Starting phenix.real_space_refine on Thu Sep 26 17:26:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/09_2024/7dlu_30713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/09_2024/7dlu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/09_2024/7dlu_30713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/09_2024/7dlu_30713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/09_2024/7dlu_30713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dlu_30713/09_2024/7dlu_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.90, per 1000 atoms: 0.36 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: 3.45 Conformation dependent library (CDL) restraints added in 1.9 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: 1.67 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: 4.50 Time building geometry restraints manager: 4.01 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.720 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 29.520 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- 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= 0.283 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 *********************** 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 fitting. rotamer outliers: 98 poor density : 217 time to evaluate : 1.502 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: 1.2869 time to fit residues: 428.2962 Evaluate side-chains 253 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 189 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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= 0.204 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 *********************** 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 fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 1.582 Fit side-chains REVERT: A 46 ARG cc_start: 0.6371 (ttm170) cc_final: 0.5828 (ttt90) REVERT: A 87 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8190 (mm-40) REVERT: A 145 ILE cc_start: 0.7776 (mt) cc_final: 0.7511 (pp) REVERT: A 154 ASP cc_start: 0.7123 (t70) cc_final: 0.6911 (t0) REVERT: A 232 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8004 (mtt-85) REVERT: B 46 ARG cc_start: 0.6075 (ttm170) cc_final: 0.5350 (ttt90) REVERT: B 145 ILE cc_start: 0.7764 (mt) cc_final: 0.7475 (pp) REVERT: B 206 ASP cc_start: 0.8450 (t70) cc_final: 0.8226 (t70) REVERT: B 232 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7969 (mtt-85) REVERT: B 270 LYS cc_start: 0.8904 (tttt) cc_final: 0.8679 (tttt) REVERT: C 46 ARG cc_start: 0.6571 (ttm170) cc_final: 0.5834 (ttt90) REVERT: C 145 ILE cc_start: 0.7768 (mt) cc_final: 0.7312 (pp) REVERT: C 232 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: C 270 LYS cc_start: 0.8877 (tttt) cc_final: 0.8486 (tttp) REVERT: D 46 ARG cc_start: 0.6351 (ttm170) cc_final: 0.5564 (ttp80) REVERT: D 95 ILE cc_start: 0.7872 (mp) cc_final: 0.7513 (mt) REVERT: D 126 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8548 (pttt) REVERT: D 145 ILE cc_start: 0.7760 (mt) cc_final: 0.7398 (pp) REVERT: D 154 ASP cc_start: 0.7153 (t70) cc_final: 0.6945 (t0) REVERT: D 232 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8042 (mtt-85) REVERT: E 46 ARG cc_start: 0.6252 (ttm170) cc_final: 0.5526 (ttt90) REVERT: E 145 ILE cc_start: 0.7784 (mt) cc_final: 0.7334 (pp) REVERT: E 194 LYS cc_start: 0.8186 (tptp) cc_final: 0.7950 (tppt) REVERT: E 232 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7938 (mtt-85) REVERT: F 46 ARG cc_start: 0.6383 (ttm170) cc_final: 0.5977 (mtp-110) REVERT: F 51 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7126 (mp) REVERT: F 87 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8199 (mm-40) REVERT: F 95 ILE cc_start: 0.7914 (mp) cc_final: 0.7703 (mt) REVERT: F 126 LYS cc_start: 0.8756 (ptpp) cc_final: 0.8540 (pttt) REVERT: F 141 ASP cc_start: 0.8025 (t0) cc_final: 0.7784 (t70) REVERT: F 145 ILE cc_start: 0.7608 (mt) cc_final: 0.7321 (pp) REVERT: F 154 ASP cc_start: 0.7089 (t70) cc_final: 0.6799 (t0) REVERT: F 232 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8037 (mtt-85) REVERT: G 46 ARG cc_start: 0.6374 (ttm170) cc_final: 0.5746 (ttt-90) REVERT: G 95 ILE cc_start: 0.7848 (mp) cc_final: 0.7638 (mt) REVERT: G 126 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8624 (pttt) REVERT: G 145 ILE cc_start: 0.7777 (mt) cc_final: 0.7402 (pp) REVERT: G 270 LYS cc_start: 0.8875 (tttt) cc_final: 0.8442 (tttp) outliers start: 51 outliers final: 22 residues processed: 273 average time/residue: 1.2966 time to fit residues: 384.5901 Evaluate side-chains 231 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 91 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 165 optimal weight: 0.4980 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 132 optimal weight: 7.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13972 Z= 0.159 Angle : 0.581 8.093 19033 Z= 0.310 Chirality : 0.044 0.142 2324 Planarity : 0.005 0.065 2380 Dihedral : 6.041 58.386 1957 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.26 % Favored : 93.96 % Rotamer: Outliers : 3.30 % Allowed : 22.12 % Favored : 74.59 % 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: 0.76 (0.21), residues: 1806 helix: 1.94 (0.17), residues: 938 sheet: -1.38 (0.28), residues: 266 loop : -0.86 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 15 HIS 0.002 0.001 HIS F 147 PHE 0.012 0.001 PHE D 63 TYR 0.006 0.001 TYR E 173 ARG 0.004 0.000 ARG A 123 *********************** 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 274 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 1.543 Fit side-chains REVERT: A 46 ARG cc_start: 0.6365 (ttm170) cc_final: 0.5832 (ttt90) REVERT: A 87 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8125 (mm-40) REVERT: A 232 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7483 (mtt-85) REVERT: B 46 ARG cc_start: 0.6067 (ttm170) cc_final: 0.5351 (ttt90) REVERT: B 154 ASP cc_start: 0.6745 (t70) cc_final: 0.6538 (t70) REVERT: B 232 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7501 (mtt-85) REVERT: B 270 LYS cc_start: 0.8897 (tttt) cc_final: 0.8673 (tttt) REVERT: C 46 ARG cc_start: 0.6506 (ttm170) cc_final: 0.5799 (ttt90) REVERT: C 232 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7448 (mtt-85) REVERT: C 270 LYS cc_start: 0.8875 (tttt) cc_final: 0.8486 (tttp) REVERT: D 46 ARG cc_start: 0.6394 (ttm170) cc_final: 0.5627 (ttp80) REVERT: D 51 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7420 (mp) REVERT: D 95 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7549 (mt) REVERT: D 123 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7197 (mtt90) REVERT: D 126 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8510 (pttt) REVERT: D 145 ILE cc_start: 0.7714 (mt) cc_final: 0.7445 (pp) REVERT: D 206 ASP cc_start: 0.8308 (t70) cc_final: 0.8074 (t70) REVERT: D 232 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7544 (mtt-85) REVERT: E 46 ARG cc_start: 0.6263 (ttm170) cc_final: 0.5547 (ttp80) REVERT: E 145 ILE cc_start: 0.7607 (mt) cc_final: 0.7269 (pp) REVERT: E 154 ASP cc_start: 0.7093 (t0) cc_final: 0.6850 (t0) REVERT: E 194 LYS cc_start: 0.8330 (tptp) cc_final: 0.8073 (tptt) REVERT: F 51 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7121 (mp) REVERT: F 83 MET cc_start: 0.8209 (ttm) cc_final: 0.8007 (ttp) REVERT: F 87 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8121 (mm-40) REVERT: F 95 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7776 (mt) REVERT: F 145 ILE cc_start: 0.7549 (mt) cc_final: 0.7346 (pp) REVERT: F 154 ASP cc_start: 0.6977 (t70) cc_final: 0.6728 (t70) REVERT: F 216 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8518 (m) REVERT: F 232 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7527 (mtt-85) REVERT: G 46 ARG cc_start: 0.6406 (ttm170) cc_final: 0.5783 (ttt-90) REVERT: G 95 ILE cc_start: 0.7875 (mp) cc_final: 0.7642 (mt) REVERT: G 145 ILE cc_start: 0.7579 (mt) cc_final: 0.7293 (pp) REVERT: G 154 ASP cc_start: 0.6856 (t70) cc_final: 0.6651 (t70) REVERT: G 206 ASP cc_start: 0.8188 (t70) cc_final: 0.7988 (t70) REVERT: G 270 LYS cc_start: 0.8858 (tttt) cc_final: 0.8431 (tttp) outliers start: 48 outliers final: 17 residues processed: 259 average time/residue: 1.2479 time to fit residues: 352.6420 Evaluate side-chains 240 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 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 95 ILE 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 192 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 216 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 272 VAL 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 163 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13972 Z= 0.217 Angle : 0.627 8.960 19033 Z= 0.337 Chirality : 0.045 0.149 2324 Planarity : 0.005 0.066 2380 Dihedral : 5.804 58.885 1952 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.48 % Favored : 92.75 % Rotamer: Outliers : 3.16 % Allowed : 22.94 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1806 helix: 2.06 (0.17), residues: 945 sheet: -0.83 (0.30), residues: 280 loop : -0.66 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 241 HIS 0.001 0.001 HIS F 147 PHE 0.015 0.002 PHE F 63 TYR 0.010 0.001 TYR E 173 ARG 0.006 0.000 ARG A 54 *********************** 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 276 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 230 time to evaluate : 1.589 Fit side-chains REVERT: A 46 ARG cc_start: 0.6389 (ttm170) cc_final: 0.5841 (ttt90) REVERT: A 87 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8178 (mm-40) REVERT: A 184 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6320 (m-30) REVERT: A 232 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7938 (mtt-85) REVERT: B 46 ARG cc_start: 0.6112 (ttm170) cc_final: 0.5396 (ttt90) REVERT: B 232 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7802 (mtt-85) REVERT: B 270 LYS cc_start: 0.8897 (tttt) cc_final: 0.8663 (tttt) REVERT: C 46 ARG cc_start: 0.6527 (ttm170) cc_final: 0.5808 (ttt90) REVERT: C 194 LYS cc_start: 0.8116 (tppt) cc_final: 0.7692 (tptp) REVERT: C 216 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8426 (m) REVERT: C 232 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: C 270 LYS cc_start: 0.8890 (tttt) cc_final: 0.8497 (tttp) REVERT: D 46 ARG cc_start: 0.6417 (ttm170) cc_final: 0.5642 (ttp80) REVERT: D 51 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7306 (mp) REVERT: D 95 ILE cc_start: 0.7900 (mp) cc_final: 0.7569 (mt) REVERT: D 123 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7240 (mtt90) REVERT: D 126 LYS cc_start: 0.8791 (ptpp) cc_final: 0.8568 (pttt) REVERT: D 145 ILE cc_start: 0.7797 (mt) cc_final: 0.7516 (pp) REVERT: D 206 ASP cc_start: 0.8354 (t70) cc_final: 0.8075 (t70) REVERT: D 232 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7890 (mtt-85) REVERT: E 46 ARG cc_start: 0.6281 (ttm170) cc_final: 0.5546 (ttp80) REVERT: E 145 ILE cc_start: 0.7733 (mt) cc_final: 0.7391 (pp) REVERT: E 194 LYS cc_start: 0.8294 (tptp) cc_final: 0.8013 (tptt) REVERT: E 250 LYS cc_start: 0.7250 (mttm) cc_final: 0.7016 (mtpm) REVERT: F 46 ARG cc_start: 0.6661 (ttm110) cc_final: 0.6364 (mtp-110) REVERT: F 51 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7109 (mp) REVERT: F 87 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8149 (mm-40) REVERT: F 95 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7700 (mt) REVERT: F 154 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6765 (t70) REVERT: F 232 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7930 (mtt-85) REVERT: G 46 ARG cc_start: 0.6505 (ttm170) cc_final: 0.5860 (ttt-90) REVERT: G 95 ILE cc_start: 0.7890 (mp) cc_final: 0.7680 (mt) REVERT: G 145 ILE cc_start: 0.7642 (mt) cc_final: 0.7356 (pp) REVERT: G 154 ASP cc_start: 0.6932 (t70) cc_final: 0.6721 (t70) REVERT: G 206 ASP cc_start: 0.8203 (t70) cc_final: 0.7985 (t70) REVERT: G 270 LYS cc_start: 0.8862 (tttt) cc_final: 0.8428 (tttp) outliers start: 46 outliers final: 20 residues processed: 261 average time/residue: 1.3819 time to fit residues: 394.5889 Evaluate side-chains 227 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 B residue 59 THR Chi-restraints excluded: chain B residue 109 SER 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 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 232 ARG Chi-restraints excluded: chain D residue 272 VAL 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 59 THR Chi-restraints excluded: chain F residue 95 ILE 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 180 ARG 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 146 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1918 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= 0.188 Angle : 0.610 8.512 19033 Z= 0.328 Chirality : 0.044 0.176 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.604 59.106 1949 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.15 % Favored : 93.08 % Rotamer: Outliers : 3.98 % Allowed : 22.05 % Favored : 73.97 % 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: 1.25 (0.21), residues: 1806 helix: 2.14 (0.17), residues: 952 sheet: -0.78 (0.30), residues: 280 loop : -0.50 (0.28), 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 0.015 0.001 PHE D 63 TYR 0.008 0.001 TYR E 173 ARG 0.005 0.000 ARG A 54 *********************** 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 273 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 215 time to evaluate : 1.587 Fit side-chains REVERT: A 46 ARG cc_start: 0.6391 (ttm170) cc_final: 0.5840 (ttt90) REVERT: A 87 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8196 (mm-40) REVERT: A 184 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.6198 (m-30) REVERT: A 232 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7782 (mtt-85) REVERT: B 46 ARG cc_start: 0.6116 (ttm170) cc_final: 0.5397 (ttt90) REVERT: B 232 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7675 (mtt-85) REVERT: B 270 LYS cc_start: 0.8848 (tttt) cc_final: 0.8611 (tttt) REVERT: C 46 ARG cc_start: 0.6581 (ttm170) cc_final: 0.5832 (ttt90) REVERT: C 87 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8351 (mm-40) REVERT: C 194 LYS cc_start: 0.8067 (tppt) cc_final: 0.7683 (tptp) REVERT: C 232 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7799 (mtt-85) REVERT: C 270 LYS cc_start: 0.8864 (tttt) cc_final: 0.8481 (tttp) REVERT: D 46 ARG cc_start: 0.6420 (ttm170) cc_final: 0.5639 (ttp80) REVERT: D 95 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7560 (mt) REVERT: D 123 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7216 (mtt90) REVERT: D 126 LYS cc_start: 0.8777 (ptpp) cc_final: 0.8561 (pttt) REVERT: D 232 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7803 (mtt-85) REVERT: E 46 ARG cc_start: 0.6300 (ttm170) cc_final: 0.5556 (ttp80) REVERT: E 145 ILE cc_start: 0.7661 (mt) cc_final: 0.7328 (pp) REVERT: E 194 LYS cc_start: 0.8384 (tptp) cc_final: 0.8089 (tptt) REVERT: E 206 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8067 (t70) REVERT: E 250 LYS cc_start: 0.7124 (mttm) cc_final: 0.6878 (mtpm) REVERT: F 51 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7081 (mp) REVERT: F 87 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8101 (mm-40) REVERT: F 145 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7038 (pp) REVERT: F 154 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6788 (t70) REVERT: F 206 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7997 (t70) REVERT: F 232 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7866 (mtt-85) REVERT: G 46 ARG cc_start: 0.6484 (ttm170) cc_final: 0.5832 (ttt-90) REVERT: G 95 ILE cc_start: 0.7883 (mp) cc_final: 0.7675 (mt) REVERT: G 145 ILE cc_start: 0.7790 (mt) cc_final: 0.7430 (pp) REVERT: G 154 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6683 (t70) REVERT: G 232 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8246 (mtt180) REVERT: G 270 LYS cc_start: 0.8853 (tttt) cc_final: 0.8419 (tttp) outliers start: 58 outliers final: 20 residues processed: 257 average time/residue: 1.2618 time to fit residues: 352.8009 Evaluate side-chains 233 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 232 ARG Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain C residue 109 SER 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 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 272 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 145 ILE 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 59 THR 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 59 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN E 195 ASN G 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2040 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= 0.177 Angle : 0.593 8.238 19033 Z= 0.319 Chirality : 0.044 0.184 2324 Planarity : 0.005 0.065 2380 Dihedral : 5.429 59.466 1947 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.20 % Favored : 93.02 % Rotamer: Outliers : 3.43 % Allowed : 22.12 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1806 helix: 2.23 (0.17), residues: 952 sheet: -0.69 (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 E 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 0.005 0.000 ARG F 46 *********************** 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 256 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 206 time to evaluate : 1.556 Fit side-chains REVERT: A 46 ARG cc_start: 0.6394 (ttm170) cc_final: 0.5840 (ttt90) REVERT: A 87 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8203 (mm-40) REVERT: A 184 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.6023 (m-30) REVERT: A 232 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: B 46 ARG cc_start: 0.6121 (ttm170) cc_final: 0.5399 (ttt90) REVERT: B 232 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7551 (mtt-85) REVERT: B 250 LYS cc_start: 0.6713 (mtmt) cc_final: 0.6459 (mtmm) REVERT: B 270 LYS cc_start: 0.8831 (tttt) cc_final: 0.8595 (tttt) REVERT: C 46 ARG cc_start: 0.6583 (ttm170) cc_final: 0.5829 (ttt90) REVERT: C 51 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7087 (mp) REVERT: C 194 LYS cc_start: 0.8046 (tppt) cc_final: 0.7728 (tptp) REVERT: C 232 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7717 (mtt-85) REVERT: C 270 LYS cc_start: 0.8865 (tttt) cc_final: 0.8480 (tttp) REVERT: D 46 ARG cc_start: 0.6446 (ttm170) cc_final: 0.5638 (ttp80) REVERT: D 51 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7327 (mp) REVERT: D 95 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7520 (mt) REVERT: D 123 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7173 (mtt90) REVERT: D 126 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8552 (pttt) REVERT: D 206 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8016 (t70) REVERT: D 232 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7682 (mtt-85) REVERT: E 46 ARG cc_start: 0.6318 (ttm170) cc_final: 0.5551 (ttp80) REVERT: E 194 LYS cc_start: 0.8391 (tptp) cc_final: 0.8110 (tptt) REVERT: E 206 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8018 (t70) REVERT: E 250 LYS cc_start: 0.7040 (mttm) cc_final: 0.6795 (mtpm) REVERT: F 46 ARG cc_start: 0.6573 (ttm110) cc_final: 0.6268 (mtp-110) REVERT: F 51 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7109 (mp) REVERT: F 87 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8129 (mm-40) REVERT: F 145 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6997 (pp) REVERT: F 154 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6794 (t70) REVERT: F 206 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (t70) REVERT: F 232 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: G 46 ARG cc_start: 0.6455 (ttm170) cc_final: 0.5775 (ttt-90) REVERT: G 51 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7299 (mp) REVERT: G 95 ILE cc_start: 0.7882 (mp) cc_final: 0.7657 (mt) REVERT: G 154 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6642 (t70) REVERT: G 206 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7783 (t70) REVERT: G 270 LYS cc_start: 0.8896 (tttt) cc_final: 0.8446 (tttp) outliers start: 50 outliers final: 20 residues processed: 245 average time/residue: 1.2918 time to fit residues: 343.8790 Evaluate side-chains 234 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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 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 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 206 ASP 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 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 145 ILE 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 51 LEU Chi-restraints excluded: chain G residue 59 THR 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 169 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2053 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= 0.190 Angle : 0.602 8.380 19033 Z= 0.325 Chirality : 0.044 0.184 2324 Planarity : 0.005 0.066 2380 Dihedral : 5.418 59.941 1947 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.42 % Favored : 92.80 % Rotamer: Outliers : 3.16 % Allowed : 22.46 % Favored : 74.38 % 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: 1.44 (0.21), residues: 1806 helix: 2.26 (0.17), residues: 952 sheet: -0.67 (0.30), residues: 280 loop : -0.37 (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 0.009 0.001 TYR E 173 ARG 0.004 0.000 ARG F 46 *********************** 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 248 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 1.547 Fit side-chains REVERT: A 46 ARG cc_start: 0.6397 (ttm170) cc_final: 0.5841 (ttt90) REVERT: A 87 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8191 (mm-40) REVERT: A 184 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.6051 (m-30) REVERT: A 232 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7758 (mtt-85) REVERT: B 46 ARG cc_start: 0.6123 (ttm170) cc_final: 0.5401 (ttt90) REVERT: B 126 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8563 (pttt) REVERT: B 232 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7623 (mtt-85) REVERT: B 270 LYS cc_start: 0.8837 (tttt) cc_final: 0.8601 (tttt) REVERT: C 46 ARG cc_start: 0.6587 (ttm170) cc_final: 0.5830 (ttt90) REVERT: C 51 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7086 (mp) REVERT: C 194 LYS cc_start: 0.8113 (tppt) cc_final: 0.7720 (tptp) REVERT: C 232 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7734 (mtt-85) REVERT: C 270 LYS cc_start: 0.8865 (tttt) cc_final: 0.8479 (tttp) REVERT: D 46 ARG cc_start: 0.6506 (ttm170) cc_final: 0.5704 (ttp80) REVERT: D 51 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7213 (mp) REVERT: D 95 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7521 (mt) REVERT: D 123 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7193 (mtt90) REVERT: D 126 LYS cc_start: 0.8795 (ptpp) cc_final: 0.8567 (pttt) REVERT: D 206 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8028 (t70) REVERT: D 232 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7780 (mtt-85) REVERT: E 46 ARG cc_start: 0.6328 (ttm170) cc_final: 0.5564 (ttp80) REVERT: E 51 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7118 (mp) REVERT: E 194 LYS cc_start: 0.8396 (tptp) cc_final: 0.8113 (tptt) REVERT: E 206 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7996 (t70) REVERT: E 250 LYS cc_start: 0.7126 (mttm) cc_final: 0.6874 (mtpm) REVERT: F 46 ARG cc_start: 0.6532 (ttm110) cc_final: 0.5735 (ttt180) REVERT: F 51 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7103 (mp) REVERT: F 87 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8175 (mm-40) REVERT: F 145 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7094 (pp) REVERT: F 154 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6796 (t70) REVERT: F 206 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7959 (t70) REVERT: F 232 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7736 (mtt-85) REVERT: G 46 ARG cc_start: 0.6459 (ttm170) cc_final: 0.5777 (ttt-90) REVERT: G 51 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7326 (mp) REVERT: G 95 ILE cc_start: 0.7851 (mp) cc_final: 0.7628 (mt) REVERT: G 154 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6649 (t70) REVERT: G 206 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7805 (t70) REVERT: G 270 LYS cc_start: 0.8896 (tttt) cc_final: 0.8447 (tttp) outliers start: 46 outliers final: 22 residues processed: 238 average time/residue: 1.3204 time to fit residues: 341.0198 Evaluate side-chains 237 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 126 LYS 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 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 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 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 109 SER Chi-restraints excluded: chain F residue 145 ILE 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 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 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 108 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.0010 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 overall best weight: 1.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13972 Z= 0.244 Angle : 0.641 8.950 19033 Z= 0.348 Chirality : 0.046 0.194 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.510 58.919 1947 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.70 % Favored : 92.52 % Rotamer: Outliers : 2.82 % Allowed : 23.01 % Favored : 74.18 % 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: 1.35 (0.21), residues: 1806 helix: 2.21 (0.17), residues: 952 sheet: -0.71 (0.30), residues: 280 loop : -0.46 (0.29), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 241 HIS 0.002 0.001 HIS F 147 PHE 0.015 0.002 PHE D 63 TYR 0.011 0.002 TYR E 173 ARG 0.004 0.000 ARG F 46 *********************** 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 266 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 1.627 Fit side-chains REVERT: A 46 ARG cc_start: 0.6405 (ttm170) cc_final: 0.5830 (ttt90) REVERT: A 87 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8182 (mm-40) REVERT: A 232 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8068 (mtt-85) REVERT: B 46 ARG cc_start: 0.6120 (ttm170) cc_final: 0.5394 (ttt90) REVERT: B 126 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8282 (pttp) REVERT: B 232 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7958 (mtt-85) REVERT: B 270 LYS cc_start: 0.8845 (tttt) cc_final: 0.8612 (tttt) REVERT: C 46 ARG cc_start: 0.6631 (ttm170) cc_final: 0.5866 (ttt90) REVERT: C 51 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7079 (mp) REVERT: C 194 LYS cc_start: 0.8059 (tppt) cc_final: 0.7712 (tptp) REVERT: C 232 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8027 (mtt-85) REVERT: C 270 LYS cc_start: 0.8909 (tttt) cc_final: 0.8506 (tttp) REVERT: D 46 ARG cc_start: 0.6560 (ttm170) cc_final: 0.5755 (ttt-90) REVERT: D 51 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7301 (mp) REVERT: D 95 ILE cc_start: 0.7837 (mp) cc_final: 0.7504 (mt) REVERT: D 123 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7343 (mtt90) REVERT: D 126 LYS cc_start: 0.8822 (ptpp) cc_final: 0.8599 (pttt) REVERT: D 206 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8121 (t70) REVERT: D 232 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7943 (mtt-85) REVERT: E 46 ARG cc_start: 0.6318 (ttm170) cc_final: 0.5560 (ttp80) REVERT: E 51 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7117 (mp) REVERT: E 194 LYS cc_start: 0.8384 (tptp) cc_final: 0.8131 (tptt) REVERT: E 206 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8091 (t70) REVERT: E 250 LYS cc_start: 0.7360 (mttm) cc_final: 0.7105 (mtpm) REVERT: F 51 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7113 (mp) REVERT: F 87 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8417 (mm-40) REVERT: F 145 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7143 (pp) REVERT: F 154 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6813 (t70) REVERT: F 232 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8063 (mtt-85) REVERT: G 46 ARG cc_start: 0.6464 (ttm170) cc_final: 0.5781 (ttt-90) REVERT: G 51 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7271 (mp) REVERT: G 154 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6662 (t70) REVERT: G 206 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7901 (t70) REVERT: G 270 LYS cc_start: 0.8909 (tttt) cc_final: 0.8451 (tttp) outliers start: 41 outliers final: 22 residues processed: 255 average time/residue: 1.3340 time to fit residues: 370.3751 Evaluate side-chains 261 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 221 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 180 ARG 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 126 LYS 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 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 109 SER Chi-restraints excluded: chain D residue 123 ARG 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 109 SER Chi-restraints excluded: chain F residue 145 ILE 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 59 THR 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 159 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 147 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13972 Z= 0.171 Angle : 0.601 8.137 19033 Z= 0.325 Chirality : 0.045 0.203 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.435 59.053 1947 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.26 % Favored : 92.97 % Rotamer: Outliers : 2.82 % Allowed : 23.42 % Favored : 73.76 % 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: 1.52 (0.21), residues: 1806 helix: 2.38 (0.17), residues: 945 sheet: -0.64 (0.30), residues: 280 loop : -0.42 (0.29), 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 0.011 0.001 PHE D 63 TYR 0.007 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 *********************** 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 253 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 212 time to evaluate : 1.444 Fit side-chains REVERT: A 46 ARG cc_start: 0.6405 (ttm170) cc_final: 0.5829 (ttt90) REVERT: A 51 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7231 (mp) REVERT: A 87 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8219 (mm-40) REVERT: A 232 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7694 (mtt-85) REVERT: B 46 ARG cc_start: 0.6119 (ttm170) cc_final: 0.5393 (ttt90) REVERT: B 126 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8558 (pttt) REVERT: B 232 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7588 (mtt-85) REVERT: B 250 LYS cc_start: 0.6701 (mtmt) cc_final: 0.6437 (mtmm) REVERT: B 270 LYS cc_start: 0.8841 (tttt) cc_final: 0.8612 (tttt) REVERT: C 46 ARG cc_start: 0.6644 (ttm170) cc_final: 0.5859 (ttt90) REVERT: C 51 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7084 (mp) REVERT: C 194 LYS cc_start: 0.8046 (tppt) cc_final: 0.7704 (tptp) REVERT: C 232 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7679 (mtt-85) REVERT: C 270 LYS cc_start: 0.8867 (tttt) cc_final: 0.8475 (tttp) REVERT: D 46 ARG cc_start: 0.6547 (ttm170) cc_final: 0.5744 (ttt-90) REVERT: D 51 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7194 (mp) REVERT: D 95 ILE cc_start: 0.7830 (mp) cc_final: 0.7518 (mt) REVERT: D 123 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7182 (mtt90) REVERT: D 126 LYS cc_start: 0.8787 (ptpp) cc_final: 0.8561 (pttt) REVERT: D 206 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8022 (t70) REVERT: D 232 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7768 (mtt-85) REVERT: E 46 ARG cc_start: 0.6325 (ttm170) cc_final: 0.5562 (ttp80) REVERT: E 51 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7125 (mp) REVERT: E 194 LYS cc_start: 0.8378 (tptp) cc_final: 0.8080 (tptt) REVERT: E 206 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8009 (t70) REVERT: F 46 ARG cc_start: 0.6572 (ttm110) cc_final: 0.6265 (mtp-110) REVERT: F 51 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7115 (mp) REVERT: F 87 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8358 (mm-40) REVERT: F 145 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7239 (tp) REVERT: F 154 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6734 (t70) REVERT: F 232 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7709 (mtt-85) REVERT: G 46 ARG cc_start: 0.6459 (ttm170) cc_final: 0.5776 (ttt-90) REVERT: G 51 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7247 (mp) REVERT: G 154 ASP cc_start: 0.6810 (OUTLIER) cc_final: 0.6609 (t70) REVERT: G 206 ASP cc_start: 0.8052 (t70) cc_final: 0.7799 (t70) REVERT: G 239 ASP cc_start: 0.8764 (m-30) cc_final: 0.8516 (m-30) REVERT: G 270 LYS cc_start: 0.8895 (tttt) cc_final: 0.8443 (tttp) outliers start: 41 outliers final: 21 residues processed: 246 average time/residue: 1.2800 time to fit residues: 342.2900 Evaluate side-chains 248 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 209 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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 232 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 126 LYS 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 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 109 SER Chi-restraints excluded: chain D residue 123 ARG 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 145 ILE 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 59 THR 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 107 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 GLN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2064 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= 0.223 Angle : 0.635 8.733 19033 Z= 0.344 Chirality : 0.045 0.190 2324 Planarity : 0.005 0.066 2380 Dihedral : 5.458 58.977 1947 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.48 % Favored : 92.75 % Rotamer: Outliers : 3.02 % Allowed : 23.42 % 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: 1.43 (0.21), residues: 1806 helix: 2.29 (0.17), residues: 952 sheet: -0.67 (0.30), residues: 280 loop : -0.45 (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 0.014 0.002 PHE D 63 TYR 0.010 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 ********************** 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 263 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 1.379 Fit side-chains REVERT: A 46 ARG cc_start: 0.6421 (ttm170) cc_final: 0.5841 (ttt90) REVERT: A 51 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 87 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8185 (mm-40) REVERT: A 195 ASN cc_start: 0.8592 (t0) cc_final: 0.8165 (t0) REVERT: A 232 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7936 (mtt-85) REVERT: B 46 ARG cc_start: 0.6121 (ttm170) cc_final: 0.5395 (ttt90) REVERT: B 126 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8570 (pttt) REVERT: B 232 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7916 (mtt-85) REVERT: B 270 LYS cc_start: 0.8841 (tttt) cc_final: 0.8616 (tttt) REVERT: C 46 ARG cc_start: 0.6629 (ttm170) cc_final: 0.5847 (ttt90) REVERT: C 51 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7100 (mp) REVERT: C 194 LYS cc_start: 0.8060 (tppt) cc_final: 0.7707 (tptp) REVERT: C 232 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7928 (mtt-85) REVERT: C 250 LYS cc_start: 0.7304 (mtmt) cc_final: 0.7058 (mttt) REVERT: C 270 LYS cc_start: 0.8900 (tttt) cc_final: 0.8502 (tttp) REVERT: D 46 ARG cc_start: 0.6582 (ttm170) cc_final: 0.5755 (ttt-90) REVERT: D 51 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 95 ILE cc_start: 0.7833 (mp) cc_final: 0.7499 (mt) REVERT: D 123 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7278 (mtt90) REVERT: D 126 LYS cc_start: 0.8805 (ptpp) cc_final: 0.8586 (pttt) REVERT: D 206 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8109 (t70) REVERT: D 232 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: E 46 ARG cc_start: 0.6359 (ttm170) cc_final: 0.5601 (ttp80) REVERT: E 51 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7104 (mp) REVERT: E 184 ASP cc_start: 0.7223 (m-30) cc_final: 0.7019 (m-30) REVERT: E 194 LYS cc_start: 0.8356 (tptp) cc_final: 0.8122 (tptt) REVERT: E 206 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8055 (t70) REVERT: E 250 LYS cc_start: 0.7298 (mttm) cc_final: 0.7050 (mtpm) REVERT: F 46 ARG cc_start: 0.6571 (ttm110) cc_final: 0.6264 (mtp-110) REVERT: F 51 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7131 (mp) REVERT: F 87 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8410 (mm-40) REVERT: F 145 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7099 (pp) REVERT: F 154 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6799 (t70) REVERT: F 232 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8007 (mtt-85) REVERT: G 46 ARG cc_start: 0.6490 (ttm170) cc_final: 0.5793 (ttt-90) REVERT: G 51 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7072 (mp) REVERT: G 154 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6653 (t70) REVERT: G 206 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (t70) REVERT: G 270 LYS cc_start: 0.8903 (tttt) cc_final: 0.8448 (tttp) outliers start: 44 outliers final: 24 residues processed: 252 average time/residue: 1.2872 time to fit residues: 353.1173 Evaluate side-chains 264 residues out of total 1456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 126 LYS Chi-restraints excluded: chain A residue 180 ARG 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 90 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 126 LYS 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 232 ARG 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 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 57 ASP 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 145 ILE 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 59 THR 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 114 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3584 r_free = 0.3584 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098145 restraints weight = 15550.348| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.72 r_work: 0.3013 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13972 Z= 0.180 Angle : 0.609 8.243 19033 Z= 0.330 Chirality : 0.045 0.194 2324 Planarity : 0.005 0.067 2380 Dihedral : 5.425 58.809 1947 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.78 % Allowed : 6.42 % Favored : 92.80 % Rotamer: Outliers : 2.82 % Allowed : 23.49 % Favored : 73.70 % 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: 1.51 (0.21), residues: 1806 helix: 2.31 (0.17), residues: 959 sheet: -0.63 (0.30), residues: 280 loop : -0.37 (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 0.008 0.001 TYR E 173 ARG 0.006 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.29 seconds wall clock time: 101 minutes 28.75 seconds (6088.75 seconds total)