Starting phenix.real_space_refine on Thu Mar 14 08:12:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/03_2024/8ibn_35344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/03_2024/8ibn_35344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/03_2024/8ibn_35344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/03_2024/8ibn_35344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/03_2024/8ibn_35344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/03_2024/8ibn_35344_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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 K 4 8.98 5 P 12 5.49 5 S 44 5.16 5 C 5520 2.51 5 N 1552 2.21 5 O 1808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 122": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8940 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "B" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "D" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8940 At special positions: 0 Unit cell: (65.1672, 58.9608, 202.742, 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) K 4 19.00 S 44 16.00 P 12 15.00 O 1808 8.00 N 1552 7.00 C 5520 6.00 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 37.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 85 through 91 removed outlier: 3.765A pdb=" N ALA A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.669A pdb=" N PHE A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.649A pdb=" N MET A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 272 through 282 Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.723A pdb=" N MET B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.776A pdb=" N ALA B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.918A pdb=" N ALA B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.928A pdb=" N PHE B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 201 removed outlier: 4.151A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 272 through 281 removed outlier: 4.016A pdb=" N THR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 29 removed outlier: 3.831A pdb=" N HIS C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.531A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.712A pdb=" N ALA C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 removed outlier: 3.909A pdb=" N ALA C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix Processing helix chain 'C' and resid 142 through 154 removed outlier: 3.806A pdb=" N THR C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 178 through 201 removed outlier: 3.500A pdb=" N ALA C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 272 through 280 Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.736A pdb=" N MET D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.763A pdb=" N ALA D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 122 removed outlier: 3.911A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 141 through 154 removed outlier: 3.976A pdb=" N PHE D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 178 through 201 removed outlier: 4.026A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 removed outlier: 4.120A pdb=" N THR D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 216 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET D 217 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU D 219 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 244 Processing helix chain 'D' and resid 272 through 283 removed outlier: 3.613A pdb=" N VAL D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.519A pdb=" N ILE A 13 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE A 40 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 15 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 42 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 17 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 126 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 100 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 128 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER A 159 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 131 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 161 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 225 through 230 removed outlier: 6.898A pdb=" N THR A 291 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N VAL A 262 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 293 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 37 through 42 removed outlier: 6.670A pdb=" N ILE B 13 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE B 40 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 15 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 42 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY B 17 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 126 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE B 100 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL B 128 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER B 159 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 131 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 161 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.540A pdb=" N GLY B 226 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR B 291 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N VAL B 262 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 293 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE B 264 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.952A pdb=" N SER C 159 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS C 14 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ALA C 101 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 16 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 225 through 230 removed outlier: 6.881A pdb=" N THR C 291 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N VAL C 262 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 293 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE C 264 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.929A pdb=" N SER D 159 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 98 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL D 130 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 100 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS D 14 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ALA D 101 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 16 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLY D 226 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR D 291 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL D 262 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 293 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE D 264 " --> pdb=" O VAL D 293 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3123 1.34 - 1.46: 1549 1.46 - 1.58: 4236 1.58 - 1.70: 20 1.70 - 1.81: 96 Bond restraints: 9024 Sorted by residual: bond pdb=" O3B G2P B 401 " pdb=" PG G2P B 401 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O3B G2P C 401 " pdb=" PG G2P C 401 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" O3B G2P D 401 " pdb=" PG G2P D 401 " ideal model delta sigma weight residual 1.716 1.609 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3B G2P A 401 " pdb=" PG G2P A 401 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1B G2P A 401 " pdb=" PB G2P A 401 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.98: 148 105.98 - 113.39: 5096 113.39 - 120.80: 4015 120.80 - 128.21: 2945 128.21 - 135.62: 24 Bond angle restraints: 12228 Sorted by residual: angle pdb=" C VAL D 30 " pdb=" N ARG D 31 " pdb=" CA ARG D 31 " ideal model delta sigma weight residual 123.91 131.28 -7.37 1.66e+00 3.63e-01 1.97e+01 angle pdb=" C3A G2P D 401 " pdb=" PA G2P D 401 " pdb=" O5' G2P D 401 " ideal model delta sigma weight residual 99.14 111.06 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C3A G2P C 401 " pdb=" PA G2P C 401 " pdb=" O5' G2P C 401 " ideal model delta sigma weight residual 99.14 110.99 -11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C VAL A 30 " pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 125.66 132.92 -7.26 1.85e+00 2.92e-01 1.54e+01 angle pdb=" C3A G2P B 401 " pdb=" PA G2P B 401 " pdb=" O5' G2P B 401 " ideal model delta sigma weight residual 99.14 110.59 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4908 17.90 - 35.80: 452 35.80 - 53.70: 71 53.70 - 71.60: 10 71.60 - 89.49: 15 Dihedral angle restraints: 5456 sinusoidal: 2112 harmonic: 3344 Sorted by residual: dihedral pdb=" CA LEU B 205 " pdb=" C LEU B 205 " pdb=" N MET B 206 " pdb=" CA MET B 206 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 205 " pdb=" C LEU A 205 " pdb=" N MET A 206 " pdb=" CA MET A 206 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU C 205 " pdb=" C LEU C 205 " pdb=" N MET C 206 " pdb=" CA MET C 206 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1208 0.072 - 0.144: 238 0.144 - 0.215: 8 0.215 - 0.287: 0 0.287 - 0.359: 2 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE A 16 " pdb=" CA ILE A 16 " pdb=" CG1 ILE A 16 " pdb=" CG2 ILE A 16 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1453 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 202 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 203 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 145 " 0.017 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE A 145 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 145 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 145 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 202 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ARG A 202 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG A 202 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 203 " 0.011 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 3160 2.86 - 3.43: 9534 3.43 - 4.00: 16328 4.00 - 4.57: 22058 4.57 - 5.14: 32285 Nonbonded interactions: 83365 Sorted by model distance: nonbonded pdb=" O1B G2P B 401 " pdb=" O2A G2P B 401 " model vdw 2.296 3.040 nonbonded pdb=" O1B G2P C 401 " pdb=" O2A G2P C 401 " model vdw 2.301 3.040 nonbonded pdb=" O ARG A 202 " pdb=" K K A 402 " model vdw 2.303 2.850 nonbonded pdb=" O ARG C 202 " pdb=" K K C 402 " model vdw 2.303 2.850 nonbonded pdb=" O ARG B 202 " pdb=" K K B 402 " model vdw 2.304 2.850 ... (remaining 83360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.050 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.410 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 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 : 0.007 0.108 9024 Z= 0.463 Angle : 0.990 11.922 12228 Z= 0.458 Chirality : 0.055 0.359 1456 Planarity : 0.005 0.090 1604 Dihedral : 14.424 89.494 3336 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -1.98 (0.21), residues: 1216 helix: -2.12 (0.18), residues: 432 sheet: 1.00 (0.36), residues: 248 loop : -1.68 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 28 PHE 0.039 0.003 PHE A 145 TYR 0.006 0.001 TYR D 222 ARG 0.004 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.999 Fit side-chains REVERT: B 104 MET cc_start: 0.5212 (mtp) cc_final: 0.4643 (mmm) REVERT: B 209 ASP cc_start: 0.6687 (m-30) cc_final: 0.6462 (m-30) REVERT: D 29 MET cc_start: 0.3931 (mtt) cc_final: 0.3643 (mtt) REVERT: D 242 MET cc_start: 0.7492 (tpp) cc_final: 0.7243 (tpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1587 time to fit residues: 31.6121 Evaluate side-chains 108 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN B 24 ASN C 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5228 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9024 Z= 0.172 Angle : 0.515 5.504 12228 Z= 0.276 Chirality : 0.047 0.180 1456 Planarity : 0.004 0.056 1604 Dihedral : 8.331 79.762 1412 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.78 % Allowed : 10.16 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1216 helix: -0.64 (0.24), residues: 408 sheet: 0.69 (0.32), residues: 292 loop : -1.46 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 156 PHE 0.027 0.002 PHE C 145 TYR 0.004 0.001 TYR D 222 ARG 0.004 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.025 Fit side-chains REVERT: B 104 MET cc_start: 0.5144 (mtp) cc_final: 0.4781 (mmm) outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 0.1650 time to fit residues: 27.0384 Evaluate side-chains 109 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 0.0470 chunk 117 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5264 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9024 Z= 0.181 Angle : 0.497 5.756 12228 Z= 0.265 Chirality : 0.046 0.165 1456 Planarity : 0.003 0.049 1604 Dihedral : 7.706 81.401 1412 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.34 % Allowed : 14.62 % Favored : 84.04 % 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: -0.83 (0.23), residues: 1216 helix: -0.26 (0.25), residues: 412 sheet: 0.77 (0.32), residues: 288 loop : -1.54 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 156 PHE 0.024 0.002 PHE A 145 TYR 0.005 0.001 TYR D 222 ARG 0.004 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: B 104 MET cc_start: 0.5084 (mtp) cc_final: 0.4819 (mmm) REVERT: B 302 MET cc_start: 0.3427 (ppp) cc_final: 0.3015 (ptt) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.1555 time to fit residues: 27.4443 Evaluate side-chains 112 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN B 165 ASN C 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5281 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9024 Z= 0.177 Angle : 0.494 5.706 12228 Z= 0.263 Chirality : 0.046 0.155 1456 Planarity : 0.003 0.053 1604 Dihedral : 7.486 81.050 1412 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.79 % Allowed : 17.41 % Favored : 80.80 % 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: -0.64 (0.23), residues: 1216 helix: 0.04 (0.26), residues: 416 sheet: 0.68 (0.32), residues: 292 loop : -1.45 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 156 PHE 0.021 0.002 PHE A 145 TYR 0.004 0.001 TYR D 222 ARG 0.004 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 225 MET cc_start: 0.7014 (ptm) cc_final: 0.6766 (ptp) REVERT: B 104 MET cc_start: 0.5116 (mtp) cc_final: 0.4851 (mmm) REVERT: D 29 MET cc_start: 0.4293 (mtt) cc_final: 0.3772 (mtt) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.1765 time to fit residues: 31.0069 Evaluate side-chains 118 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN C 280 ASN D 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9024 Z= 0.149 Angle : 0.466 5.750 12228 Z= 0.248 Chirality : 0.045 0.143 1456 Planarity : 0.003 0.051 1604 Dihedral : 7.310 83.326 1412 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.01 % Allowed : 18.86 % Favored : 79.13 % 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 (0.23), residues: 1216 helix: 0.36 (0.26), residues: 416 sheet: 0.76 (0.31), residues: 292 loop : -1.39 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 156 PHE 0.019 0.002 PHE A 145 TYR 0.003 0.001 TYR D 222 ARG 0.006 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: B 104 MET cc_start: 0.4939 (mtp) cc_final: 0.4738 (mmm) REVERT: D 29 MET cc_start: 0.4303 (mtt) cc_final: 0.3881 (mtt) REVERT: D 220 MET cc_start: 0.3497 (mmt) cc_final: 0.2074 (ttm) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.1664 time to fit residues: 31.2574 Evaluate side-chains 120 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9024 Z= 0.217 Angle : 0.540 6.381 12228 Z= 0.284 Chirality : 0.047 0.159 1456 Planarity : 0.003 0.051 1604 Dihedral : 7.487 79.503 1412 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.46 % Allowed : 20.31 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1216 helix: 0.13 (0.26), residues: 424 sheet: 0.60 (0.31), residues: 292 loop : -1.43 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 156 PHE 0.023 0.002 PHE D 145 TYR 0.007 0.001 TYR D 222 ARG 0.005 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: C 34 ILE cc_start: 0.4494 (mm) cc_final: 0.3749 (mt) REVERT: C 258 ARG cc_start: 0.6282 (mmp-170) cc_final: 0.6054 (mmt180) REVERT: C 292 VAL cc_start: 0.7582 (t) cc_final: 0.7325 (t) REVERT: D 29 MET cc_start: 0.4378 (mtt) cc_final: 0.4008 (mtt) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.1728 time to fit residues: 31.8103 Evaluate side-chains 125 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 0.2980 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5270 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9024 Z= 0.151 Angle : 0.487 9.575 12228 Z= 0.258 Chirality : 0.046 0.155 1456 Planarity : 0.003 0.057 1604 Dihedral : 7.242 84.090 1412 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.68 % Allowed : 20.87 % Favored : 76.45 % 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: -0.39 (0.23), residues: 1216 helix: 0.39 (0.27), residues: 416 sheet: 0.73 (0.31), residues: 292 loop : -1.39 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 156 PHE 0.018 0.001 PHE A 145 TYR 0.004 0.001 TYR D 222 ARG 0.006 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.5509 (mt) cc_final: 0.5066 (mt) REVERT: C 258 ARG cc_start: 0.6227 (mmp-170) cc_final: 0.6021 (mmt180) REVERT: C 292 VAL cc_start: 0.7505 (t) cc_final: 0.7289 (t) REVERT: D 29 MET cc_start: 0.4374 (mtt) cc_final: 0.3926 (mtt) outliers start: 24 outliers final: 15 residues processed: 121 average time/residue: 0.1611 time to fit residues: 29.3698 Evaluate side-chains 118 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.0170 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5225 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9024 Z= 0.141 Angle : 0.481 8.589 12228 Z= 0.250 Chirality : 0.045 0.141 1456 Planarity : 0.004 0.079 1604 Dihedral : 6.980 89.765 1412 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.79 % Allowed : 22.10 % Favored : 76.12 % 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: -0.11 (0.24), residues: 1216 helix: 0.66 (0.27), residues: 412 sheet: 0.85 (0.32), residues: 284 loop : -1.19 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 28 PHE 0.017 0.001 PHE A 145 TYR 0.003 0.001 TYR A 222 ARG 0.005 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.5329 (mt) cc_final: 0.4964 (mt) REVERT: B 303 ASN cc_start: 0.4959 (p0) cc_final: 0.4651 (m-40) REVERT: C 97 MET cc_start: 0.5649 (tpt) cc_final: 0.5421 (tpt) REVERT: C 292 VAL cc_start: 0.7370 (t) cc_final: 0.7154 (t) REVERT: D 29 MET cc_start: 0.4356 (mtt) cc_final: 0.4015 (mtt) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.1795 time to fit residues: 31.5675 Evaluate side-chains 115 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9024 Z= 0.175 Angle : 0.523 8.351 12228 Z= 0.269 Chirality : 0.046 0.167 1456 Planarity : 0.004 0.070 1604 Dihedral : 7.080 87.814 1412 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.67 % Allowed : 22.77 % Favored : 75.56 % 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: -0.16 (0.24), residues: 1216 helix: 0.47 (0.26), residues: 424 sheet: 0.85 (0.32), residues: 284 loop : -1.12 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 156 PHE 0.019 0.002 PHE A 145 TYR 0.005 0.001 TYR D 222 ARG 0.005 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.5499 (mt) cc_final: 0.5092 (mt) REVERT: B 303 ASN cc_start: 0.5167 (p0) cc_final: 0.4680 (m-40) REVERT: C 258 ARG cc_start: 0.5982 (mmt180) cc_final: 0.5503 (mmp-170) REVERT: C 292 VAL cc_start: 0.7349 (t) cc_final: 0.7134 (t) REVERT: D 29 MET cc_start: 0.4398 (mtt) cc_final: 0.4063 (mtt) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.1698 time to fit residues: 28.1192 Evaluate side-chains 114 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.0570 chunk 95 optimal weight: 0.0670 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9024 Z= 0.154 Angle : 0.508 7.977 12228 Z= 0.260 Chirality : 0.045 0.174 1456 Planarity : 0.003 0.064 1604 Dihedral : 6.794 80.394 1412 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.56 % Allowed : 22.77 % Favored : 75.67 % 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: -0.05 (0.24), residues: 1216 helix: 0.60 (0.27), residues: 424 sheet: 0.87 (0.32), residues: 284 loop : -1.07 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 156 PHE 0.018 0.001 PHE A 145 TYR 0.004 0.001 TYR D 222 ARG 0.005 0.000 ARG D 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.5238 (mt) cc_final: 0.4899 (mt) REVERT: B 303 ASN cc_start: 0.4969 (p0) cc_final: 0.4628 (m-40) REVERT: C 258 ARG cc_start: 0.5924 (mmt180) cc_final: 0.5480 (mmp-170) REVERT: C 292 VAL cc_start: 0.7454 (t) cc_final: 0.7244 (t) REVERT: D 29 MET cc_start: 0.4413 (mtt) cc_final: 0.4109 (mtt) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.1715 time to fit residues: 27.9914 Evaluate side-chains 113 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.205259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.191237 restraints weight = 16323.310| |-----------------------------------------------------------------------------| r_work (start): 0.4958 rms_B_bonded: 2.73 r_work: 0.4852 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9024 Z= 0.149 Angle : 0.497 7.733 12228 Z= 0.255 Chirality : 0.045 0.181 1456 Planarity : 0.003 0.061 1604 Dihedral : 6.433 67.171 1412 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.12 % Allowed : 22.21 % Favored : 75.67 % 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: 0.02 (0.24), residues: 1216 helix: 0.68 (0.27), residues: 424 sheet: 0.89 (0.32), residues: 284 loop : -1.05 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 156 PHE 0.017 0.001 PHE B 145 TYR 0.004 0.001 TYR D 222 ARG 0.005 0.000 ARG D 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.04 seconds wall clock time: 340 minutes 7.47 seconds (20407.47 seconds total)