Starting phenix.real_space_refine on Thu Jul 31 17:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dlu_30713/07_2025/7dlu_30713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dlu_30713/07_2025/7dlu_30713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dlu_30713/07_2025/7dlu_30713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dlu_30713/07_2025/7dlu_30713.map" model { file = "/net/cci-nas-00/data/ceres_data/7dlu_30713/07_2025/7dlu_30713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dlu_30713/07_2025/7dlu_30713.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 8911 2.51 5 N 2345 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13727 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1961 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 5.45, per 1000 atoms: 0.40 Number of scatterers: 13727 At special positions: 0 Unit cell: (101.091, 100.004, 141.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2443 8.00 N 2345 7.00 C 8911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.67 Conformation dependent library (CDL) restraints added in 2.0 seconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 54.2% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL A 19 " --> pdb=" O TRP A 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.510A pdb=" N GLY A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 105 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'B' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL B 19 " --> pdb=" O TRP B 15 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 85 removed outlier: 3.510A pdb=" N GLY B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 105 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 239 through 256 removed outlier: 4.751A pdb=" N ARG B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'C' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 25 " --> pdb=" O GLU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 105 Processing helix chain 'C' and resid 106 through 122 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'D' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 105 Processing helix chain 'D' and resid 106 through 122 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 239 through 256 removed outlier: 4.751A pdb=" N ARG D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'E' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL E 19 " --> pdb=" O TRP E 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE E 63 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 67 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 Processing helix chain 'E' and resid 106 through 122 Processing helix chain 'E' and resid 162 through 167 Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'F' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL F 19 " --> pdb=" O TRP F 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 85 removed outlier: 3.510A pdb=" N GLY F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 67 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 105 Processing helix chain 'F' and resid 106 through 122 Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 259 No H-bonds generated for 'chain 'F' and resid 257 through 259' Processing helix chain 'G' and resid 15 through 54 removed outlier: 3.701A pdb=" N VAL G 19 " --> pdb=" O TRP G 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 25 " --> pdb=" O GLU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 85 removed outlier: 3.511A pdb=" N GLY G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 67 " --> pdb=" O PHE G 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 105 Processing helix chain 'G' and resid 106 through 122 Processing helix chain 'G' and resid 162 through 167 Processing helix chain 'G' and resid 192 through 202 Processing helix chain 'G' and resid 239 through 256 removed outlier: 4.752A pdb=" N ARG G 252 " --> pdb=" O ASN G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 259 No H-bonds generated for 'chain 'G' and resid 257 through 259' Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 6.798A pdb=" N VAL A 149 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 143 " --> pdb=" O HIS A 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 149 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 143 " --> pdb=" O HIS B 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 149 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE C 143 " --> pdb=" O HIS C 147 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 149 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE D 143 " --> pdb=" O HIS D 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E 149 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE E 143 " --> pdb=" O HIS E 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL F 149 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE F 143 " --> pdb=" O HIS F 147 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N HIS F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL G 149 " --> pdb=" O ASP G 141 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE G 143 " --> pdb=" O HIS G 147 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS G 147 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR A 228 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 272 removed outlier: 6.827A pdb=" N ARG A 267 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL B 272 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 269 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 267 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL C 272 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 269 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG C 267 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL D 272 " --> pdb=" O ARG C 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL C 269 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG D 267 " --> pdb=" O LYS E 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL E 272 " --> pdb=" O ARG D 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 269 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG E 267 " --> pdb=" O LYS F 270 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL F 272 " --> pdb=" O ARG E 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL E 269 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG F 267 " --> pdb=" O LYS G 270 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL G 272 " --> pdb=" O ARG F 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL F 269 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AA6, first strand: chain 'B' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR B 228 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.613A pdb=" N THR C 228 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR D 228 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 178 through 181 Processing sheet with id=AB3, first strand: chain 'E' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR E 228 " --> pdb=" O SER E 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB5, first strand: chain 'F' and resid 178 through 181 removed outlier: 4.613A pdb=" N THR F 228 " --> pdb=" O SER F 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 178 through 181 Processing sheet with id=AB7, first strand: chain 'G' and resid 178 through 181 removed outlier: 4.614A pdb=" N THR G 228 " --> pdb=" O SER G 220 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2745 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: 4.29 Time building geometry restraints manager: 4.28 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: 4422 1.34 - 1.46: 1847 1.46 - 1.57: 7647 1.57 - 1.69: 0 1.69 - 1.80: 56 Bond restraints: 13972 Sorted by residual: bond pdb=" C GLU F 249 " pdb=" O GLU F 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.42e+00 bond pdb=" C GLU B 249 " pdb=" O GLU B 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.41e+00 bond pdb=" C GLU E 249 " pdb=" O GLU E 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.38e+00 bond pdb=" C GLU D 249 " pdb=" O GLU D 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.38e+00 bond pdb=" C GLU A 249 " pdb=" O GLU A 249 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.10e-02 8.26e+03 2.38e+00 ... (remaining 13967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 18594 1.90 - 3.80: 327 3.80 - 5.70: 84 5.70 - 7.60: 14 7.60 - 9.50: 14 Bond angle restraints: 19033 Sorted by residual: angle pdb=" C VAL C 181 " pdb=" N ILE C 182 " pdb=" CA ILE C 182 " ideal model delta sigma weight residual 121.97 112.47 9.50 1.80e+00 3.09e-01 2.79e+01 angle pdb=" C VAL F 181 " pdb=" N ILE F 182 " pdb=" CA ILE F 182 " ideal model delta sigma weight residual 121.97 112.47 9.50 1.80e+00 3.09e-01 2.79e+01 angle pdb=" C VAL E 181 " pdb=" N ILE E 182 " pdb=" CA ILE E 182 " ideal model delta sigma weight residual 121.97 112.48 9.49 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C VAL G 181 " pdb=" N ILE G 182 " pdb=" CA ILE G 182 " ideal model delta sigma weight residual 121.97 112.48 9.49 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C VAL A 181 " pdb=" N ILE A 182 " pdb=" CA ILE A 182 " ideal model delta sigma weight residual 121.97 112.48 9.49 1.80e+00 3.09e-01 2.78e+01 ... (remaining 19028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 6732 11.72 - 23.45: 920 23.45 - 35.17: 342 35.17 - 46.90: 161 46.90 - 58.62: 70 Dihedral angle restraints: 8225 sinusoidal: 3094 harmonic: 5131 Sorted by residual: dihedral pdb=" CA ASP G 212 " pdb=" C ASP G 212 " pdb=" N PRO G 213 " pdb=" CA PRO G 213 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP E 212 " pdb=" C ASP E 212 " pdb=" N PRO E 213 " pdb=" CA PRO E 213 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ASP F 212 " pdb=" C ASP F 212 " pdb=" N PRO F 213 " pdb=" CA PRO F 213 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 8222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1284 0.031 - 0.063: 651 0.063 - 0.094: 231 0.094 - 0.125: 137 0.125 - 0.156: 21 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA VAL G 181 " pdb=" N VAL G 181 " pdb=" C VAL G 181 " pdb=" CB VAL G 181 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA VAL C 181 " pdb=" N VAL C 181 " pdb=" C VAL C 181 " pdb=" CB VAL C 181 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA VAL B 181 " pdb=" N VAL B 181 " pdb=" C VAL B 181 " pdb=" CB VAL B 181 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2321 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 264 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO B 265 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 264 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO E 265 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 265 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 265 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 264 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO C 265 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.040 5.00e-02 4.00e+02 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 14 2.28 - 2.94: 5922 2.94 - 3.59: 19242 3.59 - 4.25: 30076 4.25 - 4.90: 52046 Nonbonded interactions: 107300 Sorted by model distance: nonbonded pdb=" OD2 ASP A 154 " pdb=" NH2 ARG B 179 " model vdw 1.627 3.120 nonbonded pdb=" OD2 ASP C 154 " pdb=" NH2 ARG D 179 " model vdw 1.627 3.120 nonbonded pdb=" OD2 ASP E 154 " pdb=" NH2 ARG F 179 " model vdw 1.627 3.120 nonbonded pdb=" OD2 ASP B 154 " pdb=" NH2 ARG C 179 " model vdw 1.627 3.120 nonbonded pdb=" NH2 ARG A 179 " pdb=" OD2 ASP G 154 " model vdw 1.627 3.120 ... (remaining 107295 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 0.024 13972 Z= 0.199 Angle : 0.717 9.502 19033 Z= 0.409 Chirality : 0.047 0.156 2324 Planarity : 0.005 0.072 2380 Dihedral : 15.055 58.623 4935 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.59 % Favored : 92.64 % Rotamer: Outliers : 6.73 % Allowed : 16.35 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1806 helix: 0.20 (0.16), residues: 938 sheet: -2.35 (0.26), residues: 273 loop : -1.67 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 130 HIS 0.001 0.000 HIS D 147 PHE 0.021 0.002 PHE E 63 TYR 0.005 0.001 TYR E 173 ARG 0.009 0.001 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.10700 ( 929) hydrogen bonds : angle 4.39802 ( 2745) covalent geometry : bond 0.00427 (13972) covalent geometry : angle 0.71715 (19033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 217 time to evaluate : 1.904 Fit side-chains REVERT: A 46 ARG cc_start: 0.6345 (ttm170) cc_final: 0.5881 (ttt90) REVERT: A 87 GLN cc_start: 0.8645 (mm110) cc_final: 0.8092 (mm-40) REVERT: A 145 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7616 (pp) REVERT: B 46 ARG cc_start: 0.6089 (ttm170) cc_final: 0.5405 (ttt90) REVERT: B 145 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7594 (pp) REVERT: B 270 LYS cc_start: 0.8943 (tttt) cc_final: 0.8722 (tttt) REVERT: C 46 ARG cc_start: 0.6610 (ttm170) cc_final: 0.5959 (ttt90) REVERT: C 51 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7148 (mp) REVERT: C 145 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7436 (pp) REVERT: C 180 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8410 (ttt180) REVERT: C 270 LYS cc_start: 0.8921 (tttt) cc_final: 0.8672 (tttm) REVERT: D 46 ARG cc_start: 0.6415 (ttm170) cc_final: 0.5716 (ttt-90) REVERT: D 95 ILE cc_start: 0.8017 (mp) cc_final: 0.7678 (mt) REVERT: D 126 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8567 (pttt) REVERT: D 145 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7563 (pp) REVERT: E 46 ARG cc_start: 0.6440 (ttm170) cc_final: 0.5685 (ttt90) REVERT: E 51 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7014 (mp) REVERT: E 145 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7341 (pp) REVERT: F 46 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5661 (ttt90) REVERT: F 54 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6829 (mtt-85) REVERT: F 87 GLN cc_start: 0.8736 (mm110) cc_final: 0.8268 (mm-40) REVERT: F 126 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8541 (pttt) REVERT: F 141 ASP cc_start: 0.8054 (t0) cc_final: 0.7816 (t70) REVERT: F 145 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7424 (pp) REVERT: G 46 ARG cc_start: 0.6425 (ttm170) cc_final: 0.5765 (ttt-90) REVERT: G 51 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7337 (mp) REVERT: G 145 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7511 (pp) REVERT: G 270 LYS cc_start: 0.8883 (tttt) cc_final: 0.8461 (tttp) outliers start: 98 outliers final: 53 residues processed: 306 average time/residue: 1.3411 time to fit residues: 445.1895 Evaluate side-chains 253 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 87 GLN A 147 HIS A 155 ASN A 248 ASN B 61 GLN B 147 HIS B 155 ASN B 248 ASN C 61 GLN C 147 HIS C 155 ASN C 248 ASN D 61 GLN D 147 HIS D 155 ASN D 248 ASN E 61 GLN E 147 HIS E 155 ASN E 197 GLN E 248 ASN F 61 GLN F 87 GLN F 147 HIS F 155 ASN F 248 ASN G 61 GLN G 147 HIS G 155 ASN G 248 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096118 restraints weight = 15680.987| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.83 r_work: 0.2976 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.149 Angle : 0.650 9.105 19033 Z= 0.350 Chirality : 0.045 0.141 2324 Planarity : 0.005 0.069 2380 Dihedral : 8.531 59.602 2045 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.20 % Favored : 93.02 % Rotamer: Outliers : 3.50 % Allowed : 21.22 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1806 helix: 1.31 (0.17), residues: 945 sheet: -1.83 (0.27), residues: 273 loop : -1.09 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 15 HIS 0.001 0.001 HIS E 147 PHE 0.013 0.001 PHE G 63 TYR 0.010 0.001 TYR E 173 ARG 0.004 0.000 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 929) hydrogen bonds : angle 3.92983 ( 2745) covalent geometry : bond 0.00312 (13972) covalent geometry : angle 0.64983 (19033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 1.606 Fit side-chains REVERT: A 46 ARG cc_start: 0.6334 (ttm170) cc_final: 0.5676 (ttt90) REVERT: A 87 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8219 (mm-40) REVERT: A 145 ILE cc_start: 0.8036 (mt) cc_final: 0.7686 (pp) REVERT: A 154 ASP cc_start: 0.7751 (t70) cc_final: 0.7407 (t0) REVERT: A 232 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8098 (mtt-85) REVERT: B 46 ARG cc_start: 0.5990 (ttm170) cc_final: 0.5185 (ttt90) REVERT: B 145 ILE cc_start: 0.8006 (mt) cc_final: 0.7670 (pp) REVERT: B 206 ASP cc_start: 0.8474 (t70) cc_final: 0.8255 (t70) REVERT: B 232 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8052 (mtt-85) REVERT: B 270 LYS cc_start: 0.8811 (tttt) cc_final: 0.8591 (tttt) REVERT: C 46 ARG cc_start: 0.6549 (ttm170) cc_final: 0.5704 (ttt90) REVERT: C 145 ILE cc_start: 0.8011 (mt) cc_final: 0.7503 (pp) REVERT: C 232 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8073 (mtt-85) REVERT: C 270 LYS cc_start: 0.8771 (tttt) cc_final: 0.8350 (tttp) REVERT: D 46 ARG cc_start: 0.6217 (ttm170) cc_final: 0.5363 (ttp80) REVERT: D 95 ILE cc_start: 0.8020 (mp) cc_final: 0.7648 (mt) REVERT: D 145 ILE cc_start: 0.8074 (mt) cc_final: 0.7634 (pp) REVERT: D 154 ASP cc_start: 0.7845 (t70) cc_final: 0.7512 (t0) REVERT: D 232 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8116 (mtt-85) REVERT: E 46 ARG cc_start: 0.6161 (ttm170) cc_final: 0.5354 (ttt90) REVERT: E 145 ILE cc_start: 0.8055 (mt) cc_final: 0.7580 (pp) REVERT: E 154 ASP cc_start: 0.7661 (t70) cc_final: 0.7396 (t0) REVERT: E 194 LYS cc_start: 0.8227 (tptp) cc_final: 0.8011 (tppt) REVERT: E 232 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8014 (mtt-85) REVERT: F 46 ARG cc_start: 0.6298 (ttm170) cc_final: 0.5880 (mtp-110) REVERT: F 51 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6971 (mp) REVERT: F 87 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8274 (mm-40) REVERT: F 95 ILE cc_start: 0.7989 (mp) cc_final: 0.7770 (mt) REVERT: F 141 ASP cc_start: 0.8757 (t0) cc_final: 0.8536 (t70) REVERT: F 145 ILE cc_start: 0.7879 (mt) cc_final: 0.7533 (pp) REVERT: F 154 ASP cc_start: 0.7827 (t70) cc_final: 0.7418 (t0) REVERT: F 232 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8109 (mtt-85) REVERT: G 46 ARG cc_start: 0.6313 (ttm170) cc_final: 0.5609 (ttt-90) REVERT: G 95 ILE cc_start: 0.7973 (mp) cc_final: 0.7749 (mt) REVERT: G 145 ILE cc_start: 0.8033 (mt) cc_final: 0.7589 (pp) REVERT: G 270 LYS cc_start: 0.8783 (tttt) cc_final: 0.8313 (tttp) outliers start: 51 outliers final: 22 residues processed: 273 average time/residue: 1.3254 time to fit residues: 392.8259 Evaluate side-chains 231 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 chunk 113 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN D 197 GLN F 197 GLN G 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096878 restraints weight = 15761.385| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.81 r_work: 0.2997 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13972 Z= 0.136 Angle : 0.611 8.726 19033 Z= 0.327 Chirality : 0.045 0.143 2324 Planarity : 0.005 0.066 2380 Dihedral : 6.215 57.810 1957 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.81 % Favored : 93.41 % Rotamer: Outliers : 2.88 % Allowed : 22.39 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1806 helix: 1.85 (0.17), residues: 945 sheet: -1.52 (0.28), residues: 273 loop : -0.78 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 241 HIS 0.001 0.001 HIS F 147 PHE 0.013 0.001 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.004 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 929) hydrogen bonds : angle 3.78628 ( 2745) covalent geometry : bond 0.00284 (13972) covalent geometry : angle 0.61097 (19033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 1.444 Fit side-chains REVERT: A 46 ARG cc_start: 0.6421 (ttm170) cc_final: 0.5768 (ttt90) REVERT: A 87 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8147 (mm-40) REVERT: A 145 ILE cc_start: 0.8033 (mt) cc_final: 0.7718 (pp) REVERT: A 232 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.7939 (mtt-85) REVERT: B 46 ARG cc_start: 0.6166 (ttm170) cc_final: 0.5373 (ttt90) REVERT: B 145 ILE cc_start: 0.7965 (mt) cc_final: 0.7663 (pp) REVERT: B 154 ASP cc_start: 0.7560 (t70) cc_final: 0.7303 (t70) REVERT: B 232 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7866 (mtt-85) REVERT: B 270 LYS cc_start: 0.8851 (tttt) cc_final: 0.8628 (tttt) REVERT: C 46 ARG cc_start: 0.6598 (ttm170) cc_final: 0.5766 (ttt90) REVERT: C 87 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8308 (mm-40) REVERT: C 145 ILE cc_start: 0.8114 (mt) cc_final: 0.7529 (pp) REVERT: C 154 ASP cc_start: 0.7924 (t70) cc_final: 0.7712 (t70) REVERT: C 232 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7990 (mtt-85) REVERT: C 270 LYS cc_start: 0.8831 (tttt) cc_final: 0.8428 (tttp) REVERT: D 46 ARG cc_start: 0.6347 (ttm170) cc_final: 0.5493 (ttp80) REVERT: D 51 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7283 (mp) REVERT: D 95 ILE cc_start: 0.8085 (mp) cc_final: 0.7723 (mt) REVERT: D 123 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7832 (mtt90) REVERT: D 145 ILE cc_start: 0.8117 (mt) cc_final: 0.7723 (pp) REVERT: D 154 ASP cc_start: 0.7683 (t70) cc_final: 0.7482 (t70) REVERT: D 216 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8670 (m) REVERT: D 232 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7992 (mtt-85) REVERT: E 46 ARG cc_start: 0.6277 (ttm170) cc_final: 0.5465 (ttp80) REVERT: E 145 ILE cc_start: 0.8021 (mt) cc_final: 0.7579 (pp) REVERT: E 154 ASP cc_start: 0.7665 (t70) cc_final: 0.7444 (t70) REVERT: E 194 LYS cc_start: 0.8412 (tptp) cc_final: 0.8163 (tptt) REVERT: E 216 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8624 (m) REVERT: E 232 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7686 (mtt-85) REVERT: F 46 ARG cc_start: 0.6322 (ttm170) cc_final: 0.5955 (mtp-110) REVERT: F 51 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7028 (mp) REVERT: F 87 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8329 (mm-40) REVERT: F 95 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7860 (mt) REVERT: F 145 ILE cc_start: 0.7955 (mt) cc_final: 0.7620 (pp) REVERT: F 154 ASP cc_start: 0.7749 (t70) cc_final: 0.7481 (t70) REVERT: F 232 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8036 (mtt-85) REVERT: G 46 ARG cc_start: 0.6424 (ttm170) cc_final: 0.5721 (ttt-90) REVERT: G 95 ILE cc_start: 0.8064 (mp) cc_final: 0.7838 (mt) REVERT: G 145 ILE cc_start: 0.7951 (mt) cc_final: 0.7506 (pp) REVERT: G 154 ASP cc_start: 0.7546 (t70) cc_final: 0.7294 (t70) REVERT: G 206 ASP cc_start: 0.8225 (t70) cc_final: 0.8011 (t70) REVERT: G 270 LYS cc_start: 0.8811 (tttt) cc_final: 0.8341 (tttp) outliers start: 42 outliers final: 19 residues processed: 266 average time/residue: 1.3126 time to fit residues: 379.5200 Evaluate side-chains 252 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 90 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN E 195 ASN F 195 ASN G 41 ASN G 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.096825 restraints weight = 15746.731| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.81 r_work: 0.2996 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13972 Z= 0.141 Angle : 0.616 8.793 19033 Z= 0.330 Chirality : 0.045 0.144 2324 Planarity : 0.005 0.067 2380 Dihedral : 6.029 58.476 1956 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.48 % Favored : 92.75 % Rotamer: Outliers : 3.50 % Allowed : 22.18 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1806 helix: 2.04 (0.17), residues: 945 sheet: -0.86 (0.30), residues: 280 loop : -0.65 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.014 0.002 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.006 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.05241 ( 929) hydrogen bonds : angle 3.76282 ( 2745) covalent geometry : bond 0.00299 (13972) covalent geometry : angle 0.61566 (19033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 1.420 Fit side-chains REVERT: A 46 ARG cc_start: 0.6389 (ttm170) cc_final: 0.5722 (ttt90) REVERT: A 87 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8213 (mm-40) REVERT: A 145 ILE cc_start: 0.8014 (mt) cc_final: 0.7704 (pp) REVERT: A 184 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: A 232 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: B 46 ARG cc_start: 0.6054 (ttm170) cc_final: 0.5259 (ttt90) REVERT: B 145 ILE cc_start: 0.7935 (mt) cc_final: 0.7667 (pp) REVERT: B 154 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7321 (t70) REVERT: B 232 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: B 270 LYS cc_start: 0.8812 (tttt) cc_final: 0.8588 (tttt) REVERT: C 46 ARG cc_start: 0.6608 (ttm170) cc_final: 0.5752 (ttt90) REVERT: C 87 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8299 (mm-40) REVERT: C 145 ILE cc_start: 0.8108 (mt) cc_final: 0.7838 (tp) REVERT: C 154 ASP cc_start: 0.7977 (t70) cc_final: 0.7733 (t70) REVERT: C 194 LYS cc_start: 0.8206 (tppt) cc_final: 0.7836 (tptp) REVERT: C 232 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7962 (mtt-85) REVERT: C 270 LYS cc_start: 0.8804 (tttt) cc_final: 0.8396 (tttp) REVERT: D 46 ARG cc_start: 0.6314 (ttm170) cc_final: 0.5462 (ttp80) REVERT: D 95 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7698 (mt) REVERT: D 123 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7820 (mtt90) REVERT: D 145 ILE cc_start: 0.8149 (mt) cc_final: 0.7753 (pp) REVERT: D 154 ASP cc_start: 0.7723 (t70) cc_final: 0.7484 (t70) REVERT: D 206 ASP cc_start: 0.8393 (t70) cc_final: 0.8097 (t70) REVERT: D 232 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8050 (mtt-85) REVERT: E 46 ARG cc_start: 0.6222 (ttm170) cc_final: 0.5412 (ttp80) REVERT: E 145 ILE cc_start: 0.8049 (mt) cc_final: 0.7611 (pp) REVERT: E 184 ASP cc_start: 0.7903 (m-30) cc_final: 0.7694 (m-30) REVERT: E 206 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8091 (t70) REVERT: E 232 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7593 (mtt-85) REVERT: E 250 LYS cc_start: 0.7412 (mttm) cc_final: 0.7148 (mtpm) REVERT: F 46 ARG cc_start: 0.6342 (ttm170) cc_final: 0.5927 (mtp-110) REVERT: F 51 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6958 (mp) REVERT: F 87 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8246 (mm-40) REVERT: F 95 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7843 (mt) REVERT: F 145 ILE cc_start: 0.8038 (mt) cc_final: 0.7720 (pp) REVERT: F 154 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7500 (t70) REVERT: F 216 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (m) REVERT: F 232 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8033 (mtt-85) REVERT: G 46 ARG cc_start: 0.6443 (ttm170) cc_final: 0.5721 (ttt-90) REVERT: G 95 ILE cc_start: 0.8022 (mp) cc_final: 0.7795 (mt) REVERT: G 145 ILE cc_start: 0.7964 (mt) cc_final: 0.7545 (pp) REVERT: G 154 ASP cc_start: 0.7574 (t70) cc_final: 0.7317 (t70) REVERT: G 270 LYS cc_start: 0.8767 (tttt) cc_final: 0.8294 (tttp) outliers start: 51 outliers final: 21 residues processed: 263 average time/residue: 1.2472 time to fit residues: 357.3409 Evaluate side-chains 249 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 56 optimal weight: 0.0570 chunk 161 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 GLN E 195 ASN F 197 GLN G 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097774 restraints weight = 15830.628| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.83 r_work: 0.3008 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13972 Z= 0.133 Angle : 0.598 8.443 19033 Z= 0.321 Chirality : 0.044 0.148 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.675 58.826 1952 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.09 % Favored : 93.13 % Rotamer: Outliers : 4.05 % Allowed : 21.63 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1806 helix: 2.12 (0.17), residues: 952 sheet: -0.75 (0.30), residues: 280 loop : -0.48 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.013 0.001 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.005 0.000 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.05006 ( 929) hydrogen bonds : angle 3.71174 ( 2745) covalent geometry : bond 0.00279 (13972) covalent geometry : angle 0.59819 (19033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 1.418 Fit side-chains REVERT: A 46 ARG cc_start: 0.6382 (ttm170) cc_final: 0.5714 (ttt90) REVERT: A 87 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8212 (mm-40) REVERT: A 145 ILE cc_start: 0.7978 (mt) cc_final: 0.7683 (pp) REVERT: A 184 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: A 232 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7854 (mtt-85) REVERT: B 46 ARG cc_start: 0.6038 (ttm170) cc_final: 0.5240 (ttt90) REVERT: B 145 ILE cc_start: 0.7910 (mt) cc_final: 0.7647 (pp) REVERT: B 154 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7281 (t70) REVERT: B 232 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7718 (mtt-85) REVERT: B 270 LYS cc_start: 0.8752 (tttt) cc_final: 0.8511 (tttt) REVERT: C 46 ARG cc_start: 0.6597 (ttm170) cc_final: 0.5736 (ttt90) REVERT: C 145 ILE cc_start: 0.8099 (mt) cc_final: 0.7877 (tp) REVERT: C 154 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7710 (t70) REVERT: C 194 LYS cc_start: 0.8142 (tppt) cc_final: 0.7758 (tptp) REVERT: C 232 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7895 (mtt-85) REVERT: C 270 LYS cc_start: 0.8783 (tttt) cc_final: 0.8373 (tttp) REVERT: D 46 ARG cc_start: 0.6315 (ttm170) cc_final: 0.5442 (ttp80) REVERT: D 51 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7122 (mp) REVERT: D 95 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7691 (mt) REVERT: D 123 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7831 (mtt90) REVERT: D 145 ILE cc_start: 0.8001 (mt) cc_final: 0.7708 (pp) REVERT: D 154 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7441 (t70) REVERT: D 206 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8029 (t70) REVERT: D 232 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7946 (mtt-85) REVERT: E 46 ARG cc_start: 0.6230 (ttm170) cc_final: 0.5396 (ttp80) REVERT: E 51 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7025 (mp) REVERT: E 145 ILE cc_start: 0.8014 (mt) cc_final: 0.7567 (pp) REVERT: E 154 ASP cc_start: 0.7786 (t70) cc_final: 0.7431 (t0) REVERT: E 194 LYS cc_start: 0.8463 (tptp) cc_final: 0.8180 (tptt) REVERT: E 206 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8087 (t70) REVERT: E 250 LYS cc_start: 0.7318 (mttm) cc_final: 0.7050 (mtpm) REVERT: F 51 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6915 (mp) REVERT: F 87 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8203 (mm-40) REVERT: F 95 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7790 (mt) REVERT: F 145 ILE cc_start: 0.8013 (mt) cc_final: 0.7706 (pp) REVERT: F 154 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7512 (t70) REVERT: F 232 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7820 (mtt-85) REVERT: G 46 ARG cc_start: 0.6369 (ttm170) cc_final: 0.5631 (ttt-90) REVERT: G 51 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7111 (mp) REVERT: G 95 ILE cc_start: 0.8013 (mp) cc_final: 0.7772 (mt) REVERT: G 145 ILE cc_start: 0.8202 (mt) cc_final: 0.7717 (pp) REVERT: G 154 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7248 (t70) REVERT: G 206 ASP cc_start: 0.8075 (t70) cc_final: 0.7802 (t70) REVERT: G 232 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8345 (mtt180) REVERT: G 270 LYS cc_start: 0.8757 (tttt) cc_final: 0.8289 (tttp) outliers start: 59 outliers final: 21 residues processed: 269 average time/residue: 1.2970 time to fit residues: 379.4744 Evaluate side-chains 253 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 21 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098837 restraints weight = 15834.539| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.83 r_work: 0.3024 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.125 Angle : 0.587 8.113 19033 Z= 0.314 Chirality : 0.044 0.184 2324 Planarity : 0.005 0.065 2380 Dihedral : 5.429 59.605 1947 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.04 % Favored : 93.19 % Rotamer: Outliers : 3.23 % Allowed : 22.87 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1806 helix: 2.22 (0.17), residues: 952 sheet: -0.68 (0.30), residues: 280 loop : -0.40 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.013 0.001 PHE D 63 TYR 0.007 0.001 TYR E 173 ARG 0.009 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 929) hydrogen bonds : angle 3.67906 ( 2745) covalent geometry : bond 0.00257 (13972) covalent geometry : angle 0.58672 (19033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 1.444 Fit side-chains REVERT: A 46 ARG cc_start: 0.6360 (ttm170) cc_final: 0.5696 (ttt90) REVERT: A 87 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8241 (mm-40) REVERT: A 145 ILE cc_start: 0.7959 (mt) cc_final: 0.7692 (pp) REVERT: A 184 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: A 232 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7793 (mtt-85) REVERT: B 46 ARG cc_start: 0.6023 (ttm170) cc_final: 0.5228 (ttt90) REVERT: B 145 ILE cc_start: 0.7879 (mt) cc_final: 0.7631 (pp) REVERT: B 154 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7284 (t70) REVERT: B 232 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: B 250 LYS cc_start: 0.6843 (mtmt) cc_final: 0.6588 (mtmm) REVERT: B 270 LYS cc_start: 0.8744 (tttt) cc_final: 0.8504 (tttt) REVERT: C 46 ARG cc_start: 0.6575 (ttm170) cc_final: 0.5717 (ttt90) REVERT: C 51 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6870 (mp) REVERT: C 87 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8463 (mm-40) REVERT: C 154 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7596 (t70) REVERT: C 194 LYS cc_start: 0.8101 (tppt) cc_final: 0.7701 (tptp) REVERT: C 232 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7713 (mtt-85) REVERT: C 270 LYS cc_start: 0.8799 (tttt) cc_final: 0.8392 (tttp) REVERT: D 46 ARG cc_start: 0.6296 (ttm170) cc_final: 0.5422 (ttp80) REVERT: D 51 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7119 (mp) REVERT: D 95 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7653 (mt) REVERT: D 123 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7799 (mtt90) REVERT: D 145 ILE cc_start: 0.7984 (mt) cc_final: 0.7704 (pp) REVERT: D 154 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7428 (t70) REVERT: D 206 ASP cc_start: 0.8325 (t70) cc_final: 0.8022 (t70) REVERT: D 232 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7786 (mtt-85) REVERT: E 46 ARG cc_start: 0.6221 (ttm170) cc_final: 0.5385 (ttp80) REVERT: E 51 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6980 (mp) REVERT: E 154 ASP cc_start: 0.7767 (t70) cc_final: 0.7451 (t0) REVERT: E 194 LYS cc_start: 0.8474 (tptp) cc_final: 0.8214 (tptt) REVERT: E 206 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8059 (t70) REVERT: F 46 ARG cc_start: 0.6472 (ttm110) cc_final: 0.6148 (mtp-110) REVERT: F 51 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6899 (mp) REVERT: F 87 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8265 (mm-40) REVERT: F 95 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7815 (mt) REVERT: F 145 ILE cc_start: 0.8014 (mt) cc_final: 0.7712 (pp) REVERT: F 154 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7503 (t70) REVERT: F 206 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7958 (t70) REVERT: F 232 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7764 (mtt-85) REVERT: G 46 ARG cc_start: 0.6372 (ttm170) cc_final: 0.5632 (ttt-90) REVERT: G 95 ILE cc_start: 0.8011 (mp) cc_final: 0.7768 (mt) REVERT: G 145 ILE cc_start: 0.8148 (mt) cc_final: 0.7919 (tp) REVERT: G 154 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7233 (t70) REVERT: G 206 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7772 (t70) REVERT: G 239 ASP cc_start: 0.9104 (m-30) cc_final: 0.8885 (m-30) REVERT: G 270 LYS cc_start: 0.8820 (tttt) cc_final: 0.8329 (tttp) outliers start: 47 outliers final: 20 residues processed: 255 average time/residue: 1.3151 time to fit residues: 364.4809 Evaluate side-chains 248 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096512 restraints weight = 15831.780| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.81 r_work: 0.2989 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13972 Z= 0.146 Angle : 0.612 8.651 19033 Z= 0.329 Chirality : 0.045 0.185 2324 Planarity : 0.005 0.066 2380 Dihedral : 5.459 59.891 1947 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.48 % Favored : 92.75 % Rotamer: Outliers : 3.37 % Allowed : 22.87 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1806 helix: 2.23 (0.17), residues: 952 sheet: -0.64 (0.30), residues: 280 loop : -0.41 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.013 0.002 PHE F 63 TYR 0.009 0.001 TYR E 173 ARG 0.008 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 929) hydrogen bonds : angle 3.68430 ( 2745) covalent geometry : bond 0.00317 (13972) covalent geometry : angle 0.61164 (19033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 1.567 Fit side-chains REVERT: A 46 ARG cc_start: 0.6365 (ttm170) cc_final: 0.5698 (ttt90) REVERT: A 87 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8229 (mm-40) REVERT: A 145 ILE cc_start: 0.8000 (mt) cc_final: 0.7710 (pp) REVERT: A 184 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: A 232 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7956 (mtt-85) REVERT: B 46 ARG cc_start: 0.6032 (ttm170) cc_final: 0.5237 (ttt90) REVERT: B 145 ILE cc_start: 0.7917 (mt) cc_final: 0.7680 (pp) REVERT: B 154 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7313 (t70) REVERT: B 232 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7829 (mtt-85) REVERT: B 270 LYS cc_start: 0.8763 (tttt) cc_final: 0.8524 (tttt) REVERT: C 46 ARG cc_start: 0.6578 (ttm170) cc_final: 0.5742 (ttt90) REVERT: C 51 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6881 (mp) REVERT: C 87 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8489 (mm-40) REVERT: C 154 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7659 (t70) REVERT: C 194 LYS cc_start: 0.8138 (tppt) cc_final: 0.7755 (tptp) REVERT: C 232 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7981 (mtt-85) REVERT: C 270 LYS cc_start: 0.8812 (tttt) cc_final: 0.8396 (tttp) REVERT: D 46 ARG cc_start: 0.6354 (ttm170) cc_final: 0.5486 (ttp80) REVERT: D 51 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6926 (mp) REVERT: D 95 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7684 (mt) REVERT: D 123 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7826 (mtt90) REVERT: D 145 ILE cc_start: 0.8184 (mt) cc_final: 0.7866 (pp) REVERT: D 154 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7458 (t70) REVERT: D 206 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8076 (t70) REVERT: D 232 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7987 (mtt-85) REVERT: E 46 ARG cc_start: 0.6229 (ttm170) cc_final: 0.5395 (ttp80) REVERT: E 51 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6967 (mp) REVERT: E 154 ASP cc_start: 0.7847 (t70) cc_final: 0.7483 (t0) REVERT: E 194 LYS cc_start: 0.8466 (tptp) cc_final: 0.8227 (tptt) REVERT: E 206 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8047 (t70) REVERT: E 250 LYS cc_start: 0.7468 (mttm) cc_final: 0.7201 (mtpm) REVERT: F 46 ARG cc_start: 0.6538 (ttm110) cc_final: 0.6252 (mtp-110) REVERT: F 51 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6955 (mp) REVERT: F 87 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8338 (mm-40) REVERT: F 145 ILE cc_start: 0.8044 (mt) cc_final: 0.7726 (pp) REVERT: F 154 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7516 (t70) REVERT: F 232 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8049 (mtt-85) REVERT: G 46 ARG cc_start: 0.6370 (ttm170) cc_final: 0.5628 (ttt-90) REVERT: G 51 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7132 (mp) REVERT: G 95 ILE cc_start: 0.8019 (mp) cc_final: 0.7781 (mt) REVERT: G 145 ILE cc_start: 0.8152 (mt) cc_final: 0.7932 (tp) REVERT: G 154 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7260 (t70) REVERT: G 206 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7823 (t70) REVERT: G 270 LYS cc_start: 0.8767 (tttt) cc_final: 0.8275 (tttp) outliers start: 49 outliers final: 21 residues processed: 252 average time/residue: 1.3486 time to fit residues: 368.9486 Evaluate side-chains 248 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 115 optimal weight: 0.0070 chunk 176 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 52 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN D 197 GLN G 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098383 restraints weight = 15708.376| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.81 r_work: 0.3019 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.129 Angle : 0.590 8.248 19033 Z= 0.317 Chirality : 0.044 0.192 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.437 59.712 1947 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.26 % Favored : 92.97 % Rotamer: Outliers : 2.95 % Allowed : 23.21 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.21), residues: 1806 helix: 2.27 (0.17), residues: 959 sheet: -0.59 (0.30), residues: 280 loop : -0.35 (0.29), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.011 0.001 PHE D 63 TYR 0.007 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 929) hydrogen bonds : angle 3.66192 ( 2745) covalent geometry : bond 0.00270 (13972) covalent geometry : angle 0.59025 (19033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 1.445 Fit side-chains REVERT: A 46 ARG cc_start: 0.6401 (ttm170) cc_final: 0.5722 (ttt90) REVERT: A 87 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8296 (mm-40) REVERT: A 145 ILE cc_start: 0.7961 (mt) cc_final: 0.7687 (pp) REVERT: A 184 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: A 232 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7763 (mtt-85) REVERT: B 46 ARG cc_start: 0.6049 (ttm170) cc_final: 0.5246 (ttt90) REVERT: B 145 ILE cc_start: 0.7960 (mt) cc_final: 0.7651 (pp) REVERT: B 154 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7285 (t70) REVERT: B 232 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7669 (mtt-85) REVERT: B 270 LYS cc_start: 0.8742 (tttt) cc_final: 0.8505 (tttt) REVERT: C 46 ARG cc_start: 0.6602 (ttm170) cc_final: 0.5763 (ttt90) REVERT: C 51 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6889 (mp) REVERT: C 154 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7642 (t70) REVERT: C 194 LYS cc_start: 0.8115 (tppt) cc_final: 0.7709 (tptp) REVERT: C 232 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7734 (mtt-85) REVERT: C 270 LYS cc_start: 0.8788 (tttt) cc_final: 0.8366 (tttp) REVERT: D 46 ARG cc_start: 0.6378 (ttm170) cc_final: 0.5507 (ttp80) REVERT: D 51 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6974 (mp) REVERT: D 95 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7639 (mt) REVERT: D 123 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7795 (mtt90) REVERT: D 154 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7431 (t70) REVERT: D 206 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8015 (t70) REVERT: D 232 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7833 (mtt-85) REVERT: E 46 ARG cc_start: 0.6266 (ttm170) cc_final: 0.5429 (ttp80) REVERT: E 51 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6981 (mp) REVERT: E 154 ASP cc_start: 0.7789 (t70) cc_final: 0.7271 (t0) REVERT: E 194 LYS cc_start: 0.8455 (tptp) cc_final: 0.8207 (tptt) REVERT: E 206 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8053 (t70) REVERT: F 46 ARG cc_start: 0.6563 (ttm110) cc_final: 0.6289 (mtp-110) REVERT: F 51 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6950 (mp) REVERT: F 87 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8454 (mm-40) REVERT: F 145 ILE cc_start: 0.7996 (mt) cc_final: 0.7696 (pp) REVERT: F 154 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7474 (t70) REVERT: F 232 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7728 (mtt-85) REVERT: G 46 ARG cc_start: 0.6410 (ttm170) cc_final: 0.5664 (ttt-90) REVERT: G 95 ILE cc_start: 0.8002 (mp) cc_final: 0.7762 (mt) REVERT: G 145 ILE cc_start: 0.8121 (mt) cc_final: 0.7911 (tp) REVERT: G 154 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7219 (t70) REVERT: G 206 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7726 (t70) REVERT: G 270 LYS cc_start: 0.8802 (tttt) cc_final: 0.8308 (tttp) outliers start: 43 outliers final: 21 residues processed: 249 average time/residue: 1.2706 time to fit residues: 343.9979 Evaluate side-chains 249 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 232 ARG Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 14 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 20 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.089915 restraints weight = 15585.405| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.73 r_work: 0.2893 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 13972 Z= 0.281 Angle : 0.760 10.588 19033 Z= 0.412 Chirality : 0.051 0.189 2324 Planarity : 0.006 0.069 2380 Dihedral : 5.841 56.929 1947 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.76 % Favored : 92.47 % Rotamer: Outliers : 2.54 % Allowed : 23.90 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1806 helix: 1.92 (0.17), residues: 952 sheet: -0.77 (0.30), residues: 280 loop : -0.67 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 234 HIS 0.004 0.002 HIS A 147 PHE 0.030 0.004 PHE D 183 TYR 0.015 0.003 TYR E 173 ARG 0.006 0.001 ARG G 58 Details of bonding type rmsd hydrogen bonds : bond 0.07705 ( 929) hydrogen bonds : angle 3.94815 ( 2745) covalent geometry : bond 0.00666 (13972) covalent geometry : angle 0.76036 (19033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 1.398 Fit side-chains REVERT: A 46 ARG cc_start: 0.6449 (ttm170) cc_final: 0.5769 (ttt90) REVERT: A 51 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7153 (mp) REVERT: A 87 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8350 (mm-40) REVERT: A 145 ILE cc_start: 0.8208 (mt) cc_final: 0.7909 (OUTLIER) REVERT: B 46 ARG cc_start: 0.6259 (ttm170) cc_final: 0.5449 (ttt90) REVERT: B 145 ILE cc_start: 0.8102 (mt) cc_final: 0.7831 (OUTLIER) REVERT: B 270 LYS cc_start: 0.8846 (tttt) cc_final: 0.8621 (tttt) REVERT: C 46 ARG cc_start: 0.6763 (ttm170) cc_final: 0.5905 (ttt90) REVERT: C 51 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6950 (mp) REVERT: C 87 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8456 (mm-40) REVERT: C 132 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8591 (tm-30) REVERT: C 154 ASP cc_start: 0.7961 (t70) cc_final: 0.7739 (t70) REVERT: C 194 LYS cc_start: 0.8190 (tppt) cc_final: 0.7834 (tptp) REVERT: C 270 LYS cc_start: 0.8912 (tttt) cc_final: 0.8452 (tttp) REVERT: D 46 ARG cc_start: 0.6573 (ttm170) cc_final: 0.5738 (ttt-90) REVERT: D 51 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7192 (mp) REVERT: D 95 ILE cc_start: 0.8119 (mp) cc_final: 0.7798 (mt) REVERT: D 123 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8063 (mtt90) REVERT: D 154 ASP cc_start: 0.7824 (t70) cc_final: 0.7579 (t70) REVERT: D 206 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8514 (t70) REVERT: E 46 ARG cc_start: 0.6435 (ttm170) cc_final: 0.5600 (ttp80) REVERT: E 51 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7003 (mp) REVERT: E 154 ASP cc_start: 0.7828 (t70) cc_final: 0.7536 (t0) REVERT: F 46 ARG cc_start: 0.6539 (ttm110) cc_final: 0.6302 (mtp-110) REVERT: F 51 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7039 (mp) REVERT: F 87 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8542 (mm-40) REVERT: F 145 ILE cc_start: 0.8170 (mt) cc_final: 0.7803 (pp) REVERT: F 154 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7545 (t70) REVERT: G 46 ARG cc_start: 0.6589 (ttm170) cc_final: 0.5817 (ttt-90) REVERT: G 51 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6953 (mp) REVERT: G 145 ILE cc_start: 0.8238 (mt) cc_final: 0.7806 (pp) REVERT: G 154 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7487 (t70) REVERT: G 206 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8338 (t70) REVERT: G 270 LYS cc_start: 0.8739 (tttt) cc_final: 0.8257 (tttp) outliers start: 37 outliers final: 23 residues processed: 243 average time/residue: 1.4283 time to fit residues: 375.0417 Evaluate side-chains 247 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 130 optimal weight: 30.0000 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.131871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.096342 restraints weight = 15650.553| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.79 r_work: 0.2992 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13972 Z= 0.137 Angle : 0.616 8.640 19033 Z= 0.333 Chirality : 0.045 0.198 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.653 58.271 1947 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.04 % Favored : 93.19 % Rotamer: Outliers : 2.34 % Allowed : 24.38 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1806 helix: 2.25 (0.17), residues: 945 sheet: -0.66 (0.30), residues: 280 loop : -0.56 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.002 0.001 HIS B 147 PHE 0.012 0.001 PHE D 63 TYR 0.007 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 929) hydrogen bonds : angle 3.80413 ( 2745) covalent geometry : bond 0.00279 (13972) covalent geometry : angle 0.61627 (19033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 1.999 Fit side-chains REVERT: A 46 ARG cc_start: 0.6431 (ttm170) cc_final: 0.5747 (ttt90) REVERT: A 87 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8238 (mm-40) REVERT: A 145 ILE cc_start: 0.8022 (mt) cc_final: 0.7734 (pp) REVERT: B 46 ARG cc_start: 0.6185 (ttm170) cc_final: 0.5383 (ttt90) REVERT: B 145 ILE cc_start: 0.8001 (mt) cc_final: 0.7719 (pp) REVERT: B 270 LYS cc_start: 0.8789 (tttt) cc_final: 0.8545 (tttt) REVERT: C 46 ARG cc_start: 0.6654 (ttm170) cc_final: 0.5772 (ttt90) REVERT: C 51 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6895 (mp) REVERT: C 87 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8468 (mm-40) REVERT: C 154 ASP cc_start: 0.7868 (t70) cc_final: 0.7621 (t70) REVERT: C 194 LYS cc_start: 0.8123 (tppt) cc_final: 0.7726 (tptp) REVERT: C 270 LYS cc_start: 0.8841 (tttt) cc_final: 0.8427 (tttp) REVERT: D 46 ARG cc_start: 0.6467 (ttm170) cc_final: 0.5641 (ttt-90) REVERT: D 51 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7113 (mp) REVERT: D 95 ILE cc_start: 0.7990 (mp) cc_final: 0.7639 (mt) REVERT: D 123 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7730 (mtt90) REVERT: D 154 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7452 (t70) REVERT: D 206 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8159 (t70) REVERT: E 46 ARG cc_start: 0.6320 (ttm170) cc_final: 0.5470 (ttp80) REVERT: E 51 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6986 (mp) REVERT: E 154 ASP cc_start: 0.7609 (t70) cc_final: 0.7292 (t0) REVERT: F 46 ARG cc_start: 0.6477 (ttm110) cc_final: 0.6253 (mtp-110) REVERT: F 51 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6999 (mp) REVERT: F 87 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8468 (mm-40) REVERT: F 145 ILE cc_start: 0.8085 (mt) cc_final: 0.7709 (pp) REVERT: F 154 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7497 (t70) REVERT: F 270 LYS cc_start: 0.8851 (tttm) cc_final: 0.8466 (tttp) REVERT: G 46 ARG cc_start: 0.6454 (ttm170) cc_final: 0.5697 (ttt-90) REVERT: G 51 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6968 (mp) REVERT: G 145 ILE cc_start: 0.8119 (mt) cc_final: 0.7912 (tp) REVERT: G 154 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7276 (t70) REVERT: G 206 ASP cc_start: 0.8308 (t70) cc_final: 0.8037 (t70) REVERT: G 270 LYS cc_start: 0.8799 (tttt) cc_final: 0.8307 (tttp) outliers start: 34 outliers final: 21 residues processed: 252 average time/residue: 1.2621 time to fit residues: 347.7407 Evaluate side-chains 255 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 123 ARG Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097617 restraints weight = 15836.268| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.75 r_work: 0.3009 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.133 Angle : 0.611 8.369 19033 Z= 0.329 Chirality : 0.045 0.202 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.512 58.366 1947 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.15 % Favored : 93.08 % Rotamer: Outliers : 2.20 % Allowed : 24.38 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1806 helix: 2.33 (0.17), residues: 952 sheet: -0.62 (0.30), residues: 280 loop : -0.47 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 241 HIS 0.002 0.001 HIS F 147 PHE 0.012 0.001 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 929) hydrogen bonds : angle 3.74495 ( 2745) covalent geometry : bond 0.00274 (13972) covalent geometry : angle 0.61094 (19033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11752.76 seconds wall clock time: 199 minutes 55.86 seconds (11995.86 seconds total)