Starting phenix.real_space_refine on Thu Apr 11 09:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2024/7mxy_24076_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2024/7mxy_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_24076/04_2024/7mxy_24076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2024/7mxy_24076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2024/7mxy_24076_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2024/7mxy_24076_trim_updated.pdb" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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-5288/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: 10.45, per 1000 atoms: 0.47 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: 20.65 Conformation dependent library (CDL) restraints added in 2.3 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: 3.94 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: 8.74 Time building geometry restraints manager: 21.23 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: 9308 18.00 - 36.00: 883 36.00 - 54.00: 370 54.00 - 71.99: 103 71.99 - 89.99: 12 Dihedral angle restraints: 10676 sinusoidal: 5398 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 10673 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 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: 0.050 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: 1.760 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 77.900 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 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 : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 30.88 % Favored : 65.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 230 PHE 0.019 0.001 PHE E 223 TYR 0.018 0.001 TYR B 228 ARG 0.005 0.001 ARG B 290 *********************** 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 : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8332 (t) REVERT: A 83 VAL cc_start: 0.7988 (t) cc_final: 0.7713 (t) REVERT: B 279 PHE cc_start: 0.7429 (m-80) cc_final: 0.6323 (t80) REVERT: C 258 LEU cc_start: 0.7748 (mt) cc_final: 0.7344 (mt) REVERT: D 261 THR cc_start: 0.7959 (m) cc_final: 0.7748 (m) REVERT: E 158 VAL cc_start: 0.7326 (t) cc_final: 0.7108 (m) REVERT: E 283 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4410 (mt-10) outliers start: 37 outliers final: 27 residues processed: 405 average time/residue: 1.2799 time to fit residues: 609.4445 Evaluate side-chains 383 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU 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: 10.0000 chunk 35 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 overall best weight: 4.9586 ------------------------------------------------------------------------------- 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: 0.6607 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11424 Z= 0.291 Angle : 0.545 5.463 15507 Z= 0.308 Chirality : 0.038 0.161 1757 Planarity : 0.004 0.041 1886 Dihedral : 8.530 86.516 1596 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.93 % Allowed : 28.81 % Favored : 66.26 % 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: 1.14 (0.22), residues: 1396 helix: 1.42 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.016 0.002 TYR C 38 ARG 0.002 0.000 ARG D 27 *********************** 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 413 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 356 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6176 (mt-10) REVERT: B 279 PHE cc_start: 0.7498 (m-80) cc_final: 0.6363 (t80) REVERT: C 23 GLU cc_start: 0.6977 (mp0) cc_final: 0.6753 (mp0) REVERT: E 158 VAL cc_start: 0.7334 (t) cc_final: 0.7117 (m) REVERT: E 173 ILE cc_start: 0.8431 (mm) cc_final: 0.7944 (mt) REVERT: E 283 GLU cc_start: 0.5373 (OUTLIER) cc_final: 0.4497 (mt-10) outliers start: 57 outliers final: 41 residues processed: 390 average time/residue: 1.3383 time to fit residues: 609.6788 Evaluate side-chains 391 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 348 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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 164 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS E 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11424 Z= 0.352 Angle : 0.575 5.363 15507 Z= 0.328 Chirality : 0.040 0.176 1757 Planarity : 0.004 0.051 1886 Dihedral : 7.930 88.372 1582 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 7.01 % Allowed : 26.73 % Favored : 66.26 % 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: 0.84 (0.22), residues: 1396 helix: 1.19 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.020 0.002 TYR D 138 ARG 0.002 0.000 ARG E 74 *********************** 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 434 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 353 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7406 (mmt) cc_final: 0.7120 (mmm) REVERT: A 95 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6718 (mpp) REVERT: B 118 GLU cc_start: 0.5303 (mm-30) cc_final: 0.5033 (mm-30) REVERT: B 175 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6214 (mt-10) REVERT: B 279 PHE cc_start: 0.7555 (m-80) cc_final: 0.6351 (t80) REVERT: C 23 GLU cc_start: 0.7012 (mp0) cc_final: 0.6772 (mp0) REVERT: C 86 TYR cc_start: 0.7928 (t80) cc_final: 0.7383 (t80) REVERT: E 86 TYR cc_start: 0.7769 (t80) cc_final: 0.7250 (t80) REVERT: E 158 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7133 (m) REVERT: E 283 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.4570 (mt-10) outliers start: 81 outliers final: 54 residues processed: 400 average time/residue: 1.4091 time to fit residues: 664.5626 Evaluate side-chains 406 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 348 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.6623 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11424 Z= 0.300 Angle : 0.543 5.304 15507 Z= 0.309 Chirality : 0.038 0.170 1757 Planarity : 0.004 0.042 1886 Dihedral : 7.754 87.231 1582 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 7.01 % Allowed : 26.99 % Favored : 66.00 % 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: 0.94 (0.22), residues: 1396 helix: 1.27 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.81 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 284 PHE 0.020 0.002 PHE E 223 TYR 0.018 0.002 TYR D 236 ARG 0.002 0.000 ARG B 290 *********************** 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 441 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 360 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7960 (pttm) cc_final: 0.7673 (pttp) REVERT: A 81 MET cc_start: 0.7429 (mmt) cc_final: 0.7048 (mmm) REVERT: A 95 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6721 (mpp) REVERT: B 175 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6184 (mt-10) REVERT: B 279 PHE cc_start: 0.7571 (m-80) cc_final: 0.6340 (t80) REVERT: C 23 GLU cc_start: 0.6888 (mp0) cc_final: 0.6499 (mp0) REVERT: C 86 TYR cc_start: 0.7974 (t80) cc_final: 0.7426 (t80) REVERT: C 163 LYS cc_start: 0.7260 (mptt) cc_final: 0.6952 (mptp) REVERT: C 201 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: D 289 GLU cc_start: 0.4267 (OUTLIER) cc_final: 0.3987 (tt0) REVERT: E 86 TYR cc_start: 0.7802 (t80) cc_final: 0.7279 (t80) REVERT: E 158 VAL cc_start: 0.7333 (OUTLIER) cc_final: 0.7112 (m) REVERT: E 173 ILE cc_start: 0.8433 (mm) cc_final: 0.7980 (mt) REVERT: E 283 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4656 (mt-10) outliers start: 81 outliers final: 55 residues processed: 408 average time/residue: 1.3379 time to fit residues: 637.3749 Evaluate side-chains 417 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 356 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 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: 8.1588 ------------------------------------------------------------------------------- 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: 0.6666 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 11424 Z= 0.443 Angle : 0.622 5.464 15507 Z= 0.357 Chirality : 0.042 0.176 1757 Planarity : 0.004 0.067 1886 Dihedral : 7.942 85.777 1581 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 7.27 % Allowed : 26.73 % Favored : 66.00 % 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: 0.40 (0.22), residues: 1396 helix: 0.87 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.020 0.002 TYR D 236 ARG 0.005 0.001 ARG B 290 *********************** 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 446 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 362 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7964 (pttm) cc_final: 0.7677 (pttp) REVERT: A 81 MET cc_start: 0.7439 (mmt) cc_final: 0.7081 (mmm) REVERT: A 95 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6773 (mpp) REVERT: B 175 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: B 223 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7531 (t80) REVERT: B 279 PHE cc_start: 0.7562 (m-80) cc_final: 0.6375 (t80) REVERT: C 23 GLU cc_start: 0.6978 (mp0) cc_final: 0.6621 (mp0) REVERT: C 86 TYR cc_start: 0.8131 (t80) cc_final: 0.7484 (t80) REVERT: C 201 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: E 86 TYR cc_start: 0.7942 (t80) cc_final: 0.7372 (t80) REVERT: E 158 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7109 (m) REVERT: E 173 ILE cc_start: 0.8461 (mm) cc_final: 0.7993 (mt) REVERT: E 283 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4352 (mm-30) outliers start: 84 outliers final: 60 residues processed: 411 average time/residue: 1.2892 time to fit residues: 621.3605 Evaluate side-chains 419 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 353 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU 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: 10.0000 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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 D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11424 Z= 0.272 Angle : 0.536 5.197 15507 Z= 0.304 Chirality : 0.038 0.164 1757 Planarity : 0.004 0.038 1886 Dihedral : 7.583 82.942 1579 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.75 % Allowed : 28.03 % Favored : 65.22 % 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: 0.89 (0.22), residues: 1396 helix: 1.22 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 284 PHE 0.020 0.001 PHE E 223 TYR 0.018 0.002 TYR D 138 ARG 0.002 0.000 ARG D 27 *********************** 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 442 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 364 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7951 (pttm) cc_final: 0.7663 (pttp) REVERT: A 81 MET cc_start: 0.7438 (mmt) cc_final: 0.7173 (mmm) REVERT: A 95 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6739 (mpp) REVERT: B 175 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6160 (mt-10) REVERT: B 223 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7316 (t80) REVERT: B 279 PHE cc_start: 0.7491 (m-80) cc_final: 0.6354 (t80) REVERT: C 23 GLU cc_start: 0.6766 (mp0) cc_final: 0.6418 (mp0) REVERT: C 86 TYR cc_start: 0.8138 (t80) cc_final: 0.7557 (t80) REVERT: C 201 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: D 289 GLU cc_start: 0.4272 (OUTLIER) cc_final: 0.3995 (tt0) REVERT: E 86 TYR cc_start: 0.7975 (t80) cc_final: 0.7395 (t80) REVERT: E 158 VAL cc_start: 0.7322 (t) cc_final: 0.7111 (m) REVERT: E 283 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4673 (mt-10) outliers start: 78 outliers final: 51 residues processed: 411 average time/residue: 1.4209 time to fit residues: 689.3020 Evaluate side-chains 412 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 355 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 overall best weight: 3.5184 ------------------------------------------------------------------------------- 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 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: 0.6601 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11424 Z= 0.238 Angle : 0.524 5.022 15507 Z= 0.295 Chirality : 0.037 0.160 1757 Planarity : 0.003 0.039 1886 Dihedral : 7.278 82.741 1578 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.88 % Allowed : 28.55 % Favored : 65.57 % 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: 1.16 (0.22), residues: 1396 helix: 1.43 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 284 PHE 0.020 0.001 PHE E 223 TYR 0.016 0.001 TYR D 236 ARG 0.003 0.000 ARG D 27 *********************** 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 438 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 370 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7941 (pttm) cc_final: 0.7657 (pttp) REVERT: A 81 MET cc_start: 0.7407 (mmt) cc_final: 0.7167 (mmm) REVERT: A 83 VAL cc_start: 0.8126 (t) cc_final: 0.7919 (t) REVERT: A 95 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6609 (mpp) REVERT: B 223 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7407 (t80) REVERT: B 279 PHE cc_start: 0.7471 (m-80) cc_final: 0.6330 (t80) REVERT: C 23 GLU cc_start: 0.6697 (mp0) cc_final: 0.6309 (mp0) REVERT: C 86 TYR cc_start: 0.8155 (t80) cc_final: 0.7555 (t80) REVERT: C 163 LYS cc_start: 0.7220 (mptt) cc_final: 0.6967 (mptp) REVERT: C 201 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: E 86 TYR cc_start: 0.7952 (t80) cc_final: 0.7372 (t80) REVERT: E 158 VAL cc_start: 0.7372 (t) cc_final: 0.7154 (m) outliers start: 68 outliers final: 49 residues processed: 408 average time/residue: 1.2935 time to fit residues: 618.7103 Evaluate side-chains 410 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 358 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU 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: 4.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** 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: 0.6619 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11424 Z= 0.292 Angle : 0.554 6.257 15507 Z= 0.313 Chirality : 0.038 0.164 1757 Planarity : 0.004 0.041 1886 Dihedral : 6.964 84.448 1573 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 6.06 % Allowed : 29.07 % Favored : 64.88 % 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: 1.05 (0.22), residues: 1396 helix: 1.35 (0.15), residues: 1105 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.019 0.002 TYR B 286 ARG 0.002 0.000 ARG D 27 *********************** 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 430 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 360 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7940 (pttm) cc_final: 0.7658 (pttp) REVERT: A 81 MET cc_start: 0.7427 (mmt) cc_final: 0.7194 (mmm) REVERT: A 95 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6690 (mpp) REVERT: B 223 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7477 (t80) REVERT: B 258 LEU cc_start: 0.7426 (mt) cc_final: 0.7213 (mt) REVERT: B 279 PHE cc_start: 0.7501 (m-80) cc_final: 0.6353 (t80) REVERT: C 23 GLU cc_start: 0.6767 (mp0) cc_final: 0.6380 (mp0) REVERT: C 86 TYR cc_start: 0.8211 (t80) cc_final: 0.7571 (t80) REVERT: C 163 LYS cc_start: 0.7250 (mptt) cc_final: 0.6983 (mptp) REVERT: C 201 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: D 289 GLU cc_start: 0.4265 (OUTLIER) cc_final: 0.4011 (tt0) REVERT: E 86 TYR cc_start: 0.7981 (t80) cc_final: 0.7394 (t80) REVERT: E 158 VAL cc_start: 0.7317 (t) cc_final: 0.7094 (m) outliers start: 70 outliers final: 52 residues processed: 401 average time/residue: 1.2948 time to fit residues: 608.9973 Evaluate side-chains 413 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 357 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU 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: 0.5980 chunk 124 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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: 0.6628 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11424 Z= 0.320 Angle : 0.566 5.696 15507 Z= 0.321 Chirality : 0.039 0.167 1757 Planarity : 0.004 0.047 1886 Dihedral : 7.025 85.146 1573 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.31 % Allowed : 28.89 % Favored : 64.79 % 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: 0.94 (0.22), residues: 1396 helix: 1.26 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 284 PHE 0.020 0.002 PHE E 223 TYR 0.018 0.002 TYR D 236 ARG 0.002 0.000 ARG B 290 *********************** 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 432 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 359 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7951 (pttm) cc_final: 0.7674 (pttp) REVERT: A 81 MET cc_start: 0.7439 (mmt) cc_final: 0.7135 (mmm) REVERT: A 83 VAL cc_start: 0.8150 (t) cc_final: 0.7944 (t) REVERT: A 95 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6714 (mpp) REVERT: B 223 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 279 PHE cc_start: 0.7537 (m-80) cc_final: 0.6367 (t80) REVERT: C 23 GLU cc_start: 0.6790 (mp0) cc_final: 0.6485 (mp0) REVERT: C 86 TYR cc_start: 0.8242 (t80) cc_final: 0.7609 (t80) REVERT: C 163 LYS cc_start: 0.7260 (mptt) cc_final: 0.6993 (mptp) REVERT: C 201 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: D 22 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: D 289 GLU cc_start: 0.4139 (OUTLIER) cc_final: 0.3883 (tt0) REVERT: E 86 TYR cc_start: 0.8012 (t80) cc_final: 0.7433 (t80) REVERT: E 158 VAL cc_start: 0.7329 (t) cc_final: 0.7096 (m) outliers start: 73 outliers final: 55 residues processed: 401 average time/residue: 1.3104 time to fit residues: 614.7209 Evaluate side-chains 415 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 355 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11424 Z= 0.226 Angle : 0.522 6.565 15507 Z= 0.293 Chirality : 0.037 0.162 1757 Planarity : 0.003 0.039 1886 Dihedral : 6.728 78.606 1573 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.93 % Allowed : 30.28 % Favored : 64.79 % 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: 1.29 (0.22), residues: 1396 helix: 1.50 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 284 PHE 0.020 0.001 PHE E 223 TYR 0.022 0.001 TYR B 286 ARG 0.002 0.000 ARG D 27 ********************** 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 421 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 364 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7401 (mmt) cc_final: 0.7163 (mmm) REVERT: A 83 VAL cc_start: 0.8137 (t) cc_final: 0.7926 (t) REVERT: A 122 LYS cc_start: 0.5862 (OUTLIER) cc_final: 0.5559 (mptt) REVERT: B 223 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 279 PHE cc_start: 0.7468 (m-80) cc_final: 0.6337 (t80) REVERT: C 23 GLU cc_start: 0.6678 (mp0) cc_final: 0.6324 (mp0) REVERT: C 86 TYR cc_start: 0.8224 (t80) cc_final: 0.7563 (t80) REVERT: C 201 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: D 95 MET cc_start: 0.6768 (tpp) cc_final: 0.6473 (mmm) REVERT: D 289 GLU cc_start: 0.4216 (OUTLIER) cc_final: 0.3949 (tt0) REVERT: E 86 TYR cc_start: 0.7996 (t80) cc_final: 0.7390 (t80) REVERT: E 158 VAL cc_start: 0.7311 (t) cc_final: 0.7098 (m) outliers start: 57 outliers final: 47 residues processed: 398 average time/residue: 1.3242 time to fit residues: 620.5719 Evaluate side-chains 408 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 357 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.244867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.236310 restraints weight = 33127.689| |-----------------------------------------------------------------------------| r_work (start): 0.4663 rms_B_bonded: 0.81 r_work: 0.4614 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.4546 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11424 Z= 0.380 Angle : 0.603 5.910 15507 Z= 0.344 Chirality : 0.041 0.172 1757 Planarity : 0.004 0.060 1886 Dihedral : 6.920 79.315 1570 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.45 % Allowed : 30.28 % Favored : 64.27 % 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: 0.71 (0.22), residues: 1396 helix: 1.09 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 284 PHE 0.021 0.002 PHE A 202 TYR 0.019 0.002 TYR D 236 ARG 0.004 0.000 ARG B 290 =============================================================================== Job complete usr+sys time: 9604.53 seconds wall clock time: 171 minutes 13.37 seconds (10273.37 seconds total)