Starting phenix.real_space_refine (version: dev) on Wed Dec 14 19:26:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/12_2022/7mxy_24076_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/12_2022/7mxy_24076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/12_2022/7mxy_24076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/12_2022/7mxy_24076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/12_2022/7mxy_24076_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/12_2022/7mxy_24076_trim_updated.pdb" } resolution = 2.18 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= -0.000 sd= 0.432 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 22": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22265 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4457 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain: "B" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4433 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "C" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4400 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain: "D" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4446 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "E" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4422 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 11.39, per 1000 atoms: 0.51 Number of scatterers: 22265 At special positions: 0 Unit cell: (87.74, 99.51, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 F 25 9.00 O 1911 8.00 N 1714 7.00 C 7416 6.00 H 11129 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 22.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.801A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 69 Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.916A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 99 Proline residue: A 91 - end of helix removed outlier: 5.167A pdb=" N PHE A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 4.167A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 147 Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.369A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 275 through 290 removed outlier: 5.481A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.605A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 67 Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.835A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 Proline residue: B 91 - end of helix removed outlier: 5.064A pdb=" N PHE B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.821A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 151 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.042A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.843A pdb=" N LYS B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 274 through 291 removed outlier: 5.487A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.602A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 69 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.820A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 100 Proline residue: C 91 - end of helix removed outlier: 5.233A pdb=" N PHE C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.970A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 147 Processing helix chain 'C' and resid 149 through 152 No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 209 through 225 removed outlier: 3.951A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 274 through 288 removed outlier: 6.026A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.716A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.664A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 100 Proline residue: D 91 - end of helix removed outlier: 5.231A pdb=" N PHE D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.971A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 147 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 165 through 178 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.871A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.721A pdb=" N TYR D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 254' Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 274 through 288 removed outlier: 5.953A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.703A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.590A pdb=" N GLU E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 99 Proline residue: E 91 - end of helix removed outlier: 5.020A pdb=" N PHE E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 removed outlier: 4.114A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 152 removed outlier: 4.267A pdb=" N LEU E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.090A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 258 through 270 Processing helix chain 'E' and resid 274 through 288 removed outlier: 5.628A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2223 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: 9.14 Time building geometry restraints manager: 23.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 11089 1.00 - 1.20: 49 1.20 - 1.40: 4971 1.40 - 1.61: 6344 1.61 - 1.81: 100 Bond restraints: 22553 Sorted by residual: bond pdb=" SG CYS D 96 " pdb=" HG CYS D 96 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" SG CYS D 192 " pdb=" HG CYS D 192 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" ND2 ASN E 108 " pdb="HD21 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" ND2 ASN E 108 " pdb="HD22 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" ND2 ASN D 193 " pdb="HD21 ASN D 193 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 22548 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.18: 44 103.18 - 110.39: 21698 110.39 - 117.60: 7385 117.60 - 124.81: 10280 124.81 - 132.02: 1184 Bond angle restraints: 40591 Sorted by residual: angle pdb=" N ILE D 194 " pdb=" CA ILE D 194 " pdb=" C ILE D 194 " ideal model delta sigma weight residual 110.62 102.71 7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" N LEU E 262 " pdb=" CA LEU E 262 " pdb=" C LEU E 262 " ideal model delta sigma weight residual 111.28 106.27 5.01 1.09e+00 8.42e-01 2.12e+01 angle pdb=" N THR D 109 " pdb=" CA THR D 109 " pdb=" CB THR D 109 " ideal model delta sigma weight residual 110.32 116.71 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N GLY E 264 " pdb=" CA GLY E 264 " pdb=" C GLY E 264 " ideal model delta sigma weight residual 112.77 108.12 4.65 1.28e+00 6.10e-01 1.32e+01 angle pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" C PHE D 94 " ideal model delta sigma weight residual 111.28 107.38 3.90 1.09e+00 8.42e-01 1.28e+01 ... (remaining 40586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7993 18.00 - 36.00: 846 36.00 - 54.00: 241 54.00 - 71.99: 50 71.99 - 89.99: 12 Dihedral angle restraints: 9142 sinusoidal: 3864 harmonic: 5278 Sorted by residual: dihedral pdb=" CA PHE C 90 " pdb=" C PHE C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL C 158 " pdb=" C VAL C 158 " pdb=" N HIS C 159 " pdb=" CA HIS C 159 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL E 213 " pdb=" C VAL E 213 " pdb=" N PHE E 214 " pdb=" CA PHE E 214 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 9139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1665 0.078 - 0.155: 81 0.155 - 0.233: 6 0.233 - 0.311: 3 0.311 - 0.388: 2 Chirality restraints: 1757 Sorted by residual: chirality pdb=" CA ASN D 193 " pdb=" N ASN D 193 " pdb=" C ASN D 193 " pdb=" CB ASN D 193 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA THR E 261 " pdb=" N THR E 261 " pdb=" C THR E 261 " pdb=" CB THR E 261 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA THR D 109 " pdb=" N THR D 109 " pdb=" C THR D 109 " pdb=" CB THR D 109 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1754 not shown) Planarity restraints: 3269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 108 " 0.192 2.00e-02 2.50e+03 1.92e-01 5.51e+02 pdb=" CG ASN E 108 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 108 " -0.180 2.00e-02 2.50e+03 pdb=" ND2 ASN E 108 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 108 " -0.272 2.00e-02 2.50e+03 pdb="HD22 ASN E 108 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 193 " 0.180 2.00e-02 2.50e+03 1.79e-01 4.79e+02 pdb=" CG ASN D 193 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 193 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN D 193 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN D 193 " 0.261 2.00e-02 2.50e+03 pdb="HD22 ASN D 193 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 265 " -0.068 2.00e-02 2.50e+03 6.66e-02 6.65e+01 pdb=" CG ASN E 265 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN E 265 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN E 265 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN E 265 " 0.094 2.00e-02 2.50e+03 pdb="HD22 ASN E 265 " -0.094 2.00e-02 2.50e+03 ... (remaining 3266 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1909 2.21 - 2.81: 47886 2.81 - 3.40: 67334 3.40 - 4.00: 90008 4.00 - 4.60: 137907 Nonbonded interactions: 345044 Sorted by model distance: nonbonded pdb=" O ASN B 257 " pdb=" HG1 THR B 261 " model vdw 1.611 1.850 nonbonded pdb=" O THR C 106 " pdb=" HG1 THR C 109 " model vdw 1.628 1.850 nonbonded pdb=" OE1 GLU C 229 " pdb="HD21 ASN C 234 " model vdw 1.634 1.850 nonbonded pdb=" OD1 ASN B 157 " pdb="HD22 ASN B 164 " model vdw 1.638 1.850 nonbonded pdb=" O CYS C 96 " pdb=" HG1 THR C 100 " model vdw 1.659 1.850 ... (remaining 345039 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' and (resid 12 through 289 or resid 1001)) selection = (chain 'B' and (resid 12 through 289 or resid 401)) selection = (chain 'C' and (resid 12 through 289 or resid 401)) selection = (chain 'D' and (resid 12 through 289 or resid 401)) selection = (chain 'E' and (resid 12 through 289 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 70 5.16 5 C 7416 2.51 5 N 1714 2.21 5 O 1911 1.98 5 F 25 1.80 5 H 11129 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.130 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: 0.360 Extract box with map and model: 2.670 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.190 Process input model: 77.530 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 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 : 0.006 0.090 11424 Z= 0.397 Angle : 0.655 8.012 15507 Z= 0.369 Chirality : 0.042 0.388 1757 Planarity : 0.004 0.042 1886 Dihedral : 18.004 89.992 3862 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1396 helix: 1.49 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 373 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 405 average time/residue: 1.1142 time to fit residues: 538.4977 Evaluate side-chains 380 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.2689 time to fit residues: 4.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 35 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11424 Z= 0.205 Angle : 0.500 5.392 15507 Z= 0.279 Chirality : 0.036 0.155 1757 Planarity : 0.003 0.041 1886 Dihedral : 6.201 87.794 1555 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 5.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1396 helix: 1.67 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 365 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 46 residues processed: 402 average time/residue: 1.1220 time to fit residues: 538.3634 Evaluate side-chains 397 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 351 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 30 residues processed: 16 average time/residue: 0.5250 time to fit residues: 13.9736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11424 Z= 0.229 Angle : 0.502 4.957 15507 Z= 0.284 Chirality : 0.036 0.164 1757 Planarity : 0.003 0.040 1886 Dihedral : 5.999 89.270 1555 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 6.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1396 helix: 1.69 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -1.71 (0.34), residues: 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 367 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 43 residues processed: 409 average time/residue: 1.1572 time to fit residues: 561.0120 Evaluate side-chains 399 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 356 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 27 residues processed: 17 average time/residue: 0.8046 time to fit residues: 19.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.2980 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 11424 Z= 0.275 Angle : 0.527 5.195 15507 Z= 0.299 Chirality : 0.038 0.170 1757 Planarity : 0.003 0.040 1886 Dihedral : 5.906 89.986 1555 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 6.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1396 helix: 1.55 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -1.72 (0.34), residues: 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 357 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 51 residues processed: 400 average time/residue: 1.1610 time to fit residues: 551.1356 Evaluate side-chains 405 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 354 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 34 residues processed: 18 average time/residue: 0.7095 time to fit residues: 18.8523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.096 11424 Z= 0.498 Angle : 0.655 5.393 15507 Z= 0.376 Chirality : 0.044 0.178 1757 Planarity : 0.005 0.076 1886 Dihedral : 6.341 88.284 1555 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 7.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.22), residues: 1396 helix: 0.82 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 362 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 54 residues processed: 409 average time/residue: 1.1205 time to fit residues: 547.6134 Evaluate side-chains 410 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 356 time to evaluate : 1.780 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 38 residues processed: 18 average time/residue: 0.5663 time to fit residues: 16.3518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 193 ASN B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 11424 Z= 0.362 Angle : 0.586 6.305 15507 Z= 0.333 Chirality : 0.040 0.170 1757 Planarity : 0.004 0.051 1886 Dihedral : 6.191 86.025 1555 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 6.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.22), residues: 1396 helix: 0.96 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.86 (0.33), residues: 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 362 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 54 residues processed: 410 average time/residue: 1.1081 time to fit residues: 541.7634 Evaluate side-chains 409 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 355 time to evaluate : 1.831 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 41 residues processed: 15 average time/residue: 0.6005 time to fit residues: 14.4318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 overall best weight: 7.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 193 ASN B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 11424 Z= 0.417 Angle : 0.618 5.919 15507 Z= 0.353 Chirality : 0.042 0.173 1757 Planarity : 0.004 0.062 1886 Dihedral : 6.288 85.982 1555 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 7.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.22), residues: 1396 helix: 0.76 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 364 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 61 residues processed: 418 average time/residue: 1.1110 time to fit residues: 555.1384 Evaluate side-chains 418 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 357 time to evaluate : 1.638 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 61 outliers final: 43 residues processed: 20 average time/residue: 1.0877 time to fit residues: 28.1757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 11424 Z= 0.316 Angle : 0.571 6.093 15507 Z= 0.323 Chirality : 0.039 0.167 1757 Planarity : 0.004 0.042 1886 Dihedral : 6.093 84.614 1555 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.22), residues: 1396 helix: 1.07 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -1.81 (0.33), residues: 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 365 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 51 residues processed: 415 average time/residue: 1.1200 time to fit residues: 557.2313 Evaluate side-chains 412 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 361 time to evaluate : 1.825 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 51 outliers final: 41 residues processed: 12 average time/residue: 0.6387 time to fit residues: 12.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 11424 Z= 0.385 Angle : 0.610 6.043 15507 Z= 0.348 Chirality : 0.041 0.172 1757 Planarity : 0.004 0.057 1886 Dihedral : 6.184 84.325 1555 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 5.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.22), residues: 1396 helix: 0.91 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 358 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 53 residues processed: 405 average time/residue: 1.1128 time to fit residues: 539.8629 Evaluate side-chains 407 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 354 time to evaluate : 1.901 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 43 residues processed: 12 average time/residue: 0.5214 time to fit residues: 11.0176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11424 Z= 0.213 Angle : 0.530 6.998 15507 Z= 0.295 Chirality : 0.037 0.161 1757 Planarity : 0.003 0.042 1886 Dihedral : 5.793 81.915 1555 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 5.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1396 helix: 1.42 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 369 time to evaluate : 2.005 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 45 residues processed: 415 average time/residue: 1.1337 time to fit residues: 558.6760 Evaluate side-chains 402 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 357 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 7 average time/residue: 0.9582 time to fit residues: 10.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.232347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.225182 restraints weight = 31341.686| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 0.86 r_work: 0.4592 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4523 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 11424 Z= 0.483 Angle : 0.674 8.262 15507 Z= 0.383 Chirality : 0.044 0.175 1757 Planarity : 0.005 0.069 1886 Dihedral : 6.273 84.203 1555 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.22), residues: 1396 helix: 0.82 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 293 =============================================================================== Job complete usr+sys time: 8847.13 seconds wall clock time: 156 minutes 4.03 seconds (9364.03 seconds total)