Starting phenix.real_space_refine on Fri Dec 8 18:52:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/12_2023/8ibn_35344_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/12_2023/8ibn_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_35344/12_2023/8ibn_35344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/12_2023/8ibn_35344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/12_2023/8ibn_35344_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibn_35344/12_2023/8ibn_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-1.21rc1-5172/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: 3.45 Conformation dependent library (CDL) restraints added in 1.9 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: 2.04 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: 2.35 Time building geometry restraints manager: 3.73 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: 2.260 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: 6.110 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.140 Find NCS groups from input model: 0.730 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.400 ------------------------------------------------------------------------------- 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 : 1.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1582 time to fit residues: 31.7629 Evaluate side-chains 107 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3196 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 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: 0.5227 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9024 Z= 0.171 Angle : 0.513 5.271 12228 Z= 0.275 Chirality : 0.047 0.178 1456 Planarity : 0.004 0.056 1604 Dihedral : 8.428 79.253 1412 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.67 % Allowed : 10.16 % Favored : 89.17 % 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: -1.01 (0.23), residues: 1216 helix: -0.63 (0.24), residues: 408 sheet: 0.76 (0.32), residues: 288 loop : -1.48 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 28 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 112 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.003 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.1650 time to fit residues: 26.6226 Evaluate side-chains 107 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0966 time to fit residues: 2.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.5223 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9024 Z= 0.155 Angle : 0.467 6.009 12228 Z= 0.251 Chirality : 0.046 0.162 1456 Planarity : 0.003 0.049 1604 Dihedral : 7.586 85.584 1412 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.12 % Allowed : 14.17 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.23), residues: 1216 helix: -0.13 (0.25), residues: 412 sheet: 0.86 (0.32), residues: 288 loop : -1.49 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 156 PHE 0.021 0.002 PHE A 145 TYR 0.004 0.001 TYR D 222 ARG 0.003 0.000 ARG A 283 *********************** 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 118 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.982 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 113 average time/residue: 0.1640 time to fit residues: 28.2511 Evaluate side-chains 110 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0830 time to fit residues: 1.9544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9024 Z= 0.269 Angle : 0.598 5.905 12228 Z= 0.315 Chirality : 0.049 0.165 1456 Planarity : 0.004 0.047 1604 Dihedral : 7.775 75.637 1412 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.89 % Allowed : 18.75 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1216 helix: -0.34 (0.24), residues: 440 sheet: 0.47 (0.31), residues: 292 loop : -1.44 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 156 PHE 0.027 0.003 PHE A 145 TYR 0.007 0.002 TYR D 222 ARG 0.005 0.000 ARG D 142 *********************** 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 116 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.024 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.1718 time to fit residues: 29.5111 Evaluate side-chains 110 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1026 time to fit residues: 1.9964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN D 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9024 Z= 0.291 Angle : 0.631 7.597 12228 Z= 0.332 Chirality : 0.050 0.161 1456 Planarity : 0.004 0.051 1604 Dihedral : 7.837 75.392 1412 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.34 % Allowed : 19.64 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1216 helix: -0.38 (0.25), residues: 424 sheet: 0.24 (0.31), residues: 292 loop : -1.53 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 28 PHE 0.027 0.003 PHE A 145 TYR 0.009 0.002 TYR D 222 ARG 0.004 0.001 ARG D 142 *********************** 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 121 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.982 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.1716 time to fit residues: 29.6419 Evaluate side-chains 115 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0932 time to fit residues: 2.7553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 116 optimal weight: 0.0970 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9024 Z= 0.273 Angle : 0.614 6.217 12228 Z= 0.323 Chirality : 0.049 0.162 1456 Planarity : 0.004 0.059 1604 Dihedral : 7.771 74.723 1412 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.68 % Allowed : 19.64 % Favored : 77.68 % 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: -1.22 (0.23), residues: 1216 helix: -0.51 (0.24), residues: 444 sheet: 0.15 (0.30), residues: 292 loop : -1.61 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 156 PHE 0.026 0.003 PHE B 145 TYR 0.010 0.002 TYR D 222 ARG 0.005 0.000 ARG D 142 *********************** 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 135 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.921 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 129 average time/residue: 0.1612 time to fit residues: 31.3356 Evaluate side-chains 113 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0872 time to fit residues: 2.4869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.5413 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9024 Z= 0.259 Angle : 0.605 8.849 12228 Z= 0.316 Chirality : 0.049 0.185 1456 Planarity : 0.004 0.062 1604 Dihedral : 7.735 74.033 1412 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.46 % Allowed : 20.98 % Favored : 76.56 % 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: -1.07 (0.23), residues: 1216 helix: -0.30 (0.25), residues: 424 sheet: 0.13 (0.30), residues: 296 loop : -1.53 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 156 PHE 0.025 0.002 PHE A 145 TYR 0.009 0.002 TYR D 222 ARG 0.004 0.000 ARG D 142 *********************** 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 130 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 1.065 Fit side-chains outliers start: 22 outliers final: 5 residues processed: 124 average time/residue: 0.1757 time to fit residues: 32.6805 Evaluate side-chains 111 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0832 time to fit residues: 2.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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: 0.5301 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9024 Z= 0.158 Angle : 0.520 6.771 12228 Z= 0.271 Chirality : 0.046 0.164 1456 Planarity : 0.004 0.084 1604 Dihedral : 7.160 74.056 1412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.00 % Allowed : 21.43 % Favored : 77.57 % 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: -0.64 (0.24), residues: 1216 helix: 0.19 (0.26), residues: 424 sheet: 0.40 (0.30), residues: 296 loop : -1.44 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 28 PHE 0.019 0.001 PHE B 145 TYR 0.005 0.001 TYR D 222 ARG 0.003 0.000 ARG C 202 *********************** 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 118 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.1714 time to fit residues: 30.1558 Evaluate side-chains 110 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0839 time to fit residues: 2.0081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.5401 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9024 Z= 0.252 Angle : 0.613 7.951 12228 Z= 0.313 Chirality : 0.048 0.157 1456 Planarity : 0.004 0.076 1604 Dihedral : 7.537 69.695 1412 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.56 % Allowed : 22.10 % Favored : 77.34 % 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: -0.78 (0.24), residues: 1216 helix: 0.05 (0.26), residues: 424 sheet: 0.34 (0.29), residues: 316 loop : -1.57 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 156 PHE 0.024 0.002 PHE C 145 TYR 0.008 0.002 TYR D 222 ARG 0.004 0.000 ARG D 142 *********************** 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 109 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.030 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.1878 time to fit residues: 30.1822 Evaluate side-chains 104 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1050 time to fit residues: 1.9241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.5369 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9024 Z= 0.205 Angle : 0.587 9.612 12228 Z= 0.300 Chirality : 0.047 0.170 1456 Planarity : 0.004 0.066 1604 Dihedral : 7.347 67.652 1412 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.33 % Allowed : 22.43 % 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: -0.58 (0.24), residues: 1216 helix: 0.21 (0.26), residues: 420 sheet: 0.40 (0.29), residues: 316 loop : -1.41 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 156 PHE 0.022 0.002 PHE B 145 TYR 0.007 0.001 TYR D 222 ARG 0.003 0.000 ARG D 142 ********************** 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 103 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.025 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 102 average time/residue: 0.1789 time to fit residues: 27.2612 Evaluate side-chains 102 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0846 time to fit residues: 1.6714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.5078 r_free = 0.5078 target = 0.201612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.187575 restraints weight = 16341.859| |-----------------------------------------------------------------------------| r_work (start): 0.4925 rms_B_bonded: 2.72 r_work: 0.4816 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9024 Z= 0.189 Angle : 0.557 9.685 12228 Z= 0.286 Chirality : 0.047 0.183 1456 Planarity : 0.004 0.064 1604 Dihedral : 7.101 60.195 1412 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.22 % Allowed : 22.54 % 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: -0.46 (0.24), residues: 1216 helix: 0.32 (0.26), residues: 420 sheet: 0.49 (0.29), residues: 316 loop : -1.36 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 28 PHE 0.021 0.002 PHE B 145 TYR 0.007 0.001 TYR D 222 ARG 0.003 0.000 ARG D 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.92 seconds wall clock time: 34 minutes 40.33 seconds (2080.33 seconds total)