Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 16:07:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/04_2023/7s06_24785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/04_2023/7s06_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_24785/04_2023/7s06_24785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/04_2023/7s06_24785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/04_2023/7s06_24785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s06_24785/04_2023/7s06_24785.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.22, per 1000 atoms: 0.54 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: 3.17 Conformation dependent library (CDL) restraints added in 947.9 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: 0.50 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: 2.21 Time building geometry restraints manager: 3.45 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 - 17.98: 4227 17.98 - 35.96: 428 35.96 - 53.93: 79 53.93 - 71.91: 11 71.91 - 89.89: 12 Dihedral angle restraints: 4757 sinusoidal: 2019 harmonic: 2738 Sorted by residual: dihedral pdb=" CA ARG B1127 " pdb=" C ARG B1127 " pdb=" N THR B1128 " pdb=" CA THR B1128 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG A1127 " pdb=" C ARG A1127 " pdb=" N THR A1128 " pdb=" CA THR A1128 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA THR B 918 " pdb=" C THR B 918 " pdb=" N ASP B 919 " pdb=" CA ASP B 919 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1078 0.072 - 0.145: 118 0.145 - 0.217: 7 0.217 - 0.289: 2 0.289 - 0.362: 3 Chirality restraints: 1208 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 376 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.24e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 376 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1205 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 922 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C ASN A 922 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 922 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG A 923 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 922 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN B 922 " 0.070 2.00e-02 2.50e+03 pdb=" O ASN B 922 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG B 923 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 995 " 0.014 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE B 995 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 995 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 995 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 995 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 995 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 995 " -0.006 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 555 2.74 - 3.28: 7900 3.28 - 3.82: 12910 3.82 - 4.36: 15027 4.36 - 4.90: 25810 Nonbonded interactions: 62202 Sorted by model distance: nonbonded pdb=" O LEU A1025 " pdb=" OH TYR A1078 " model vdw 2.199 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: 0.700 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: 4.170 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 22.830 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- 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 : 15.060 89.888 2962 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.905 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1972 time to fit residues: 51.2035 Evaluate side-chains 107 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4094 ------------------------------------------------------------------------------- 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: 0.8980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7579 moved from start: 0.1790 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= 0.206 Angle : 0.603 8.319 10882 Z= 0.309 Chirality : 0.047 0.293 1208 Planarity : 0.003 0.036 1388 Dihedral : 4.216 21.807 1002 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.29), residues: 898 helix: 1.90 (0.25), residues: 414 sheet: 0.68 (0.55), residues: 94 loop : -0.87 (0.34), residues: 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.908 Fit side-chains outliers start: 29 outliers final: 22 residues processed: 141 average time/residue: 0.1655 time to fit residues: 33.6495 Evaluate side-chains 122 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0732 time to fit residues: 4.2402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 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: 3.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8050 Z= 0.231 Angle : 0.588 8.168 10882 Z= 0.298 Chirality : 0.047 0.280 1208 Planarity : 0.003 0.035 1388 Dihedral : 4.201 22.280 1002 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.25), residues: 414 sheet: 0.22 (0.52), residues: 98 loop : -0.91 (0.34), residues: 386 *********************** 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 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.982 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.1755 time to fit residues: 28.0837 Evaluate side-chains 104 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0944 time to fit residues: 2.9835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.0020 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.3570 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8050 Z= 0.254 Angle : 0.587 7.859 10882 Z= 0.296 Chirality : 0.047 0.275 1208 Planarity : 0.003 0.035 1388 Dihedral : 4.273 23.468 1002 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.29), residues: 898 helix: 1.97 (0.26), residues: 402 sheet: -0.14 (0.52), residues: 98 loop : -0.95 (0.33), residues: 398 *********************** 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 122 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.862 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 119 average time/residue: 0.1844 time to fit residues: 31.1772 Evaluate side-chains 100 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0792 time to fit residues: 2.2221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- 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 983 HIS B1156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8050 Z= 0.250 Angle : 0.584 7.747 10882 Z= 0.295 Chirality : 0.047 0.270 1208 Planarity : 0.003 0.035 1388 Dihedral : 4.258 22.657 1002 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.29), residues: 898 helix: 1.96 (0.26), residues: 402 sheet: -0.32 (0.52), residues: 98 loop : -1.08 (0.32), residues: 398 *********************** 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 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.879 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 116 average time/residue: 0.2196 time to fit residues: 34.5824 Evaluate side-chains 104 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0774 time to fit residues: 2.4491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8050 Z= 0.179 Angle : 0.593 14.242 10882 Z= 0.290 Chirality : 0.047 0.271 1208 Planarity : 0.004 0.038 1388 Dihedral : 4.162 23.031 1002 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.50 % 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: 0.70 (0.29), residues: 898 helix: 2.02 (0.26), residues: 402 sheet: -0.25 (0.53), residues: 98 loop : -1.01 (0.32), residues: 398 *********************** 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 113 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.957 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 110 average time/residue: 0.2254 time to fit residues: 33.5528 Evaluate side-chains 100 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0779 time to fit residues: 2.1869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.0030 chunk 54 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8050 Z= 0.162 Angle : 0.589 9.802 10882 Z= 0.293 Chirality : 0.046 0.258 1208 Planarity : 0.003 0.038 1388 Dihedral : 4.060 24.052 1002 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.46 % 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: 2.12 (0.25), residues: 414 sheet: -0.04 (0.53), residues: 96 loop : -1.04 (0.33), residues: 388 *********************** 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 106 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.981 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 104 average time/residue: 0.2289 time to fit residues: 32.2112 Evaluate side-chains 96 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0740 time to fit residues: 1.4403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8050 Z= 0.179 Angle : 0.594 9.848 10882 Z= 0.294 Chirality : 0.046 0.261 1208 Planarity : 0.003 0.039 1388 Dihedral : 4.007 23.607 1002 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.46 % 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: 0.91 (0.29), residues: 898 helix: 2.17 (0.25), residues: 414 sheet: -0.03 (0.53), residues: 96 loop : -1.00 (0.33), residues: 388 *********************** 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 111 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.843 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 108 average time/residue: 0.2155 time to fit residues: 31.5348 Evaluate side-chains 98 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8050 Z= 0.189 Angle : 0.611 10.280 10882 Z= 0.301 Chirality : 0.046 0.260 1208 Planarity : 0.003 0.041 1388 Dihedral : 4.011 24.421 1002 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 1.04 % 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: 0.94 (0.29), residues: 898 helix: 2.20 (0.26), residues: 414 sheet: -0.04 (0.53), residues: 96 loop : -0.98 (0.33), residues: 388 *********************** 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 111 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.880 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 108 average time/residue: 0.2148 time to fit residues: 31.6256 Evaluate side-chains 102 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0718 time to fit residues: 1.7620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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** B1156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8050 Z= 0.207 Angle : 0.636 14.682 10882 Z= 0.311 Chirality : 0.047 0.261 1208 Planarity : 0.004 0.040 1388 Dihedral : 4.046 23.317 1002 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.23 % 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: 0.90 (0.29), residues: 898 helix: 2.15 (0.25), residues: 414 sheet: -0.04 (0.53), residues: 96 loop : -0.99 (0.33), residues: 388 ********************** 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 105 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.948 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.2108 time to fit residues: 29.8710 Evaluate side-chains 100 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0760 time to fit residues: 1.4818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** B 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.186666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127966 restraints weight = 9627.350| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.70 r_work: 0.3305 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8050 Z= 0.182 Angle : 0.612 10.101 10882 Z= 0.302 Chirality : 0.046 0.257 1208 Planarity : 0.003 0.041 1388 Dihedral : 3.996 22.774 1002 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.35 % 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: 0.92 (0.29), residues: 898 helix: 2.04 (0.25), residues: 426 sheet: -0.03 (0.53), residues: 96 loop : -0.92 (0.33), residues: 376 =============================================================================== Job complete usr+sys time: 1861.42 seconds wall clock time: 34 minutes 34.60 seconds (2074.60 seconds total)