0.19 (0.52), residues: 98 loop : -0.93 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 433 HIS 0.002 0.001 HIS B1156 PHE 0.012 0.001 PHE A 973 TYR 0.015 0.001 TYR A 999 ARG 0.002 0.000 ARG A 986 *********************** 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 fitting. rotamer outliers: 44 poor density : 102 time to evaluate : 0.941 Fit side-chains REVERT: A 76 ASP cc_start: 0.8093 (m-30) cc_final: 0.7707 (m-30) REVERT: A 392 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.8002 (mm) REVERT: A 1125 MET cc_start: 0.6999 (mmt) cc_final: 0.6784 (tpp) REVERT: B 76 ASP cc_start: 0.8093 (m-30) cc_final: 0.7825 (m-30) REVERT: B 93 LEU cc_start: 0.8546 (tp) cc_final: 0.8167 (pp) REVERT: B 392 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7971 (mm) REVERT: B 935 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7344 (mp) REVERT: B 978 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7749 (t70) REVERT: B 1125 MET cc_start: 0.7025 (mmt) cc_final: 0.6810 (tpp) outliers start: 44 outliers final: 28 residues processed: 135 average time/residue: 0.1664 time to fit residues: 32.0900 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 392 ILE 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 59 ASN 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 382 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 432 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.0000 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 0.0470 chunk 49 optimal weight: 0.6980 overall best weight: 0.4482 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8050 Z= 0.156 Angle : 0.613 11.252 10882 Z= 0.297 Chirality : 0.047 0.266 1208 Planarity : 0.003 0.036 1388 Dihedral : 6.741 48.586 1296 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.82 % Allowed : 17.48 % Favored : 78.70 % 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: 0.85 (0.29), residues: 898 helix: 2.08 (0.25), residues: 414 sheet: 0.04 (0.53), residues: 96 loop : -1.02 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 433 HIS 0.002 0.000 HIS B1194 PHE 0.014 0.001 PHE A 973 TYR 0.013 0.001 TYR A 999 ARG 0.002 0.000 ARG B 986 *********************** 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 141 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 0.851 Fit side-chains REVERT: A 76 ASP cc_start: 0.8086 (m-30) cc_final: 0.7830 (m-30) REVERT: A 107 MET cc_start: 0.6801 (pmm) cc_final: 0.6594 (pmm) REVERT: A 1116 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7427 (mtm) REVERT: A 1125 MET cc_start: 0.7016 (mmt) cc_final: 0.6810 (tpp) REVERT: B 76 ASP cc_start: 0.8076 (m-30) cc_final: 0.7818 (m-30) REVERT: B 93 LEU cc_start: 0.8469 (tp) cc_final: 0.8155 (pp) REVERT: B 107 MET cc_start: 0.6575 (pmm) cc_final: 0.6318 (pmm) REVERT: B 392 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7932 (mm) REVERT: B 425 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7900 (mttm) REVERT: B 978 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7713 (t70) REVERT: B 1116 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7461 (mtm) outliers start: 33 outliers final: 23 residues processed: 131 average time/residue: 0.1932 time to fit residues: 34.9326 Evaluate side-chains 130 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 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 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 59 ASN 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 382 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 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 63 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3124 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= 0.193 Angle : 0.610 8.498 10882 Z= 0.295 Chirality : 0.047 0.266 1208 Planarity : 0.003 0.037 1388 Dihedral : 6.171 41.679 1296 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.28 % Allowed : 16.90 % 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: 0.79 (0.29), residues: 898 helix: 2.06 (0.25), residues: 414 sheet: -0.16 (0.53), residues: 98 loop : -1.04 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 357 HIS 0.002 0.001 HIS B 391 PHE 0.014 0.001 PHE A 973 TYR 0.015 0.001 TYR A 999 ARG 0.003 0.000 ARG A 951 *********************** 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 140 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 1.054 Fit side-chains REVERT: A 76 ASP cc_start: 0.8075 (m-30) cc_final: 0.7823 (m-30) REVERT: A 107 MET cc_start: 0.6599 (pmm) cc_final: 0.6387 (pmm) REVERT: A 1116 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7423 (mtm) REVERT: B 76 ASP cc_start: 0.8055 (m-30) cc_final: 0.7822 (m-30) REVERT: B 93 LEU cc_start: 0.8482 (tp) cc_final: 0.8179 (pp) REVERT: B 107 MET cc_start: 0.6464 (pmm) cc_final: 0.6162 (pmm) REVERT: B 392 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7933 (mm) REVERT: B 425 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7914 (mttm) REVERT: B 972 MET cc_start: 0.8076 (tpp) cc_final: 0.7814 (ttt) REVERT: B 978 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7754 (t70) REVERT: B 1116 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7480 (mtm) REVERT: B 1197 GLU cc_start: 0.4917 (OUTLIER) cc_final: 0.4654 (mm-30) outliers start: 37 outliers final: 25 residues processed: 133 average time/residue: 0.1982 time to fit residues: 36.5052 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 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 59 ASN 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 382 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 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 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8050 Z= 0.206 Angle : 0.613 8.167 10882 Z= 0.300 Chirality : 0.047 0.268 1208 Planarity : 0.003 0.038 1388 Dihedral : 5.614 32.931 1296 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.70 % Allowed : 17.71 % 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: 0.82 (0.29), residues: 898 helix: 2.10 (0.26), residues: 402 sheet: -0.02 (0.63), residues: 74 loop : -0.93 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 357 HIS 0.002 0.001 HIS B 391 PHE 0.011 0.001 PHE A 973 TYR 0.014 0.001 TYR A 999 ARG 0.002 0.000 ARG A 986 *********************** 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 fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 0.897 Fit side-chains REVERT: A 107 MET cc_start: 0.6482 (pmm) cc_final: 0.5925 (pmm) REVERT: A 1116 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7413 (mtm) REVERT: B 93 LEU cc_start: 0.8471 (tp) cc_final: 0.8199 (pp) REVERT: B 392 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 425 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7926 (mttm) REVERT: B 978 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7781 (t70) REVERT: B 1116 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7473 (mtm) outliers start: 32 outliers final: 25 residues processed: 126 average time/residue: 0.1837 time to fit residues: 32.2645 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN 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 1017 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 59 ASN 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 392 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8050 Z= 0.222 Angle : 0.621 8.213 10882 Z= 0.305 Chirality : 0.047 0.266 1208 Planarity : 0.003 0.038 1388 Dihedral : 5.183 29.712 1296 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.82 % Allowed : 18.06 % 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 (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: 0.77 (0.29), residues: 898 helix: 2.07 (0.26), residues: 402 sheet: -0.45 (0.62), residues: 78 loop : -0.88 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 357 HIS 0.002 0.001 HIS B 391 PHE 0.014 0.001 PHE B 946 TYR 0.015 0.001 TYR A 999 ARG 0.002 0.000 ARG A 986 *********************** 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 133 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 0.892 Fit side-chains REVERT: A 107 MET cc_start: 0.6476 (pmm) cc_final: 0.6087 (pmm) REVERT: A 1116 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7417 (mtm) REVERT: B 392 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7990 (mm) REVERT: B 425 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7995 (mtpt) REVERT: B 978 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7792 (t70) REVERT: B 1116 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7455 (mtm) outliers start: 33 outliers final: 26 residues processed: 123 average time/residue: 0.1995 time to fit residues: 33.5078 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 64 SER 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 1020 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1116 MET Chi-restraints excluded: chain A residue 1132 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 59 ASN 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 377 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1077 SER Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3502 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= 0.176 Angle : 0.617 10.613 10882 Z= 0.304 Chirality : 0.046 0.260 1208 Planarity : 0.004 0.073 1388 Dihedral : 4.932 29.524 1296 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.24 % Allowed : 19.56 % 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 (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: 2.14 (0.26), residues: 402 sheet: -0.34 (0.62), residues: 78 loop : -0.81 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 357 HIS 0.002 0.000 HIS A 379 PHE 0.012 0.001 PHE B 995 TYR 0.014 0.001 TYR A 999 ARG 0.017 0.000 ARG B1127 ********************** 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 132 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.973 Fit side-chains REVERT: A 107 MET cc_start: 0.6523 (pmm) cc_final: 0.5809 (pmm) REVERT: A 1116 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7891 (mtt) REVERT: A 1153 ASN cc_start: 0.7490 (p0) cc_final: 0.7220 (p0) REVERT: B 93 LEU cc_start: 0.8407 (tp) cc_final: 0.8199 (pp) REVERT: B 392 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (mm) REVERT: B 425 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7964 (mtpt) REVERT: B 978 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7755 (t70) REVERT: B 1116 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8105 (mtt) outliers start: 28 outliers final: 22 residues processed: 124 average time/residue: 0.1891 time to fit residues: 32.7808 Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 64 SER 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 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 1156 HIS Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain B residue 59 ASN 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 377 LEU Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 943 ASN Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 0.0020 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4139 r_free = 0.4139 target = 0.185853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126861 restraints weight = 9622.830| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.70 r_work: 0.3280 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 0.054 8050 Z= 0.226 Angle : 0.623 10.077 10882 Z= 0.310 Chirality : 0.047 0.264 1208 Planarity : 0.004 0.051 1388 Dihedral : 4.810 29.512 1296 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.36 % Allowed : 19.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 898 helix: 2.14 (0.26), residues: 402 sheet: -0.31 (0.63), residues: 78 loop : -0.84 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 357 HIS 0.002 0.001 HIS B 370 PHE 0.013 0.001 PHE B 995 TYR 0.014 0.001 TYR A 999 ARG 0.012 0.000 ARG A1127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.64 seconds wall clock time: 36 minutes 50.40 seconds (2210.40 seconds total)