Starting phenix.real_space_refine on Sat Oct 11 23:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmg_41388/10_2025/8tmg_41388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmg_41388/10_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_41388/10_2025/8tmg_41388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmg_41388/10_2025/8tmg_41388.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmg_41388/10_2025/8tmg_41388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmg_41388/10_2025/8tmg_41388.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.78, per 1000 atoms: 0.27 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: 1.57 Conformation dependent library (CDL) restraints added in 684.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.73 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: 3.14 Time building geometry restraints manager: 2.07 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.620 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- 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 : 10.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG L 67 TYR 0.018 0.002 TYR B 171 PHE 0.015 0.001 PHE B 147 TRP 0.010 0.001 TRP B 226 HIS 0.006 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00389 (18151) covalent geometry : angle 0.62561 (24618) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.57887 ( 8) hydrogen bonds : bond 0.16642 ( 1079) hydrogen bonds : angle 6.58411 ( 3096) *********************** 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 : 0.479 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: 0.5495 time to fit residues: 306.8493 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 : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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 = 0.190292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.135648 restraints weight = 20114.007| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.98 r_work: 0.3212 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18155 Z= 0.200 Angle : 0.648 10.240 24626 Z= 0.343 Chirality : 0.045 0.199 2788 Planarity : 0.005 0.050 3080 Dihedral : 4.757 27.957 2399 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 2.81 % Allowed : 13.86 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 2146 helix: 2.13 (0.16), residues: 966 sheet: 1.06 (0.24), residues: 488 loop : -1.00 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 67 TYR 0.025 0.002 TYR B 171 PHE 0.013 0.002 PHE D 42 TRP 0.012 0.001 TRP B 226 HIS 0.006 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00466 (18151) covalent geometry : angle 0.64817 (24618) SS BOND : bond 0.00475 ( 4) SS BOND : angle 1.08783 ( 8) hydrogen bonds : bond 0.06448 ( 1079) hydrogen bonds : angle 5.13968 ( 3096) *********************** 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 498 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 442 time to evaluate : 0.699 Fit side-chains REVERT: G 25 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7610 (ttm110) REVERT: G 80 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7777 (mm-40) REVERT: F 1 GLU cc_start: 0.7071 (tp30) cc_final: 0.6443 (tp30) REVERT: F 6 GLU cc_start: 0.8516 (mp0) cc_final: 0.8030 (mp0) REVERT: A 100 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 138 MET cc_start: 0.8036 (ttp) cc_final: 0.7775 (ttp) REVERT: A 230 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 281 SER cc_start: 0.8007 (m) cc_final: 0.7739 (m) REVERT: A 289 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6830 (mt-10) REVERT: A 297 ILE cc_start: 0.8288 (mp) cc_final: 0.8066 (mp) REVERT: A 334 MET cc_start: 0.5516 (mmp) cc_final: 0.4863 (mmp) REVERT: B 85 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8321 (mt) REVERT: B 119 LEU cc_start: 0.7151 (pt) cc_final: 0.6539 (pt) REVERT: B 121 GLU cc_start: 0.7815 (pm20) cc_final: 0.7275 (pm20) REVERT: B 191 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6235 (mm-30) REVERT: B 215 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8167 (ttpp) REVERT: B 230 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 297 ILE cc_start: 0.8208 (tt) cc_final: 0.7907 (pt) REVERT: C 121 GLU cc_start: 0.7823 (mp0) cc_final: 0.7277 (mp0) REVERT: C 163 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7596 (mmmm) REVERT: C 189 ASP cc_start: 0.8652 (t0) cc_final: 0.8409 (t0) REVERT: C 213 GLN cc_start: 0.7943 (tp40) cc_final: 0.7691 (tp40) REVERT: C 220 GLU cc_start: 0.8048 (tp30) cc_final: 0.7709 (mm-30) REVERT: C 245 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8220 (mmmm) REVERT: D 100 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8603 (mt-10) REVERT: D 180 ASP cc_start: 0.8225 (t70) cc_final: 0.7884 (t70) REVERT: D 216 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7978 (mtp-110) REVERT: D 237 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7574 (mtm180) REVERT: D 266 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: D 297 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7465 (mp) REVERT: E 102 PHE cc_start: 0.7625 (m-80) cc_final: 0.7320 (m-80) outliers start: 56 outliers final: 22 residues processed: 459 average time/residue: 0.5452 time to fit residues: 282.6170 Evaluate side-chains 441 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 413 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 201 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 140 GLN A 285 ASN B 63 ASN C 92 ASN D 104 ASN E 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.189419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.135890 restraints weight = 20411.905| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.95 r_work: 0.3216 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18155 Z= 0.192 Angle : 0.619 8.930 24626 Z= 0.329 Chirality : 0.044 0.207 2788 Planarity : 0.005 0.044 3080 Dihedral : 4.722 26.936 2399 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 3.46 % Allowed : 16.82 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 2146 helix: 2.19 (0.16), residues: 965 sheet: 1.10 (0.24), residues: 474 loop : -1.09 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.019 0.002 TYR E 236 PHE 0.022 0.002 PHE E 27 TRP 0.012 0.001 TRP B 226 HIS 0.005 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00448 (18151) covalent geometry : angle 0.61906 (24618) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.94621 ( 8) hydrogen bonds : bond 0.06190 ( 1079) hydrogen bonds : angle 4.91442 ( 3096) *********************** 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 498 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8303 (t) REVERT: G 25 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7568 (ttm110) REVERT: G 80 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7617 (mm-40) REVERT: F 1 GLU cc_start: 0.7062 (tp30) cc_final: 0.6453 (tp30) REVERT: F 6 GLU cc_start: 0.8553 (mp0) cc_final: 0.8026 (mp0) REVERT: A 100 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 105 TYR cc_start: 0.7833 (p90) cc_final: 0.7624 (p90) REVERT: A 281 SER cc_start: 0.8026 (m) cc_final: 0.7751 (m) REVERT: A 289 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6823 (mt-10) REVERT: A 291 MET cc_start: 0.6273 (mmp) cc_final: 0.5994 (mmp) REVERT: A 334 MET cc_start: 0.5981 (mmp) cc_final: 0.5274 (mmp) REVERT: B 119 LEU cc_start: 0.7248 (pt) cc_final: 0.6570 (pt) REVERT: B 121 GLU cc_start: 0.7826 (pm20) cc_final: 0.7319 (pm20) REVERT: B 191 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6274 (mm-30) REVERT: B 215 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8191 (ttpp) REVERT: B 230 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: B 297 ILE cc_start: 0.8342 (tt) cc_final: 0.8033 (pt) REVERT: C 121 GLU cc_start: 0.7901 (mp0) cc_final: 0.7283 (mp0) REVERT: C 163 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7631 (mmmm) REVERT: C 175 ASP cc_start: 0.7865 (p0) cc_final: 0.7616 (p0) REVERT: C 213 GLN cc_start: 0.7961 (tp40) cc_final: 0.7716 (tp40) REVERT: C 245 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8132 (mmmm) REVERT: D 100 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: D 180 ASP cc_start: 0.8186 (t70) cc_final: 0.7873 (t70) REVERT: D 186 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: D 207 THR cc_start: 0.8068 (p) cc_final: 0.7834 (p) REVERT: D 237 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7595 (mtm180) REVERT: D 263 ASP cc_start: 0.7814 (m-30) cc_final: 0.7478 (m-30) REVERT: D 266 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: D 297 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7571 (mp) REVERT: E 172 SER cc_start: 0.6680 (m) cc_final: 0.6246 (t) REVERT: E 313 MET cc_start: 0.3938 (mmp) cc_final: 0.3070 (mmt) REVERT: E 318 MET cc_start: 0.6349 (pp-130) cc_final: 0.5473 (ttt) outliers start: 69 outliers final: 39 residues processed: 460 average time/residue: 0.5735 time to fit residues: 297.2660 Evaluate side-chains 460 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 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 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 57 SER Chi-restraints excluded: chain D residue 100 GLU 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 180 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 146 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 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 = 0.3988 r_free = 0.3988 target = 0.190844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.138087 restraints weight = 20280.279| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.90 r_work: 0.3230 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18155 Z= 0.157 Angle : 0.586 8.610 24626 Z= 0.311 Chirality : 0.043 0.217 2788 Planarity : 0.004 0.043 3080 Dihedral : 4.597 26.154 2399 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.07 % Allowed : 18.02 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.19), residues: 2146 helix: 2.32 (0.16), residues: 966 sheet: 1.08 (0.24), residues: 468 loop : -1.02 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 162 TYR 0.022 0.001 TYR E 236 PHE 0.022 0.001 PHE A 27 TRP 0.011 0.001 TRP B 226 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00354 (18151) covalent geometry : angle 0.58639 (24618) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.78166 ( 8) hydrogen bonds : bond 0.05715 ( 1079) hydrogen bonds : angle 4.70211 ( 3096) *********************** 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 513 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 432 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8204 (pm20) cc_final: 0.7981 (mp0) REVERT: H 65 LYS cc_start: 0.8139 (tttp) cc_final: 0.7760 (tttm) REVERT: H 98 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8673 (tmm160) REVERT: L 80 GLN cc_start: 0.7730 (mt0) cc_final: 0.7450 (mt0) REVERT: G 25 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7635 (ttm110) REVERT: G 80 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7831 (mm-40) REVERT: F 1 GLU cc_start: 0.7061 (tp30) cc_final: 0.6485 (tp30) REVERT: A 62 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7386 (mm) REVERT: A 100 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 138 MET cc_start: 0.7825 (ttp) cc_final: 0.6992 (ttp) REVERT: A 196 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 237 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6596 (mtp180) REVERT: A 281 SER cc_start: 0.8068 (m) cc_final: 0.7798 (m) REVERT: A 289 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6612 (mt-10) REVERT: A 291 MET cc_start: 0.6269 (mmp) cc_final: 0.5889 (mmp) REVERT: A 334 MET cc_start: 0.5909 (mmp) cc_final: 0.4903 (mmp) REVERT: B 85 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 119 LEU cc_start: 0.7288 (pt) cc_final: 0.6934 (pt) REVERT: B 121 GLU cc_start: 0.7884 (pm20) cc_final: 0.7526 (pm20) REVERT: B 191 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6236 (mm-30) REVERT: B 206 GLU cc_start: 0.7617 (mp0) cc_final: 0.7393 (mp0) REVERT: B 215 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8304 (ttpp) REVERT: B 230 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: B 297 ILE cc_start: 0.8499 (tt) cc_final: 0.8210 (pt) REVERT: C 121 GLU cc_start: 0.8024 (mp0) cc_final: 0.7434 (mp0) REVERT: C 162 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7582 (mmm-85) REVERT: C 163 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7657 (mmmm) REVERT: C 213 GLN cc_start: 0.8037 (tp40) cc_final: 0.7817 (tp40) REVERT: C 245 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8155 (mmmm) REVERT: D 186 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: D 237 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7686 (mtm180) REVERT: D 263 ASP cc_start: 0.7904 (m-30) cc_final: 0.7629 (m-30) REVERT: D 266 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: D 297 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7717 (mp) REVERT: E 313 MET cc_start: 0.3291 (mmp) cc_final: 0.2466 (mmt) REVERT: E 318 MET cc_start: 0.6334 (pp-130) cc_final: 0.5461 (mtt) outliers start: 81 outliers final: 47 residues processed: 467 average time/residue: 0.5482 time to fit residues: 289.7706 Evaluate side-chains 472 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 416 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 146 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 LEU 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 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 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 33 optimal weight: 0.0470 chunk 91 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.190521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.136699 restraints weight = 20186.893| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.05 r_work: 0.3210 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 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 = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18155 Z= 0.164 Angle : 0.587 9.987 24626 Z= 0.311 Chirality : 0.043 0.220 2788 Planarity : 0.004 0.043 3080 Dihedral : 4.569 25.553 2399 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 4.67 % Allowed : 19.63 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.19), residues: 2146 helix: 2.34 (0.16), residues: 966 sheet: 1.08 (0.24), residues: 456 loop : -1.08 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 67 TYR 0.038 0.002 TYR A 105 PHE 0.027 0.001 PHE A 27 TRP 0.010 0.001 TRP B 226 HIS 0.005 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00377 (18151) covalent geometry : angle 0.58648 (24618) SS BOND : bond 0.00345 ( 4) SS BOND : angle 0.86363 ( 8) hydrogen bonds : bond 0.05666 ( 1079) hydrogen bonds : angle 4.63671 ( 3096) *********************** 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 524 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 431 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8320 (pm20) cc_final: 0.8073 (mp0) REVERT: H 65 LYS cc_start: 0.8068 (tttp) cc_final: 0.7686 (tttm) REVERT: H 98 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8726 (tmm160) REVERT: L 80 GLN cc_start: 0.7659 (mt0) cc_final: 0.7326 (mt0) REVERT: G 25 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7537 (ttm110) REVERT: G 80 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7699 (mm-40) REVERT: F 1 GLU cc_start: 0.6951 (tp30) cc_final: 0.6335 (tp30) REVERT: F 6 GLU cc_start: 0.8455 (mp0) cc_final: 0.8172 (mp0) REVERT: A 62 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7232 (mm) REVERT: A 100 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 138 MET cc_start: 0.7867 (ttp) cc_final: 0.6982 (ttp) REVERT: A 281 SER cc_start: 0.7851 (m) cc_final: 0.7576 (m) REVERT: A 334 MET cc_start: 0.6221 (mmp) cc_final: 0.5629 (mmp) REVERT: B 85 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8404 (mt) REVERT: B 119 LEU cc_start: 0.7189 (pt) cc_final: 0.6600 (pt) REVERT: B 121 GLU cc_start: 0.7807 (pm20) cc_final: 0.7336 (pm20) REVERT: B 191 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6079 (mm-30) REVERT: B 215 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8211 (ttpp) REVERT: B 230 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: B 297 ILE cc_start: 0.8280 (tt) cc_final: 0.8002 (pt) REVERT: C 121 GLU cc_start: 0.7917 (mp0) cc_final: 0.7181 (mp0) REVERT: C 162 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7629 (mmm-85) REVERT: C 163 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7616 (mmmm) REVERT: C 213 GLN cc_start: 0.7933 (tp40) cc_final: 0.7673 (tp40) REVERT: C 245 LYS cc_start: 0.8284 (mmmm) cc_final: 0.8015 (mmmm) REVERT: D 100 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8589 (mt-10) REVERT: D 180 ASP cc_start: 0.8185 (t70) cc_final: 0.7849 (t70) REVERT: D 186 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: D 237 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7601 (mtm180) REVERT: D 263 ASP cc_start: 0.7917 (m-30) cc_final: 0.7590 (m-30) REVERT: D 266 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: D 297 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7553 (mp) REVERT: E 28 GLU cc_start: 0.5512 (tm-30) cc_final: 0.5208 (tm-30) REVERT: E 38 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6335 (pp20) REVERT: E 105 TYR cc_start: 0.7729 (p90) cc_final: 0.7444 (p90) REVERT: E 172 SER cc_start: 0.6660 (m) cc_final: 0.6210 (t) REVERT: E 185 LEU cc_start: 0.7864 (mp) cc_final: 0.7626 (mt) REVERT: E 313 MET cc_start: 0.3206 (mmp) cc_final: 0.2457 (mmt) REVERT: E 318 MET cc_start: 0.6436 (pp-130) cc_final: 0.5372 (mtt) outliers start: 93 outliers final: 59 residues processed: 482 average time/residue: 0.5601 time to fit residues: 304.9608 Evaluate side-chains 483 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 414 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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 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 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 109 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 133 LYS 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 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 50 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 100 GLU 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 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 38 GLU Chi-restraints excluded: chain E residue 43 LYS 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 186 GLU Chi-restraints excluded: chain E residue 280 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 46 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 187 optimal weight: 0.0030 chunk 206 optimal weight: 0.8980 chunk 1 optimal weight: 0.0370 chunk 109 optimal weight: 0.0060 chunk 100 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 198 optimal weight: 2.9990 overall best weight: 0.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN G 7 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN B 63 ASN B 126 GLN C 92 ASN D 68 HIS D 104 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.196163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.143807 restraints weight = 20398.902| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.99 r_work: 0.3326 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18155 Z= 0.125 Angle : 0.553 7.845 24626 Z= 0.294 Chirality : 0.042 0.232 2788 Planarity : 0.004 0.042 3080 Dihedral : 4.331 23.550 2399 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 3.21 % Allowed : 21.84 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.19), residues: 2146 helix: 2.53 (0.17), residues: 967 sheet: 1.25 (0.25), residues: 438 loop : -1.03 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.032 0.001 TYR A 105 PHE 0.029 0.001 PHE E 27 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00252 (18151) covalent geometry : angle 0.55349 (24618) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.57339 ( 8) hydrogen bonds : bond 0.04800 ( 1079) hydrogen bonds : angle 4.40126 ( 3096) *********************** 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 492 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 428 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7953 (tttp) cc_final: 0.7553 (tttm) REVERT: H 98 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8508 (ttt-90) REVERT: L 80 GLN cc_start: 0.7655 (mt0) cc_final: 0.7349 (mt0) REVERT: L 101 GLN cc_start: 0.7784 (pm20) cc_final: 0.7552 (pm20) REVERT: G 25 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7500 (ttm110) REVERT: G 43 LYS cc_start: 0.8120 (mptm) cc_final: 0.7802 (mptp) REVERT: G 62 ARG cc_start: 0.7990 (mpp-170) cc_final: 0.7784 (ptp-170) REVERT: G 80 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7482 (mm-40) REVERT: F 1 GLU cc_start: 0.6895 (tp30) cc_final: 0.6376 (tp30) REVERT: F 6 GLU cc_start: 0.8377 (mp0) cc_final: 0.8131 (mp0) REVERT: F 20 LEU cc_start: 0.8966 (mt) cc_final: 0.8683 (mt) REVERT: A 100 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7438 (mt-10) REVERT: A 139 PHE cc_start: 0.8067 (m-80) cc_final: 0.7722 (m-80) REVERT: A 281 SER cc_start: 0.7804 (m) cc_final: 0.7523 (m) REVERT: A 297 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 334 MET cc_start: 0.5821 (mmp) cc_final: 0.4570 (mmp) REVERT: B 85 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 119 LEU cc_start: 0.7214 (pt) cc_final: 0.6596 (pt) REVERT: B 121 GLU cc_start: 0.7642 (pm20) cc_final: 0.7199 (pm20) REVERT: B 206 GLU cc_start: 0.7448 (mp0) cc_final: 0.7204 (mp0) REVERT: B 215 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8159 (ttpp) REVERT: B 230 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: B 297 ILE cc_start: 0.8278 (tt) cc_final: 0.8012 (pt) REVERT: C 40 ARG cc_start: 0.7262 (ttp80) cc_final: 0.7041 (ttp80) REVERT: C 162 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7557 (mmm-85) REVERT: C 175 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7299 (p0) REVERT: C 189 ASP cc_start: 0.8513 (t0) cc_final: 0.8306 (t0) REVERT: C 191 GLU cc_start: 0.8174 (tt0) cc_final: 0.7963 (tt0) REVERT: C 213 GLN cc_start: 0.7826 (tp40) cc_final: 0.7609 (tp40) REVERT: C 245 LYS cc_start: 0.8290 (mmmm) cc_final: 0.8036 (mmmm) REVERT: D 186 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: D 202 ARG cc_start: 0.6454 (mpp80) cc_final: 0.6192 (mpp80) REVERT: D 237 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7483 (mtm180) REVERT: D 263 ASP cc_start: 0.7700 (m-30) cc_final: 0.7395 (m-30) REVERT: D 297 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7394 (mp) REVERT: E 28 GLU cc_start: 0.5636 (tm-30) cc_final: 0.5401 (tm-30) REVERT: E 125 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6017 (pp20) REVERT: E 164 LYS cc_start: 0.6424 (mmmm) cc_final: 0.6174 (mmmt) REVERT: E 301 PHE cc_start: 0.7166 (m-80) cc_final: 0.6901 (m-80) REVERT: E 313 MET cc_start: 0.2948 (mmp) cc_final: 0.2413 (mmt) REVERT: E 318 MET cc_start: 0.6376 (pp-130) cc_final: 0.5534 (mtt) outliers start: 64 outliers final: 26 residues processed: 464 average time/residue: 0.5644 time to fit residues: 296.2720 Evaluate side-chains 430 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 395 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 75 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 106 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 85 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 272 VAL 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 287 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 167 ASP 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 280 LEU 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 90 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 103 optimal weight: 0.4980 chunk 202 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 44 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 92 ASN E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.193010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.139765 restraints weight = 20260.322| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.97 r_work: 0.3261 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.003 0.052 18155 Z= 0.142 Angle : 0.583 9.324 24626 Z= 0.305 Chirality : 0.043 0.230 2788 Planarity : 0.004 0.042 3080 Dihedral : 4.371 24.859 2399 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 3.51 % Allowed : 23.39 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.19), residues: 2146 helix: 2.50 (0.16), residues: 961 sheet: 1.31 (0.25), residues: 443 loop : -0.94 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.036 0.001 TYR A 105 PHE 0.025 0.001 PHE A 27 TRP 0.009 0.001 TRP B 226 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00323 (18151) covalent geometry : angle 0.58290 (24618) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.96852 ( 8) hydrogen bonds : bond 0.05050 ( 1079) hydrogen bonds : angle 4.39899 ( 3096) *********************** 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 479 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 409 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7918 (tttp) cc_final: 0.7589 (tttm) REVERT: H 98 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8549 (tmm160) REVERT: L 80 GLN cc_start: 0.7635 (mt0) cc_final: 0.7337 (mt0) REVERT: G 25 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7563 (ttm110) REVERT: G 28 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: G 43 LYS cc_start: 0.8164 (mptm) cc_final: 0.7849 (mptp) REVERT: G 80 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7619 (mm-40) REVERT: F 1 GLU cc_start: 0.6943 (tp30) cc_final: 0.6278 (tp30) REVERT: F 6 GLU cc_start: 0.8422 (mp0) cc_final: 0.7968 (mp0) REVERT: A 100 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 110 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7459 (mm) REVERT: A 139 PHE cc_start: 0.8100 (m-80) cc_final: 0.7720 (m-80) REVERT: A 281 SER cc_start: 0.7825 (m) cc_final: 0.7548 (m) REVERT: A 334 MET cc_start: 0.6201 (mmp) cc_final: 0.5811 (mmp) REVERT: B 85 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 119 LEU cc_start: 0.7252 (pt) cc_final: 0.6445 (pt) REVERT: B 121 GLU cc_start: 0.7615 (pm20) cc_final: 0.7122 (pm20) REVERT: B 191 GLU cc_start: 0.7272 (mm-30) cc_final: 0.5949 (mm-30) REVERT: B 206 GLU cc_start: 0.7527 (mp0) cc_final: 0.7272 (mp0) REVERT: B 215 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8220 (ttpp) REVERT: B 230 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: B 297 ILE cc_start: 0.8242 (tt) cc_final: 0.7911 (pt) REVERT: C 40 ARG cc_start: 0.7301 (ttp80) cc_final: 0.7069 (ttp80) REVERT: C 121 GLU cc_start: 0.7944 (mp0) cc_final: 0.7219 (mp0) REVERT: C 152 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: C 162 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7707 (mmm-85) REVERT: C 175 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7276 (p0) REVERT: C 189 ASP cc_start: 0.8586 (t0) cc_final: 0.8267 (t70) REVERT: C 220 GLU cc_start: 0.7904 (tp30) cc_final: 0.7687 (mm-30) REVERT: C 245 LYS cc_start: 0.8287 (mmmm) cc_final: 0.8022 (mmmm) REVERT: D 191 GLU cc_start: 0.8046 (tp30) cc_final: 0.7440 (tp30) REVERT: D 237 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7585 (mtm180) REVERT: D 263 ASP cc_start: 0.7746 (m-30) cc_final: 0.7427 (m-30) REVERT: D 266 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6750 (tp30) REVERT: D 297 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7431 (mp) REVERT: E 28 GLU cc_start: 0.5675 (tm-30) cc_final: 0.5425 (tm-30) REVERT: E 164 LYS cc_start: 0.6542 (mmmm) cc_final: 0.6308 (mmmt) REVERT: E 189 ASP cc_start: 0.7596 (t70) cc_final: 0.7284 (t70) REVERT: E 289 GLU cc_start: 0.7932 (pt0) cc_final: 0.7714 (pt0) REVERT: E 301 PHE cc_start: 0.7252 (m-80) cc_final: 0.6981 (m-80) REVERT: E 313 MET cc_start: 0.2958 (mmp) cc_final: 0.2411 (mmt) REVERT: E 318 MET cc_start: 0.6341 (pp-130) cc_final: 0.5488 (mtt) outliers start: 70 outliers final: 41 residues processed: 455 average time/residue: 0.5628 time to fit residues: 288.8794 Evaluate side-chains 448 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 397 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 28 GLN 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 106 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 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 85 LEU Chi-restraints excluded: chain B residue 167 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 B residue 272 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 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 50 VAL Chi-restraints excluded: chain D residue 167 ASP 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 297 ILE Chi-restraints excluded: chain E residue 43 LYS 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 112 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 150 VAL 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 142 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN B 120 HIS C 92 ASN E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.192435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.139075 restraints weight = 20295.057| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.00 r_work: 0.3249 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18155 Z= 0.151 Angle : 0.593 9.283 24626 Z= 0.310 Chirality : 0.043 0.237 2788 Planarity : 0.004 0.053 3080 Dihedral : 4.422 24.714 2399 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 3.41 % Allowed : 24.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.19), residues: 2146 helix: 2.46 (0.16), residues: 960 sheet: 1.27 (0.25), residues: 444 loop : -0.93 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 69 TYR 0.037 0.001 TYR A 105 PHE 0.024 0.001 PHE A 27 TRP 0.009 0.001 TRP B 226 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00348 (18151) covalent geometry : angle 0.59286 (24618) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.16452 ( 8) hydrogen bonds : bond 0.05171 ( 1079) hydrogen bonds : angle 4.42652 ( 3096) *********************** 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 477 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 409 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7901 (tttp) cc_final: 0.7526 (tttm) REVERT: H 98 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8601 (tmm160) REVERT: L 80 GLN cc_start: 0.7633 (mt0) cc_final: 0.7329 (mt0) REVERT: G 25 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7543 (ttm110) REVERT: G 28 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: G 43 LYS cc_start: 0.8168 (mptm) cc_final: 0.7849 (mptp) REVERT: G 62 ARG cc_start: 0.8575 (ptp-170) cc_final: 0.8375 (ptp-170) REVERT: G 80 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7553 (mm-40) REVERT: F 1 GLU cc_start: 0.6931 (tp30) cc_final: 0.6263 (tp30) REVERT: A 100 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 110 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7449 (mm) REVERT: A 139 PHE cc_start: 0.8050 (m-80) cc_final: 0.7825 (m-80) REVERT: A 201 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6936 (tm-30) REVERT: A 281 SER cc_start: 0.7875 (m) cc_final: 0.7607 (m) REVERT: A 297 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7831 (mp) REVERT: A 334 MET cc_start: 0.6283 (mmp) cc_final: 0.5783 (mmp) REVERT: B 85 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 119 LEU cc_start: 0.7234 (pt) cc_final: 0.6608 (pt) REVERT: B 121 GLU cc_start: 0.7638 (pm20) cc_final: 0.7159 (pm20) REVERT: B 206 GLU cc_start: 0.7561 (mp0) cc_final: 0.7307 (mp0) REVERT: B 230 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: B 297 ILE cc_start: 0.8284 (tt) cc_final: 0.7937 (pt) REVERT: C 40 ARG cc_start: 0.7310 (ttp80) cc_final: 0.7081 (ttp80) REVERT: C 152 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: C 162 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7727 (mmm-85) REVERT: C 189 ASP cc_start: 0.8557 (t0) cc_final: 0.8237 (t70) REVERT: C 220 GLU cc_start: 0.7984 (tp30) cc_final: 0.7757 (mm-30) REVERT: C 245 LYS cc_start: 0.8290 (mmmm) cc_final: 0.8041 (mmmm) REVERT: D 191 GLU cc_start: 0.8096 (tp30) cc_final: 0.7469 (tp30) REVERT: D 202 ARG cc_start: 0.6477 (mpp80) cc_final: 0.6233 (mpp80) REVERT: D 237 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7580 (mtm180) REVERT: D 263 ASP cc_start: 0.7730 (m-30) cc_final: 0.7416 (m-30) REVERT: D 266 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6743 (tp30) REVERT: D 292 LYS cc_start: 0.8075 (tttt) cc_final: 0.7805 (tppt) REVERT: D 297 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7424 (mp) REVERT: E 69 ARG cc_start: 0.7109 (mtp-110) cc_final: 0.6038 (ptm160) REVERT: E 164 LYS cc_start: 0.6516 (mmmm) cc_final: 0.6291 (mmmt) REVERT: E 301 PHE cc_start: 0.7263 (m-80) cc_final: 0.7013 (m-80) REVERT: E 313 MET cc_start: 0.3132 (mmp) cc_final: 0.2481 (mmt) REVERT: E 318 MET cc_start: 0.6337 (pp-130) cc_final: 0.5463 (mtt) outliers start: 68 outliers final: 45 residues processed: 452 average time/residue: 0.5831 time to fit residues: 296.9398 Evaluate side-chains 457 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 402 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain G residue 28 GLN 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 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 127 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 297 ILE 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 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 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 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 50 VAL Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 43 LYS 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 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 0.0980 chunk 171 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN A 288 ASN B 63 ASN B 120 HIS C 92 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4009 r_free = 0.4009 target = 0.192918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.140971 restraints weight = 20359.903| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.96 r_work: 0.3273 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- 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 = 0.46 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18155 Z= 0.142 Angle : 0.594 8.800 24626 Z= 0.310 Chirality : 0.042 0.236 2788 Planarity : 0.004 0.055 3080 Dihedral : 4.401 23.698 2399 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 3.16 % Allowed : 24.90 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.19), residues: 2146 helix: 2.46 (0.16), residues: 961 sheet: 1.31 (0.25), residues: 444 loop : -0.95 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.029 0.001 TYR A 105 PHE 0.030 0.001 PHE A 27 TRP 0.009 0.001 TRP A 226 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00324 (18151) covalent geometry : angle 0.59370 (24618) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.05461 ( 8) hydrogen bonds : bond 0.05072 ( 1079) hydrogen bonds : angle 4.40687 ( 3096) *********************** 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 469 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 406 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7900 (tttp) cc_final: 0.7573 (tttm) REVERT: H 98 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8593 (tmm160) REVERT: G 25 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7523 (ttm110) REVERT: G 28 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: G 43 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7830 (mptt) REVERT: F 1 GLU cc_start: 0.6915 (tp30) cc_final: 0.6265 (tp30) REVERT: F 76 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7988 (ttmm) REVERT: A 100 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7357 (mt-10) REVERT: A 110 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7396 (mm) REVERT: A 139 PHE cc_start: 0.7961 (m-80) cc_final: 0.7703 (m-80) REVERT: A 281 SER cc_start: 0.7757 (m) cc_final: 0.7502 (m) REVERT: A 297 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 313 MET cc_start: 0.3140 (mmm) cc_final: 0.2596 (mmm) REVERT: B 119 LEU cc_start: 0.7248 (pt) cc_final: 0.6527 (pt) REVERT: B 121 GLU cc_start: 0.7633 (pm20) cc_final: 0.7128 (pm20) REVERT: B 206 GLU cc_start: 0.7514 (mp0) cc_final: 0.7272 (mp0) REVERT: B 230 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: B 297 ILE cc_start: 0.8339 (tt) cc_final: 0.7984 (pt) REVERT: C 40 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6916 (ttp-170) REVERT: C 152 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6447 (mt-10) REVERT: C 162 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7652 (mmm-85) REVERT: C 189 ASP cc_start: 0.8587 (t0) cc_final: 0.8284 (t70) REVERT: C 220 GLU cc_start: 0.7948 (tp30) cc_final: 0.7667 (mm-30) REVERT: C 245 LYS cc_start: 0.8275 (mmmm) cc_final: 0.8033 (mmmm) REVERT: D 191 GLU cc_start: 0.8060 (tp30) cc_final: 0.7443 (tp30) REVERT: D 202 ARG cc_start: 0.6607 (mpp80) cc_final: 0.6337 (mpp80) REVERT: D 237 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7606 (mtm180) REVERT: D 259 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8184 (mt) REVERT: D 263 ASP cc_start: 0.7776 (m-30) cc_final: 0.7482 (m-30) REVERT: D 266 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6720 (tp30) REVERT: D 297 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7428 (mp) REVERT: E 28 GLU cc_start: 0.5113 (tm-30) cc_final: 0.4906 (tm-30) REVERT: E 133 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7739 (mptt) REVERT: E 164 LYS cc_start: 0.6524 (mmmm) cc_final: 0.6306 (mmmt) REVERT: E 181 TYR cc_start: 0.5001 (m-80) cc_final: 0.4146 (m-80) REVERT: E 301 PHE cc_start: 0.7259 (m-80) cc_final: 0.7002 (m-80) REVERT: E 313 MET cc_start: 0.3183 (mmp) cc_final: 0.2566 (mmt) REVERT: E 318 MET cc_start: 0.6323 (pp-130) cc_final: 0.5461 (mtt) outliers start: 63 outliers final: 45 residues processed: 444 average time/residue: 0.5716 time to fit residues: 286.4660 Evaluate side-chains 452 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 396 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain L residue 75 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 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 127 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 28 GLU 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 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 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 180 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 50 VAL Chi-restraints excluded: chain D residue 167 ASP 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 259 ILE Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 43 LYS 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 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 5 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 26 optimal weight: 0.0040 chunk 178 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN B 63 ASN C 92 ASN E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.191940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138294 restraints weight = 20217.856| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.02 r_work: 0.3242 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2331 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= 0.160 Angle : 0.622 12.378 24626 Z= 0.323 Chirality : 0.043 0.232 2788 Planarity : 0.004 0.052 3080 Dihedral : 4.460 24.143 2399 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 3.11 % Allowed : 25.20 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.19), residues: 2146 helix: 2.38 (0.16), residues: 962 sheet: 1.24 (0.25), residues: 452 loop : -0.94 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.019 0.001 TYR B 236 PHE 0.030 0.001 PHE A 27 TRP 0.015 0.001 TRP A 226 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00374 (18151) covalent geometry : angle 0.62128 (24618) SS BOND : bond 0.00290 ( 4) SS BOND : angle 1.21070 ( 8) hydrogen bonds : bond 0.05279 ( 1079) hydrogen bonds : angle 4.44812 ( 3096) ********************** 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 467 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 65 LYS cc_start: 0.7903 (tttp) cc_final: 0.7532 (tttm) REVERT: H 98 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8659 (tmm160) REVERT: G 25 ARG cc_start: 0.7921 (ttm110) cc_final: 0.7588 (ttm110) REVERT: G 28 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: G 43 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7806 (mptt) REVERT: G 97 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9178 (mm) REVERT: F 1 GLU cc_start: 0.6906 (tp30) cc_final: 0.6240 (tp30) REVERT: F 6 GLU cc_start: 0.8604 (mp0) cc_final: 0.8254 (mp0) REVERT: F 76 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7969 (ttmm) REVERT: A 100 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7370 (mt-10) REVERT: A 110 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7439 (mm) REVERT: A 281 SER cc_start: 0.7829 (m) cc_final: 0.7591 (m) REVERT: A 297 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 313 MET cc_start: 0.3078 (mmm) cc_final: 0.2567 (mmm) REVERT: B 119 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6448 (pt) REVERT: B 121 GLU cc_start: 0.7707 (pm20) cc_final: 0.7162 (pm20) REVERT: B 206 GLU cc_start: 0.7558 (mp0) cc_final: 0.7313 (mp0) REVERT: B 230 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 297 ILE cc_start: 0.8313 (tt) cc_final: 0.7932 (pt) REVERT: C 40 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6951 (ttp-170) REVERT: C 152 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: C 189 ASP cc_start: 0.8559 (t0) cc_final: 0.8241 (t70) REVERT: C 220 GLU cc_start: 0.7996 (tp30) cc_final: 0.7711 (mm-30) REVERT: C 245 LYS cc_start: 0.8281 (mmmm) cc_final: 0.8040 (mmmm) REVERT: D 191 GLU cc_start: 0.8095 (tp30) cc_final: 0.7458 (tp30) REVERT: D 202 ARG cc_start: 0.6645 (mpp80) cc_final: 0.6367 (mpp80) REVERT: D 237 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7571 (mtm180) REVERT: D 263 ASP cc_start: 0.7829 (m-30) cc_final: 0.7532 (m-30) REVERT: D 266 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: D 297 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7438 (mp) REVERT: E 28 GLU cc_start: 0.5048 (tm-30) cc_final: 0.4843 (tm-30) REVERT: E 181 TYR cc_start: 0.5049 (m-80) cc_final: 0.4121 (m-80) REVERT: E 301 PHE cc_start: 0.7291 (m-80) cc_final: 0.7007 (m-80) REVERT: E 313 MET cc_start: 0.3247 (mmp) cc_final: 0.2500 (mmt) REVERT: E 318 MET cc_start: 0.6397 (pp-130) cc_final: 0.5476 (mtt) outliers start: 62 outliers final: 48 residues processed: 441 average time/residue: 0.5789 time to fit residues: 287.9404 Evaluate side-chains 460 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 400 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain L residue 75 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 G residue 97 ILE 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 266 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 167 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 B residue 272 VAL 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 180 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 50 VAL Chi-restraints excluded: chain D residue 167 ASP 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 259 ILE 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 43 LYS 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 305 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 18 optimal weight: 0.3980 chunk 179 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 chunk 149 optimal weight: 0.5980 chunk 195 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN B 63 ASN C 92 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** 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 = 0.4006 r_free = 0.4006 target = 0.192509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3469 r_free = 0.3469 target = 0.141474 restraints weight = 20328.476| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.93 r_work: 0.3282 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18155 Z= 0.148 Angle : 0.615 12.128 24626 Z= 0.320 Chirality : 0.043 0.231 2788 Planarity : 0.004 0.049 3080 Dihedral : 4.450 23.815 2399 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 3.16 % Allowed : 25.35 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.19), residues: 2146 helix: 2.41 (0.16), residues: 962 sheet: 1.22 (0.24), residues: 463 loop : -0.96 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 69 TYR 0.019 0.001 TYR B 236 PHE 0.029 0.001 PHE A 27 TRP 0.021 0.001 TRP A 226 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00339 (18151) covalent geometry : angle 0.61526 (24618) SS BOND : bond 0.00278 ( 4) SS BOND : angle 1.05687 ( 8) hydrogen bonds : bond 0.05163 ( 1079) hydrogen bonds : angle 4.41914 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8978.71 seconds wall clock time: 153 minutes 11.08 seconds (9191.08 seconds total)