Starting phenix.real_space_refine on Mon May 19 18:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmg_41388/05_2025/8tmg_41388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmg_41388/05_2025/8tmg_41388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmg_41388/05_2025/8tmg_41388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmg_41388/05_2025/8tmg_41388.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmg_41388/05_2025/8tmg_41388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmg_41388/05_2025/8tmg_41388.cif" } resolution = 3.0 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 65 5.16 5 C 11500 2.51 5 N 2892 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17747 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2812 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2908 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "E" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.40, per 1000 atoms: 0.64 Number of scatterers: 17747 At special positions: 0 Unit cell: (130.296, 137.772, 161.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 2 11.99 O 3288 8.00 N 2892 7.00 C 11500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.52 Conformation dependent library (CDL) restraints added in 2.4 seconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4130 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 18 sheets defined 49.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.822A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.270A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.986A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.736A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.549A pdb=" N LEU A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.647A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.715A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.518A pdb=" N LYS A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 164' Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.571A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 Proline residue: A 227 - end of helix removed outlier: 4.035A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 276 removed outlier: 4.356A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 284 through 312 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 345 Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.620A pdb=" N LEU B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.561A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 202 Processing helix chain 'B' and resid 204 through 239 Proline residue: B 227 - end of helix removed outlier: 3.728A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 311 removed outlier: 3.598A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 4.222A pdb=" N ALA B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 removed outlier: 3.823A pdb=" N LYS B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 56 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.539A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.891A pdb=" N LYS C 164 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.613A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 281 removed outlier: 3.538A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 311 removed outlier: 3.953A pdb=" N LYS C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Proline residue: C 303 - end of helix removed outlier: 3.707A pdb=" N TYR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.538A pdb=" N VAL C 329 " --> pdb=" O TRP C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.892A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.641A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 165 through 202 Processing helix chain 'D' and resid 205 through 238 removed outlier: 3.590A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 247 through 312 removed outlier: 3.564A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 349 Processing helix chain 'E' and resid 50 through 56 Processing helix chain 'E' and resid 69 through 81 removed outlier: 4.050A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.565A pdb=" N LEU E 87 " --> pdb=" O HIS E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 165 through 202 Processing helix chain 'E' and resid 204 through 239 removed outlier: 3.861A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRP E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Proline residue: E 227 - end of helix removed outlier: 3.793A pdb=" N VAL E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 312 removed outlier: 4.707A pdb=" N SER E 284 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 349 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR H 102 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN H 111 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.672A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.598A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8 removed outlier: 3.956A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.123A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.123A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.891A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.612A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 110 " --> pdb=" O TYR F 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 44 removed outlier: 6.521A pdb=" N THR A 60 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET A 138 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 62 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 44 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.737A pdb=" N VAL C 31 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 114 through 116 removed outlier: 4.157A pdb=" N ASP C 116 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU C 121 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 39 through 44 removed outlier: 6.770A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 121 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 40 through 44 removed outlier: 3.648A pdb=" N MET E 112 " --> pdb=" O GLU E 125 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3096 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: 5.84 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5467 1.34 - 1.45: 2835 1.45 - 1.57: 9732 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 18151 Sorted by residual: bond pdb=" C LEU A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.63e+00 bond pdb=" CG1 ILE D 297 " pdb=" CD1 ILE D 297 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 bond pdb=" C GLN D 95 " pdb=" N ARG D 96 " ideal model delta sigma weight residual 1.333 1.293 0.040 2.74e-02 1.33e+03 2.10e+00 bond pdb=" CG LEU B 294 " pdb=" CD1 LEU B 294 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB MET D 291 " pdb=" CG MET D 291 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 18146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 24382 2.61 - 5.22: 220 5.22 - 7.83: 10 7.83 - 10.44: 4 10.44 - 13.05: 2 Bond angle restraints: 24618 Sorted by residual: angle pdb=" CB MET D 291 " pdb=" CG MET D 291 " pdb=" SD MET D 291 " ideal model delta sigma weight residual 112.70 99.65 13.05 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CA LEU A 294 " pdb=" CB LEU A 294 " pdb=" CG LEU A 294 " ideal model delta sigma weight residual 116.30 128.97 -12.67 3.50e+00 8.16e-02 1.31e+01 angle pdb=" C VAL B 265 " pdb=" N GLU B 266 " pdb=" CA GLU B 266 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" CA LYS C 133 " pdb=" CB LYS C 133 " pdb=" CG LYS C 133 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.83e+00 angle pdb=" C LEU C 235 " pdb=" N TYR C 236 " pdb=" CA TYR C 236 " ideal model delta sigma weight residual 122.06 116.43 5.63 1.86e+00 2.89e-01 9.17e+00 ... (remaining 24613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 9718 17.30 - 34.59: 957 34.59 - 51.89: 154 51.89 - 69.19: 20 69.19 - 86.48: 26 Dihedral angle restraints: 10875 sinusoidal: 4471 harmonic: 6404 Sorted by residual: dihedral pdb=" CA GLU B 266 " pdb=" C GLU B 266 " pdb=" N THR B 267 " pdb=" CA THR B 267 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA VAL C 146 " pdb=" C VAL C 146 " pdb=" N PHE C 147 " pdb=" CA PHE C 147 " ideal model delta harmonic sigma weight residual -180.00 -156.07 -23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA SER E 284 " pdb=" C SER E 284 " pdb=" N ASN E 285 " pdb=" CA ASN E 285 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 10872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1912 0.039 - 0.077: 613 0.077 - 0.116: 222 0.116 - 0.154: 38 0.154 - 0.193: 3 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CB ILE E 160 " pdb=" CA ILE E 160 " pdb=" CG1 ILE E 160 " pdb=" CG2 ILE E 160 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ASP C 180 " pdb=" N ASP C 180 " pdb=" C ASP C 180 " pdb=" CB ASP C 180 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CG LEU A 110 " pdb=" CB LEU A 110 " pdb=" CD1 LEU A 110 " pdb=" CD2 LEU A 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 2785 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 266 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU B 266 " 0.066 2.00e-02 2.50e+03 pdb=" O GLU B 266 " -0.024 2.00e-02 2.50e+03 pdb=" N THR B 267 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 284 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C SER E 284 " -0.055 2.00e-02 2.50e+03 pdb=" O SER E 284 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN E 285 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 327 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 328 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.037 5.00e-02 4.00e+02 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 239 2.67 - 3.22: 16824 3.22 - 3.78: 27596 3.78 - 4.34: 37782 4.34 - 4.90: 62366 Nonbonded interactions: 144807 Sorted by model distance: nonbonded pdb=" OD1 ASN B 288 " pdb=" OG1 THR C 287 " model vdw 2.108 3.040 nonbonded pdb=" OG SER G 27 " pdb=" OE1 GLN G 28 " model vdw 2.117 3.040 nonbonded pdb=" O LYS B 111 " pdb=" OH TYR B 181 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR C 115 " pdb=" OE1 GLU C 191 " model vdw 2.139 3.040 nonbonded pdb=" NH2 ARG A 222 " pdb=" OE1 GLU A 266 " model vdw 2.174 3.120 ... (remaining 144802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 351) selection = (chain 'B' and resid 17 through 351) selection = chain 'C' selection = (chain 'D' and resid 17 through 351) selection = chain 'E' } ncs_group { reference = (chain 'F' and resid 1 through 122) selection = chain 'H' } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } 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=0.49 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.350 Find NCS groups from input model: 0.740 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18155 Z= 0.169 Angle : 0.626 13.051 24626 Z= 0.326 Chirality : 0.044 0.193 2788 Planarity : 0.004 0.067 3080 Dihedral : 14.003 86.484 6733 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.28 (0.19), residues: 2146 helix: 2.05 (0.16), residues: 960 sheet: 1.09 (0.25), residues: 474 loop : -1.04 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 226 HIS 0.006 0.001 HIS D 257 PHE 0.015 0.001 PHE B 147 TYR 0.018 0.002 TYR B 171 ARG 0.007 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.16642 ( 1079) hydrogen bonds : angle 6.58411 ( 3096) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.57887 ( 8) covalent geometry : bond 0.00389 (18151) covalent geometry : angle 0.62561 (24618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7541 (tptp) cc_final: 0.7302 (tttm) REVERT: G 25 ARG cc_start: 0.7348 (ttm110) cc_final: 0.7059 (ttm110) REVERT: F 1 GLU cc_start: 0.6753 (tp30) cc_final: 0.6364 (tp30) REVERT: F 6 GLU cc_start: 0.8177 (mp0) cc_final: 0.7875 (mp0) REVERT: F 83 MET cc_start: 0.8360 (mtm) cc_final: 0.8146 (mtp) REVERT: A 100 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6347 (mt-10) REVERT: A 161 ILE cc_start: 0.8329 (tp) cc_final: 0.8055 (tt) REVERT: A 230 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6577 (mt-10) REVERT: A 334 MET cc_start: 0.5634 (mmp) cc_final: 0.4996 (mmp) REVERT: B 119 LEU cc_start: 0.7586 (pt) cc_final: 0.7365 (pt) REVERT: B 191 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5841 (mm-30) REVERT: B 215 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8036 (ttpp) REVERT: C 63 ASN cc_start: 0.5641 (t0) cc_final: 0.5439 (t0) REVERT: C 163 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7785 (mmmt) REVERT: C 213 GLN cc_start: 0.7655 (tp40) cc_final: 0.7419 (tp40) REVERT: D 32 MET cc_start: 0.8573 (mtm) cc_final: 0.8208 (mtm) REVERT: D 74 GLN cc_start: 0.8636 (tt0) cc_final: 0.8382 (mt0) REVERT: D 216 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7767 (mtp-110) REVERT: E 259 ILE cc_start: 0.8320 (mm) cc_final: 0.7996 (mm) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 1.1159 time to fit residues: 624.6252 Evaluate side-chains 404 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN A 74 GLN A 140 GLN C 92 ASN D 104 ASN E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.190853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.136408 restraints weight = 20238.878| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.01 r_work: 0.3223 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18155 Z= 0.186 Angle : 0.636 10.517 24626 Z= 0.337 Chirality : 0.044 0.202 2788 Planarity : 0.005 0.049 3080 Dihedral : 4.715 27.901 2399 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.81 % Allowed : 13.60 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.42 (0.19), residues: 2146 helix: 2.17 (0.16), residues: 966 sheet: 1.06 (0.24), residues: 487 loop : -0.96 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 226 HIS 0.006 0.001 HIS D 257 PHE 0.014 0.001 PHE B 147 TYR 0.025 0.001 TYR B 171 ARG 0.010 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.06308 ( 1079) hydrogen bonds : angle 5.11762 ( 3096) SS BOND : bond 0.00475 ( 4) SS BOND : angle 1.04143 ( 8) covalent geometry : bond 0.00429 (18151) covalent geometry : angle 0.63625 (24618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 436 time to evaluate : 2.120 Fit side-chains REVERT: L 73 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8344 (t) REVERT: G 25 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7596 (ttm110) REVERT: G 80 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7790 (mm-40) REVERT: F 1 GLU cc_start: 0.7062 (tp30) cc_final: 0.6440 (tp30) REVERT: F 6 GLU cc_start: 0.8508 (mp0) cc_final: 0.8016 (mp0) REVERT: A 100 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 138 MET cc_start: 0.8065 (ttp) cc_final: 0.7788 (ttp) REVERT: A 236 TYR cc_start: 0.8309 (p90) cc_final: 0.7963 (p90) REVERT: A 281 SER cc_start: 0.7996 (m) cc_final: 0.7727 (m) REVERT: A 289 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6779 (mt-10) REVERT: A 297 ILE cc_start: 0.8231 (mp) cc_final: 0.8024 (mp) REVERT: A 334 MET cc_start: 0.5497 (mmp) cc_final: 0.4856 (mmp) REVERT: B 85 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8315 (mt) REVERT: B 119 LEU cc_start: 0.7210 (pt) cc_final: 0.6574 (pt) REVERT: B 121 GLU cc_start: 0.7802 (pm20) cc_final: 0.7254 (pm20) REVERT: B 191 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6238 (mm-30) REVERT: B 215 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8162 (ttpp) REVERT: B 230 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: B 297 ILE cc_start: 0.8181 (tt) cc_final: 0.7875 (pt) REVERT: C 163 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7592 (mmmm) REVERT: C 189 ASP cc_start: 0.8638 (t0) cc_final: 0.8380 (t0) REVERT: C 213 GLN cc_start: 0.7935 (tp40) cc_final: 0.7681 (tp40) REVERT: C 245 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8211 (mmmm) REVERT: D 100 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8613 (mt-10) REVERT: D 186 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: D 216 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7982 (mtp-110) REVERT: D 237 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7549 (mtm180) REVERT: D 266 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6772 (tp30) REVERT: D 297 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7443 (mp) REVERT: E 172 SER cc_start: 0.6628 (m) cc_final: 0.6213 (t) outliers start: 56 outliers final: 22 residues processed: 454 average time/residue: 1.0924 time to fit residues: 562.6195 Evaluate side-chains 444 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 414 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 187 optimal weight: 0.0770 chunk 155 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN G 90 GLN A 134 ASN A 285 ASN B 63 ASN C 92 ASN D 104 ASN E 288 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.190394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.136801 restraints weight = 20135.961| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.97 r_work: 0.3223 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18155 Z= 0.179 Angle : 0.610 9.273 24626 Z= 0.323 Chirality : 0.044 0.207 2788 Planarity : 0.005 0.044 3080 Dihedral : 4.669 26.649 2399 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 3.46 % Allowed : 16.92 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.44 (0.19), residues: 2146 helix: 2.24 (0.16), residues: 965 sheet: 1.13 (0.24), residues: 472 loop : -1.02 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.005 0.001 HIS D 257 PHE 0.023 0.001 PHE E 27 TYR 0.020 0.002 TYR E 236 ARG 0.009 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 1079) hydrogen bonds : angle 4.87287 ( 3096) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.01636 ( 8) covalent geometry : bond 0.00413 (18151) covalent geometry : angle 0.61022 (24618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 434 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7585 (ttm110) REVERT: G 80 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7595 (mm-40) REVERT: F 1 GLU cc_start: 0.7035 (tp30) cc_final: 0.6410 (tp30) REVERT: F 6 GLU cc_start: 0.8547 (mp0) cc_final: 0.8021 (mp0) REVERT: A 100 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7432 (mt-10) REVERT: A 217 ASN cc_start: 0.8882 (m-40) cc_final: 0.8669 (m-40) REVERT: A 281 SER cc_start: 0.7934 (m) cc_final: 0.7664 (m) REVERT: A 289 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6732 (mt-10) REVERT: A 334 MET cc_start: 0.5935 (mmp) cc_final: 0.5250 (mmp) REVERT: B 119 LEU cc_start: 0.7198 (pt) cc_final: 0.6593 (pt) REVERT: B 121 GLU cc_start: 0.7798 (pm20) cc_final: 0.7299 (pm20) REVERT: B 191 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6251 (mm-30) REVERT: B 206 GLU cc_start: 0.7565 (mp0) cc_final: 0.7344 (mp0) REVERT: B 215 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8167 (ttpp) REVERT: B 230 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: B 297 ILE cc_start: 0.8247 (tt) cc_final: 0.7916 (pt) REVERT: C 163 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7585 (mmmm) REVERT: C 175 ASP cc_start: 0.7787 (p0) cc_final: 0.7546 (p0) REVERT: C 189 ASP cc_start: 0.8575 (t0) cc_final: 0.8362 (t0) REVERT: C 213 GLN cc_start: 0.7939 (tp40) cc_final: 0.7696 (tp40) REVERT: C 245 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8126 (mmmm) REVERT: D 40 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7534 (ptm160) REVERT: D 180 ASP cc_start: 0.8135 (t70) cc_final: 0.7810 (t70) REVERT: D 186 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: D 216 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7880 (mtp-110) REVERT: D 237 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7573 (mtm180) REVERT: D 263 ASP cc_start: 0.7822 (m-30) cc_final: 0.7473 (m-30) REVERT: D 266 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: D 297 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7511 (mp) REVERT: E 28 GLU cc_start: 0.5540 (tm-30) cc_final: 0.5231 (tm-30) REVERT: E 318 MET cc_start: 0.6405 (pp-130) cc_final: 0.5861 (mmt) outliers start: 69 outliers final: 40 residues processed: 462 average time/residue: 1.0659 time to fit residues: 558.5819 Evaluate side-chains 464 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 418 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 93 optimal weight: 0.0050 chunk 113 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN B 63 ASN C 92 ASN D 104 ASN E 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.190468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.137219 restraints weight = 20205.421| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.93 r_work: 0.3233 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18155 Z= 0.165 Angle : 0.593 8.087 24626 Z= 0.314 Chirality : 0.043 0.222 2788 Planarity : 0.004 0.043 3080 Dihedral : 4.604 26.285 2399 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 4.02 % Allowed : 18.27 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.47 (0.19), residues: 2146 helix: 2.30 (0.16), residues: 966 sheet: 1.14 (0.24), residues: 462 loop : -1.04 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.004 0.001 HIS H 35 PHE 0.022 0.001 PHE A 27 TYR 0.033 0.001 TYR A 105 ARG 0.005 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.05766 ( 1079) hydrogen bonds : angle 4.73880 ( 3096) SS BOND : bond 0.00321 ( 4) SS BOND : angle 0.96509 ( 8) covalent geometry : bond 0.00377 (18151) covalent geometry : angle 0.59268 (24618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 439 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8258 (pm20) cc_final: 0.7868 (mp0) REVERT: H 98 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8705 (tmm160) REVERT: L 80 GLN cc_start: 0.7640 (mt0) cc_final: 0.7354 (mt0) REVERT: G 25 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7586 (ttm110) REVERT: G 80 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7733 (mm-40) REVERT: F 1 GLU cc_start: 0.6994 (tp30) cc_final: 0.6397 (tp30) REVERT: F 6 GLU cc_start: 0.8579 (mp0) cc_final: 0.8138 (mp0) REVERT: A 62 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7342 (mm) REVERT: A 100 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 138 MET cc_start: 0.7709 (ttp) cc_final: 0.6862 (ttp) REVERT: A 217 ASN cc_start: 0.8893 (m-40) cc_final: 0.8673 (m-40) REVERT: A 237 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6450 (mtp180) REVERT: A 281 SER cc_start: 0.7938 (m) cc_final: 0.7669 (m) REVERT: A 289 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6700 (mt-10) REVERT: A 334 MET cc_start: 0.5741 (mmp) cc_final: 0.4882 (mmp) REVERT: B 85 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8368 (mt) REVERT: B 119 LEU cc_start: 0.7183 (pt) cc_final: 0.6871 (pt) REVERT: B 121 GLU cc_start: 0.7787 (pm20) cc_final: 0.7381 (pm20) REVERT: B 191 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6106 (mm-30) REVERT: B 215 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8174 (ttpp) REVERT: B 230 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 297 ILE cc_start: 0.8312 (tt) cc_final: 0.7989 (pt) REVERT: C 121 GLU cc_start: 0.7878 (mp0) cc_final: 0.7245 (mp0) REVERT: C 163 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7592 (mmmm) REVERT: C 175 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7576 (p0) REVERT: C 189 ASP cc_start: 0.8547 (t0) cc_final: 0.8340 (t0) REVERT: C 213 GLN cc_start: 0.7941 (tp40) cc_final: 0.7690 (tp40) REVERT: C 245 LYS cc_start: 0.8357 (mmmm) cc_final: 0.8107 (mmmm) REVERT: D 180 ASP cc_start: 0.8093 (t70) cc_final: 0.7752 (t70) REVERT: D 186 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: D 202 ARG cc_start: 0.6713 (mpp80) cc_final: 0.6249 (mpp80) REVERT: D 237 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7586 (mtm180) REVERT: D 263 ASP cc_start: 0.7765 (m-30) cc_final: 0.7443 (m-30) REVERT: D 266 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: D 297 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7559 (mp) REVERT: E 28 GLU cc_start: 0.5558 (tm-30) cc_final: 0.5252 (tm-30) REVERT: E 172 SER cc_start: 0.6659 (m) cc_final: 0.6203 (t) REVERT: E 318 MET cc_start: 0.6357 (pp-130) cc_final: 0.5451 (mtt) outliers start: 80 outliers final: 50 residues processed: 476 average time/residue: 1.0749 time to fit residues: 582.3692 Evaluate side-chains 487 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 427 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN B 63 ASN C 92 ASN D 104 ASN E 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.188899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.134454 restraints weight = 20448.706| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.02 r_work: 0.3188 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18155 Z= 0.207 Angle : 0.621 10.579 24626 Z= 0.328 Chirality : 0.044 0.229 2788 Planarity : 0.005 0.043 3080 Dihedral : 4.685 27.017 2399 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.67 % Allowed : 19.43 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.37 (0.18), residues: 2146 helix: 2.23 (0.16), residues: 965 sheet: 1.06 (0.24), residues: 473 loop : -1.13 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 226 HIS 0.006 0.001 HIS D 94 PHE 0.025 0.002 PHE A 27 TYR 0.035 0.002 TYR A 105 ARG 0.007 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.06051 ( 1079) hydrogen bonds : angle 4.74891 ( 3096) SS BOND : bond 0.00372 ( 4) SS BOND : angle 1.10605 ( 8) covalent geometry : bond 0.00495 (18151) covalent geometry : angle 0.62100 (24618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 438 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 98 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8765 (tmm160) REVERT: L 80 GLN cc_start: 0.7665 (mt0) cc_final: 0.7422 (mt0) REVERT: G 25 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7558 (ttm110) REVERT: G 80 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7652 (mm-40) REVERT: F 1 GLU cc_start: 0.6974 (tp30) cc_final: 0.6359 (tp30) REVERT: A 62 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7308 (mm) REVERT: A 100 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 138 MET cc_start: 0.7933 (ttp) cc_final: 0.7081 (ttp) REVERT: A 217 ASN cc_start: 0.8916 (m-40) cc_final: 0.8690 (m-40) REVERT: A 281 SER cc_start: 0.7848 (m) cc_final: 0.7563 (m) REVERT: A 334 MET cc_start: 0.6178 (mmp) cc_final: 0.4927 (mmp) REVERT: B 41 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7729 (tt0) REVERT: B 85 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 119 LEU cc_start: 0.7187 (pt) cc_final: 0.6473 (pt) REVERT: B 121 GLU cc_start: 0.7835 (pm20) cc_final: 0.7375 (pm20) REVERT: B 191 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6090 (mm-30) REVERT: B 206 GLU cc_start: 0.7613 (mp0) cc_final: 0.7380 (mp0) REVERT: B 230 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: B 297 ILE cc_start: 0.8306 (tt) cc_final: 0.8003 (pt) REVERT: C 121 GLU cc_start: 0.7945 (mp0) cc_final: 0.7264 (mp0) REVERT: C 162 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: C 175 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7654 (p0) REVERT: C 189 ASP cc_start: 0.8609 (t0) cc_final: 0.8393 (t0) REVERT: C 213 GLN cc_start: 0.7985 (tp40) cc_final: 0.7752 (tp40) REVERT: C 220 GLU cc_start: 0.8071 (tp30) cc_final: 0.7780 (mm-30) REVERT: C 245 LYS cc_start: 0.8356 (mmmm) cc_final: 0.8095 (mmmm) REVERT: D 180 ASP cc_start: 0.8279 (t70) cc_final: 0.7979 (t70) REVERT: D 186 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: D 237 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7634 (mtm180) REVERT: D 263 ASP cc_start: 0.7809 (m-30) cc_final: 0.7475 (m-30) REVERT: D 266 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: D 297 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7637 (mp) REVERT: E 28 GLU cc_start: 0.5533 (tm-30) cc_final: 0.5246 (tm-30) REVERT: E 38 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6164 (pp20) REVERT: E 185 LEU cc_start: 0.7918 (mp) cc_final: 0.7699 (mt) REVERT: E 318 MET cc_start: 0.6409 (pp-130) cc_final: 0.5333 (mtt) outliers start: 93 outliers final: 60 residues processed: 481 average time/residue: 1.0956 time to fit residues: 601.0086 Evaluate side-chains 489 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 419 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 199 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN C 92 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.190486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.136501 restraints weight = 20347.610| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.01 r_work: 0.3222 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18155 Z= 0.164 Angle : 0.597 9.557 24626 Z= 0.314 Chirality : 0.043 0.235 2788 Planarity : 0.004 0.043 3080 Dihedral : 4.596 25.983 2399 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.22 % Allowed : 20.48 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.46 (0.19), residues: 2146 helix: 2.33 (0.16), residues: 966 sheet: 1.01 (0.24), residues: 468 loop : -1.03 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.005 0.001 HIS H 35 PHE 0.029 0.001 PHE A 27 TYR 0.037 0.001 TYR A 105 ARG 0.011 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05688 ( 1079) hydrogen bonds : angle 4.64012 ( 3096) SS BOND : bond 0.00314 ( 4) SS BOND : angle 0.84707 ( 8) covalent geometry : bond 0.00379 (18151) covalent geometry : angle 0.59676 (24618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 419 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8250 (pm20) cc_final: 0.8047 (mp0) REVERT: H 65 LYS cc_start: 0.8164 (tttp) cc_final: 0.7805 (tttm) REVERT: H 98 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8724 (tmm160) REVERT: L 80 GLN cc_start: 0.7693 (mt0) cc_final: 0.7333 (mt0) REVERT: G 25 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7511 (ttm110) REVERT: G 80 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7525 (mm-40) REVERT: F 1 GLU cc_start: 0.6948 (tp30) cc_final: 0.6350 (tp30) REVERT: A 62 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7264 (mm) REVERT: A 100 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 110 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7489 (mm) REVERT: A 138 MET cc_start: 0.7834 (ttp) cc_final: 0.6913 (ttp) REVERT: A 217 ASN cc_start: 0.8890 (m-40) cc_final: 0.8659 (m-40) REVERT: A 237 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6385 (mtp180) REVERT: A 281 SER cc_start: 0.7843 (m) cc_final: 0.7561 (m) REVERT: A 294 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7190 (tp) REVERT: A 334 MET cc_start: 0.6320 (mmp) cc_final: 0.5784 (mmp) REVERT: B 119 LEU cc_start: 0.7243 (pt) cc_final: 0.6778 (pt) REVERT: B 121 GLU cc_start: 0.7793 (pm20) cc_final: 0.7356 (pm20) REVERT: B 206 GLU cc_start: 0.7640 (mp0) cc_final: 0.7390 (mp0) REVERT: B 230 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: B 297 ILE cc_start: 0.8280 (tt) cc_final: 0.8002 (pt) REVERT: C 103 GLU cc_start: 0.7438 (tp30) cc_final: 0.7148 (mm-30) REVERT: C 121 GLU cc_start: 0.7923 (mp0) cc_final: 0.7298 (mp0) REVERT: C 162 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7593 (mmm-85) REVERT: C 175 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7504 (p0) REVERT: C 189 ASP cc_start: 0.8581 (t0) cc_final: 0.8354 (t0) REVERT: C 213 GLN cc_start: 0.7918 (tp40) cc_final: 0.7677 (tp40) REVERT: C 245 LYS cc_start: 0.8297 (mmmm) cc_final: 0.8038 (mmmm) REVERT: D 186 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: D 237 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7595 (mtm180) REVERT: D 263 ASP cc_start: 0.7837 (m-30) cc_final: 0.7542 (m-30) REVERT: D 266 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: D 297 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7548 (mp) REVERT: E 38 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: E 301 PHE cc_start: 0.7288 (m-80) cc_final: 0.7001 (m-80) REVERT: E 318 MET cc_start: 0.6358 (pp-130) cc_final: 0.5365 (mtt) outliers start: 104 outliers final: 65 residues processed: 472 average time/residue: 1.0787 time to fit residues: 578.0025 Evaluate side-chains 482 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 405 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 103 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN B 63 ASN C 92 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.191283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.138103 restraints weight = 20330.582| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.96 r_work: 0.3249 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18155 Z= 0.147 Angle : 0.583 8.506 24626 Z= 0.309 Chirality : 0.043 0.243 2788 Planarity : 0.004 0.053 3080 Dihedral : 4.518 25.343 2399 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 4.57 % Allowed : 21.74 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.52 (0.19), residues: 2146 helix: 2.41 (0.16), residues: 960 sheet: 1.13 (0.25), residues: 449 loop : -1.03 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.004 0.001 HIS H 35 PHE 0.025 0.001 PHE A 27 TYR 0.037 0.001 TYR A 105 ARG 0.014 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05419 ( 1079) hydrogen bonds : angle 4.55694 ( 3096) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.79300 ( 8) covalent geometry : bond 0.00331 (18151) covalent geometry : angle 0.58306 (24618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 435 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7994 (tttp) cc_final: 0.7659 (tttm) REVERT: H 98 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8674 (tmm160) REVERT: G 25 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7543 (ttm110) REVERT: G 80 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7563 (mm-40) REVERT: F 1 GLU cc_start: 0.6916 (tp30) cc_final: 0.6338 (tp30) REVERT: A 62 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7250 (mm) REVERT: A 100 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 110 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7406 (mm) REVERT: A 217 ASN cc_start: 0.8882 (m-40) cc_final: 0.8646 (m-40) REVERT: A 237 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6383 (mtp180) REVERT: A 281 SER cc_start: 0.7842 (m) cc_final: 0.7562 (m) REVERT: A 334 MET cc_start: 0.6193 (mmp) cc_final: 0.5684 (mmp) REVERT: B 114 THR cc_start: 0.8438 (p) cc_final: 0.8211 (m) REVERT: B 119 LEU cc_start: 0.7232 (pt) cc_final: 0.6607 (pt) REVERT: B 121 GLU cc_start: 0.7762 (pm20) cc_final: 0.7295 (pm20) REVERT: B 206 GLU cc_start: 0.7591 (mp0) cc_final: 0.7351 (mp0) REVERT: B 230 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: B 297 ILE cc_start: 0.8290 (tt) cc_final: 0.8001 (pt) REVERT: C 40 ARG cc_start: 0.7303 (ttp80) cc_final: 0.7053 (ttp80) REVERT: C 121 GLU cc_start: 0.7945 (mp0) cc_final: 0.7301 (mp0) REVERT: C 162 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7570 (mmm-85) REVERT: C 175 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7419 (p0) REVERT: C 213 GLN cc_start: 0.7922 (tp40) cc_final: 0.7674 (tp40) REVERT: C 245 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8059 (mmmm) REVERT: D 186 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: D 237 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7598 (mtm180) REVERT: D 263 ASP cc_start: 0.7794 (m-30) cc_final: 0.7500 (m-30) REVERT: D 266 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: D 297 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7548 (mp) REVERT: E 28 GLU cc_start: 0.5190 (tm-30) cc_final: 0.4975 (tm-30) REVERT: E 31 VAL cc_start: 0.7836 (m) cc_final: 0.7537 (t) REVERT: E 164 LYS cc_start: 0.6803 (mmmm) cc_final: 0.6557 (mmmt) REVERT: E 181 TYR cc_start: 0.4896 (m-80) cc_final: 0.3980 (m-10) REVERT: E 185 LEU cc_start: 0.7936 (mp) cc_final: 0.7660 (mt) REVERT: E 189 ASP cc_start: 0.7618 (t70) cc_final: 0.7346 (t70) REVERT: E 301 PHE cc_start: 0.7281 (m-80) cc_final: 0.7022 (m-80) REVERT: E 318 MET cc_start: 0.6305 (pp-130) cc_final: 0.5361 (mtt) outliers start: 91 outliers final: 63 residues processed: 483 average time/residue: 1.0564 time to fit residues: 579.8586 Evaluate side-chains 481 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 408 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 134 optimal weight: 0.0000 chunk 154 optimal weight: 0.5980 chunk 174 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN A 285 ASN B 63 ASN B 120 HIS B 126 GLN C 92 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.192966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.140031 restraints weight = 20327.107| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.99 r_work: 0.3273 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18155 Z= 0.136 Angle : 0.584 9.724 24626 Z= 0.306 Chirality : 0.042 0.254 2788 Planarity : 0.004 0.057 3080 Dihedral : 4.439 23.947 2399 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 3.92 % Allowed : 23.44 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.61 (0.19), residues: 2146 helix: 2.47 (0.16), residues: 961 sheet: 1.22 (0.25), residues: 442 loop : -0.98 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.023 0.001 PHE A 27 TYR 0.039 0.001 TYR A 105 ARG 0.014 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 1079) hydrogen bonds : angle 4.46565 ( 3096) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.92374 ( 8) covalent geometry : bond 0.00300 (18151) covalent geometry : angle 0.58422 (24618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 422 time to evaluate : 1.881 Fit side-chains revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7971 (tttp) cc_final: 0.7599 (tttm) REVERT: H 98 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8579 (tmm160) REVERT: G 25 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7573 (ttm110) REVERT: G 43 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7806 (mptt) REVERT: G 80 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7675 (mm-40) REVERT: F 1 GLU cc_start: 0.6907 (tp30) cc_final: 0.6317 (tp30) REVERT: F 5 VAL cc_start: 0.9212 (t) cc_final: 0.8933 (m) REVERT: F 6 GLU cc_start: 0.8416 (mp0) cc_final: 0.8209 (mp0) REVERT: A 100 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 110 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7388 (mm) REVERT: A 139 PHE cc_start: 0.8085 (m-80) cc_final: 0.7636 (m-80) REVERT: A 201 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: A 217 ASN cc_start: 0.8879 (m-40) cc_final: 0.8631 (m-40) REVERT: A 281 SER cc_start: 0.7818 (m) cc_final: 0.7536 (m) REVERT: A 297 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7722 (mp) REVERT: A 334 MET cc_start: 0.6480 (mmp) cc_final: 0.5884 (mmp) REVERT: B 85 LEU cc_start: 0.8712 (mt) cc_final: 0.8443 (mt) REVERT: B 119 LEU cc_start: 0.7274 (pt) cc_final: 0.6510 (pt) REVERT: B 121 GLU cc_start: 0.7646 (pm20) cc_final: 0.7181 (pm20) REVERT: B 206 GLU cc_start: 0.7537 (mp0) cc_final: 0.7292 (mp0) REVERT: B 230 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: B 297 ILE cc_start: 0.8273 (tt) cc_final: 0.7966 (pt) REVERT: C 40 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6926 (ttp-170) REVERT: C 103 GLU cc_start: 0.7258 (tp30) cc_final: 0.7029 (mm-30) REVERT: C 121 GLU cc_start: 0.7907 (mp0) cc_final: 0.7231 (mp0) REVERT: C 162 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: C 175 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7392 (p0) REVERT: C 191 GLU cc_start: 0.8194 (tt0) cc_final: 0.7992 (tt0) REVERT: C 213 GLN cc_start: 0.7915 (tp40) cc_final: 0.7658 (tp40) REVERT: C 245 LYS cc_start: 0.8298 (mmmm) cc_final: 0.8047 (mmmm) REVERT: D 186 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: D 202 ARG cc_start: 0.6612 (mpp80) cc_final: 0.6390 (mpp80) REVERT: D 237 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7591 (mtm180) REVERT: D 263 ASP cc_start: 0.7739 (m-30) cc_final: 0.7451 (m-30) REVERT: D 266 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6824 (tp30) REVERT: D 297 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7478 (mp) REVERT: E 28 GLU cc_start: 0.5094 (tm-30) cc_final: 0.4881 (tm-30) REVERT: E 164 LYS cc_start: 0.6480 (mmmm) cc_final: 0.6237 (mmmt) REVERT: E 181 TYR cc_start: 0.4932 (m-80) cc_final: 0.4023 (m-80) REVERT: E 185 LEU cc_start: 0.7937 (mp) cc_final: 0.7672 (mt) REVERT: E 301 PHE cc_start: 0.7259 (m-80) cc_final: 0.6947 (m-80) REVERT: E 318 MET cc_start: 0.6342 (pp-130) cc_final: 0.5385 (mtt) outliers start: 78 outliers final: 47 residues processed: 465 average time/residue: 1.0614 time to fit residues: 560.8705 Evaluate side-chains 463 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 405 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 138 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 92 ASN B 120 HIS C 92 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.189243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.135299 restraints weight = 20375.232| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.00 r_work: 0.3203 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 18155 Z= 0.199 Angle : 0.637 9.968 24626 Z= 0.334 Chirality : 0.044 0.242 2788 Planarity : 0.005 0.064 3080 Dihedral : 4.629 25.178 2399 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 3.61 % Allowed : 24.00 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.45 (0.19), residues: 2146 helix: 2.29 (0.16), residues: 960 sheet: 0.99 (0.24), residues: 476 loop : -0.96 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 350 HIS 0.006 0.001 HIS D 94 PHE 0.032 0.002 PHE A 27 TYR 0.039 0.002 TYR A 105 ARG 0.014 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05759 ( 1079) hydrogen bonds : angle 4.60371 ( 3096) SS BOND : bond 0.00343 ( 4) SS BOND : angle 1.65346 ( 8) covalent geometry : bond 0.00478 (18151) covalent geometry : angle 0.63611 (24618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 415 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.8137 (tttp) cc_final: 0.7823 (tttm) REVERT: H 76 LYS cc_start: 0.8590 (mttp) cc_final: 0.7994 (mtmt) REVERT: H 98 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8743 (tmm160) REVERT: G 25 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7559 (ttm110) REVERT: G 28 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: G 80 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7576 (mm-40) REVERT: F 1 GLU cc_start: 0.6906 (tp30) cc_final: 0.6299 (tp30) REVERT: F 6 GLU cc_start: 0.8498 (mp0) cc_final: 0.8280 (mp0) REVERT: A 62 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7255 (mm) REVERT: A 100 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 110 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7450 (mm) REVERT: A 201 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: A 217 ASN cc_start: 0.8910 (m-40) cc_final: 0.8695 (m-40) REVERT: A 281 SER cc_start: 0.7960 (m) cc_final: 0.7697 (m) REVERT: B 119 LEU cc_start: 0.7277 (pt) cc_final: 0.6591 (pt) REVERT: B 121 GLU cc_start: 0.7772 (pm20) cc_final: 0.7236 (pm20) REVERT: B 230 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: B 297 ILE cc_start: 0.8312 (tt) cc_final: 0.7992 (pt) REVERT: C 121 GLU cc_start: 0.7918 (mp0) cc_final: 0.7243 (mp0) REVERT: C 191 GLU cc_start: 0.8270 (tt0) cc_final: 0.8067 (tt0) REVERT: C 213 GLN cc_start: 0.7977 (tp40) cc_final: 0.7726 (tp40) REVERT: C 245 LYS cc_start: 0.8284 (mmmm) cc_final: 0.8032 (mmmm) REVERT: D 186 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: D 237 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7606 (mtm180) REVERT: D 263 ASP cc_start: 0.7825 (m-30) cc_final: 0.7544 (m-30) REVERT: D 266 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: D 297 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7577 (mp) REVERT: E 28 GLU cc_start: 0.5282 (tm-30) cc_final: 0.5045 (tm-30) REVERT: E 164 LYS cc_start: 0.6765 (mmmm) cc_final: 0.6536 (mmmt) REVERT: E 181 TYR cc_start: 0.5001 (m-80) cc_final: 0.4108 (m-80) REVERT: E 301 PHE cc_start: 0.7328 (m-80) cc_final: 0.7103 (m-80) REVERT: E 318 MET cc_start: 0.6450 (pp-130) cc_final: 0.5394 (mtt) outliers start: 72 outliers final: 52 residues processed: 457 average time/residue: 1.0809 time to fit residues: 560.1905 Evaluate side-chains 469 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 407 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 157 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 202 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS C 92 ASN D 104 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.190800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.136979 restraints weight = 20312.748| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.97 r_work: 0.3222 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18155 Z= 0.162 Angle : 0.625 9.906 24626 Z= 0.327 Chirality : 0.043 0.259 2788 Planarity : 0.005 0.066 3080 Dihedral : 4.591 24.467 2399 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 3.31 % Allowed : 24.95 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.47 (0.19), residues: 2146 helix: 2.31 (0.16), residues: 960 sheet: 1.00 (0.24), residues: 472 loop : -0.95 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 226 HIS 0.005 0.001 HIS H 35 PHE 0.030 0.001 PHE A 27 TYR 0.032 0.002 TYR A 105 ARG 0.015 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05484 ( 1079) hydrogen bonds : angle 4.55219 ( 3096) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.45939 ( 8) covalent geometry : bond 0.00377 (18151) covalent geometry : angle 0.62495 (24618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 408 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.8121 (tttp) cc_final: 0.7804 (tttm) REVERT: H 76 LYS cc_start: 0.8589 (mttp) cc_final: 0.7989 (mtmt) REVERT: H 98 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8714 (tmm160) REVERT: G 25 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7535 (ttm110) REVERT: G 28 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: G 43 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7853 (mptt) REVERT: G 80 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7613 (mm-40) REVERT: F 1 GLU cc_start: 0.6891 (tp30) cc_final: 0.6282 (tp30) REVERT: F 6 GLU cc_start: 0.8519 (mp0) cc_final: 0.8008 (mp0) REVERT: A 100 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 110 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7415 (mm) REVERT: A 201 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: A 217 ASN cc_start: 0.8908 (m-40) cc_final: 0.8670 (m-40) REVERT: A 244 GLU cc_start: 0.6711 (tp30) cc_final: 0.6091 (tt0) REVERT: A 281 SER cc_start: 0.7845 (m) cc_final: 0.7575 (m) REVERT: B 119 LEU cc_start: 0.7271 (pt) cc_final: 0.6482 (pt) REVERT: B 121 GLU cc_start: 0.7771 (pm20) cc_final: 0.7282 (pm20) REVERT: B 206 GLU cc_start: 0.7588 (mp0) cc_final: 0.7380 (mp0) REVERT: B 230 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: B 297 ILE cc_start: 0.8296 (tt) cc_final: 0.7987 (pt) REVERT: C 121 GLU cc_start: 0.7928 (mp0) cc_final: 0.7230 (mp0) REVERT: C 213 GLN cc_start: 0.7950 (tp40) cc_final: 0.7702 (tp40) REVERT: C 245 LYS cc_start: 0.8282 (mmmm) cc_final: 0.8037 (mmmm) REVERT: D 186 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: D 198 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.6036 (tp30) REVERT: D 237 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7599 (mtm180) REVERT: D 263 ASP cc_start: 0.7797 (m-30) cc_final: 0.7513 (m-30) REVERT: D 266 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: D 297 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7545 (mp) REVERT: E 164 LYS cc_start: 0.6741 (mmmm) cc_final: 0.6500 (mmmt) REVERT: E 181 TYR cc_start: 0.4987 (m-80) cc_final: 0.4170 (m-80) REVERT: E 185 LEU cc_start: 0.7968 (mp) cc_final: 0.7731 (mt) REVERT: E 301 PHE cc_start: 0.7309 (m-80) cc_final: 0.7065 (m-80) REVERT: E 318 MET cc_start: 0.6428 (pp-130) cc_final: 0.5409 (mtt) outliers start: 66 outliers final: 47 residues processed: 442 average time/residue: 1.0640 time to fit residues: 534.0683 Evaluate side-chains 461 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 403 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 0.0770 chunk 88 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN B 120 HIS C 92 ASN D 104 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.190749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.137384 restraints weight = 20272.882| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.97 r_work: 0.3224 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18155 Z= 0.163 Angle : 0.624 9.059 24626 Z= 0.327 Chirality : 0.043 0.257 2788 Planarity : 0.005 0.067 3080 Dihedral : 4.578 24.450 2399 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 3.61 % Allowed : 24.80 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 1.45 (0.19), residues: 2146 helix: 2.30 (0.16), residues: 960 sheet: 1.06 (0.24), residues: 460 loop : -0.99 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 226 HIS 0.004 0.001 HIS H 35 PHE 0.030 0.001 PHE A 27 TYR 0.037 0.002 TYR A 105 ARG 0.015 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 1079) hydrogen bonds : angle 4.53497 ( 3096) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.40306 ( 8) covalent geometry : bond 0.00381 (18151) covalent geometry : angle 0.62393 (24618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16971.41 seconds wall clock time: 291 minutes 49.38 seconds (17509.38 seconds total)