Starting phenix.real_space_refine on Fri Jun 20 02:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tk1_41321/06_2025/8tk1_41321_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tk1_41321/06_2025/8tk1_41321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tk1_41321/06_2025/8tk1_41321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tk1_41321/06_2025/8tk1_41321.map" model { file = "/net/cci-nas-00/data/ceres_data/8tk1_41321/06_2025/8tk1_41321_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tk1_41321/06_2025/8tk1_41321_neut.cif" } resolution = 2.98 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= 0.001 sd= 0.023 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 67 5.16 5 C 15057 2.51 5 N 3871 2.21 5 O 4429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23424 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "E" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2513 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain breaks: 5 Chain: "G" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 13.53, per 1000 atoms: 0.58 Number of scatterers: 23424 At special positions: 0 Unit cell: (137.76, 163.52, 189.28, 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 67 16.00 O 4429 8.00 N 3871 7.00 C 15057 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: 5.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5416 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 21 sheets defined 48.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 310 through 313 removed outlier: 3.999A pdb=" N LYS A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.643A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 removed outlier: 4.632A pdb=" N SER A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.560A pdb=" N LYS A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.869A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.535A pdb=" N GLY A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.577A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 553 through 562 Processing helix chain 'A' and resid 566 through 573 removed outlier: 4.195A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.023A pdb=" N ILE B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.750A pdb=" N VAL B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 90 removed outlier: 5.764A pdb=" N LYS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.707A pdb=" N LEU B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 195 through 201 removed outlier: 4.392A pdb=" N TRP B 199 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'C' and resid 33 through 47 removed outlier: 3.669A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 310 through 313 removed outlier: 3.997A pdb=" N LYS C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.643A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.634A pdb=" N SER C 357 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.559A pdb=" N LYS C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.870A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.539A pdb=" N GLY C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 528 removed outlier: 3.576A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 540 through 550 Processing helix chain 'C' and resid 553 through 562 Processing helix chain 'C' and resid 566 through 573 removed outlier: 4.196A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 removed outlier: 4.022A pdb=" N ILE D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 38 Processing helix chain 'D' and resid 50 through 62 Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.749A pdb=" N VAL D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 90 removed outlier: 5.764A pdb=" N LYS D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.598A pdb=" N GLY D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.681A pdb=" N LEU D 139 " --> pdb=" O PHE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 182 Processing helix chain 'D' and resid 195 through 201 removed outlier: 4.393A pdb=" N TRP D 199 " --> pdb=" O ILE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'E' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 310 through 313 removed outlier: 3.999A pdb=" N LYS E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 321 through 326 removed outlier: 3.642A pdb=" N LEU E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 326 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 removed outlier: 4.626A pdb=" N SER E 357 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.557A pdb=" N LYS E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 395 Processing helix chain 'E' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR E 419 " --> pdb=" O HIS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.865A pdb=" N LEU E 456 " --> pdb=" O ARG E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 493 Processing helix chain 'E' and resid 493 through 503 removed outlier: 3.531A pdb=" N GLY E 502 " --> pdb=" O GLY E 498 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 503 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 528 removed outlier: 3.577A pdb=" N ASP E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU E 522 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER E 523 " --> pdb=" O ALA E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 538 Processing helix chain 'E' and resid 540 through 550 removed outlier: 3.556A pdb=" N MET E 545 " --> pdb=" O LYS E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 566 through 573 removed outlier: 4.200A pdb=" N LYS E 570 " --> pdb=" O PHE E 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.063A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 38 Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 73 through 81 removed outlier: 3.752A pdb=" N VAL F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 90 removed outlier: 5.766A pdb=" N LYS F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O PHE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 3.537A pdb=" N GLY F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.681A pdb=" N LEU F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.575A pdb=" N ARG F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 195 through 201 removed outlier: 4.391A pdb=" N TRP F 199 " --> pdb=" O ILE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 229 through 239 removed outlier: 4.131A pdb=" N PHE F 239 " --> pdb=" O TYR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 247 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 452 through 459 Processing helix chain 'G' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 52 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 310 through 313 removed outlier: 3.998A pdb=" N LYS G 313 " --> pdb=" O SER G 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 310 through 313' Processing helix chain 'G' and resid 321 through 326 removed outlier: 3.644A pdb=" N LEU G 324 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 326 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 357 removed outlier: 4.628A pdb=" N SER G 357 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.560A pdb=" N LYS G 364 " --> pdb=" O LYS G 360 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 368 " --> pdb=" O LYS G 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA G 369 " --> pdb=" O ALA G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 395 Processing helix chain 'G' and resid 413 through 424 removed outlier: 3.705A pdb=" N THR G 419 " --> pdb=" O HIS G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 456 removed outlier: 3.868A pdb=" N LEU G 456 " --> pdb=" O ARG G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 493 Processing helix chain 'G' and resid 493 through 503 removed outlier: 3.533A pdb=" N GLY G 502 " --> pdb=" O GLY G 498 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 503 " --> pdb=" O GLU G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 528 removed outlier: 3.578A pdb=" N ASP G 515 " --> pdb=" O ASP G 511 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU G 522 " --> pdb=" O SER G 518 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER G 523 " --> pdb=" O ALA G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 538 Processing helix chain 'G' and resid 540 through 550 Processing helix chain 'G' and resid 553 through 562 Processing helix chain 'G' and resid 566 through 573 removed outlier: 4.194A pdb=" N LYS G 570 " --> pdb=" O PHE G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 removed outlier: 4.026A pdb=" N ILE H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 50 through 62 Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.748A pdb=" N VAL H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 5.766A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 89 " --> pdb=" O PHE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 119 removed outlier: 3.581A pdb=" N GLY H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 143 removed outlier: 3.677A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'H' and resid 168 through 182 Processing helix chain 'H' and resid 195 through 201 removed outlier: 4.397A pdb=" N TRP H 199 " --> pdb=" O ILE H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.729A pdb=" N LYS A 16 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 9 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN A 18 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A 7 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 20 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN A 5 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 2 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 6 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 72 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE A 8 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A 70 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 105 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N VAL A 104 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU A 129 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A 128 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.976A pdb=" N LYS A 24 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 334 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.511A pdb=" N ILE A 465 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.730A pdb=" N SER B 43 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE B 160 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 45 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP B 162 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL B 47 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B 185 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 13 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY B 190 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 15 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 222 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.727A pdb=" N LYS C 16 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS C 9 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN C 18 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C 7 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 20 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN C 5 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 2 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 105 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL C 104 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU C 129 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER C 128 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.978A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 403 through 407 Processing sheet with id=AA9, first strand: chain 'C' and resid 435 through 437 removed outlier: 3.512A pdb=" N ILE C 465 " --> pdb=" O TYR C 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER D 43 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE D 160 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA D 45 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP D 162 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL D 47 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 185 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 13 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY D 190 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 15 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 222 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.729A pdb=" N LYS E 16 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS E 9 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN E 18 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR E 7 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN E 20 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN E 5 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 2 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR E 74 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 6 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 72 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 8 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU E 70 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 105 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL E 104 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU E 129 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 112 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 121 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER E 128 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 154 removed outlier: 6.976A pdb=" N LYS E 24 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 334 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL E 26 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL E 336 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE E 28 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 403 through 407 Processing sheet with id=AB5, first strand: chain 'E' and resid 435 through 437 removed outlier: 3.506A pdb=" N ILE E 465 " --> pdb=" O TYR E 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER F 43 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE F 160 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA F 45 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP F 162 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL F 47 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS F 185 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 13 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY F 190 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL F 15 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 222 " --> pdb=" O THR F 16 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 256 through 259 removed outlier: 6.533A pdb=" N ILE F 257 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN F 434 " --> pdb=" O LYS F 464 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE F 466 " --> pdb=" O ASN F 434 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL F 436 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE F 468 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 438 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE F 287 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE F 310 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR F 424 " --> pdb=" O ILE F 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 14 through 20 removed outlier: 6.730A pdb=" N LYS G 16 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS G 9 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN G 18 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR G 7 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN G 20 " --> pdb=" O ASN G 5 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN G 5 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 2 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR G 74 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE G 6 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE G 72 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE G 8 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU G 70 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE G 105 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL G 104 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU G 129 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS G 112 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN G 121 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER G 128 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 149 through 154 removed outlier: 6.979A pdb=" N LYS G 24 " --> pdb=" O ARG G 332 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE G 334 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL G 26 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL G 336 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE G 28 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 403 through 407 Processing sheet with id=AC2, first strand: chain 'G' and resid 435 through 437 removed outlier: 3.506A pdb=" N ILE G 465 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER H 43 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE H 160 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA H 45 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP H 162 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL H 47 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS H 185 " --> pdb=" O PHE H 157 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE H 13 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY H 190 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL H 15 " --> pdb=" O GLY H 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 222 " --> pdb=" O THR H 16 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 2940 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: 9.85 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7366 1.34 - 1.46: 3981 1.46 - 1.58: 12386 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 23845 Sorted by residual: bond pdb=" N SER F 224 " pdb=" CA SER F 224 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.26e-02 6.30e+03 1.03e+01 bond pdb=" N ASN F 225 " pdb=" CA ASN F 225 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N CYS F 229 " pdb=" CA CYS F 229 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.32e-02 5.74e+03 7.61e+00 bond pdb=" N THR F 223 " pdb=" CA THR F 223 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 6.96e+00 bond pdb=" ND1 HIS F 426 " pdb=" CE1 HIS F 426 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.43e+00 ... (remaining 23840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 30758 1.18 - 2.36: 1006 2.36 - 3.53: 192 3.53 - 4.71: 60 4.71 - 5.89: 9 Bond angle restraints: 32025 Sorted by residual: angle pdb=" CB HIS F 426 " pdb=" CG HIS F 426 " pdb=" CD2 HIS F 426 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 angle pdb=" OE1 GLN F 314 " pdb=" CD GLN F 314 " pdb=" NE2 GLN F 314 " ideal model delta sigma weight residual 122.60 118.14 4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CB HIS F 454 " pdb=" CG HIS F 454 " pdb=" CD2 HIS F 454 " ideal model delta sigma weight residual 131.20 125.67 5.53 1.30e+00 5.92e-01 1.81e+01 angle pdb=" OE1 GLN F 254 " pdb=" CD GLN F 254 " pdb=" NE2 GLN F 254 " ideal model delta sigma weight residual 122.60 118.60 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" OD1 ASN F 240 " pdb=" CG ASN F 240 " pdb=" ND2 ASN F 240 " ideal model delta sigma weight residual 122.60 118.71 3.89 1.00e+00 1.00e+00 1.52e+01 ... (remaining 32020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 12725 16.24 - 32.49: 1352 32.49 - 48.73: 329 48.73 - 64.98: 27 64.98 - 81.22: 18 Dihedral angle restraints: 14451 sinusoidal: 6027 harmonic: 8424 Sorted by residual: dihedral pdb=" CA PHE F 423 " pdb=" C PHE F 423 " pdb=" N THR F 424 " pdb=" CA THR F 424 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER F 224 " pdb=" C SER F 224 " pdb=" N ASN F 225 " pdb=" CA ASN F 225 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LYS G 125 " pdb=" C LYS G 125 " pdb=" N TRP G 126 " pdb=" CA TRP G 126 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 14448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3022 0.057 - 0.115: 390 0.115 - 0.172: 102 0.172 - 0.230: 2 0.230 - 0.287: 1 Chirality restraints: 3517 Sorted by residual: chirality pdb=" CA THR F 243 " pdb=" N THR F 243 " pdb=" C THR F 243 " pdb=" CB THR F 243 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA VAL F 253 " pdb=" N VAL F 253 " pdb=" C VAL F 253 " pdb=" CB VAL F 253 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA GLU F 432 " pdb=" N GLU F 432 " pdb=" C GLU F 432 " pdb=" CB GLU F 432 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 3514 not shown) Planarity restraints: 4075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 126 " 0.036 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP C 126 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP C 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 126 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 126 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 126 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 126 " -0.035 2.00e-02 2.50e+03 3.21e-02 2.57e+01 pdb=" CG TRP A 126 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A 126 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 126 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 126 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 126 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 126 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 126 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.56e+01 pdb=" CG TRP G 126 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP G 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP G 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 126 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 126 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 126 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 126 " 0.005 2.00e-02 2.50e+03 ... (remaining 4072 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 176 2.60 - 3.18: 18899 3.18 - 3.75: 32696 3.75 - 4.33: 51116 4.33 - 4.90: 85193 Nonbonded interactions: 188080 Sorted by model distance: nonbonded pdb=" OE2 GLU E 393 " pdb=" OG1 THR E 554 " model vdw 2.031 3.040 nonbonded pdb=" OE2 GLU A 393 " pdb=" OG1 THR A 554 " model vdw 2.036 3.040 nonbonded pdb=" OE2 GLU C 393 " pdb=" OG1 THR C 554 " model vdw 2.039 3.040 nonbonded pdb=" OE2 GLU G 393 " pdb=" OG1 THR G 554 " model vdw 2.040 3.040 nonbonded pdb=" NZ LYS A 439 " pdb=" O ILE E 527 " model vdw 2.103 3.120 ... (remaining 188075 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 52.200 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.003 0.040 23845 Z= 0.175 Angle : 0.540 5.890 32025 Z= 0.317 Chirality : 0.043 0.287 3517 Planarity : 0.004 0.147 4075 Dihedral : 13.820 81.221 9035 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % 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: -0.10 (0.15), residues: 2837 helix: 0.43 (0.15), residues: 1113 sheet: 0.52 (0.22), residues: 554 loop : -0.74 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.010 TRP C 126 HIS 0.012 0.001 HIS F 426 PHE 0.030 0.002 PHE F 309 TYR 0.039 0.001 TYR F 418 ARG 0.008 0.000 ARG F 244 Details of bonding type rmsd hydrogen bonds : bond 0.19975 ( 1039) hydrogen bonds : angle 6.70182 ( 2940) covalent geometry : bond 0.00347 (23845) covalent geometry : angle 0.54030 (32025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 599 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8426 (tttt) cc_final: 0.7802 (ttpp) REVERT: A 328 MET cc_start: 0.8419 (ptt) cc_final: 0.8159 (ptp) REVERT: A 556 ASP cc_start: 0.7211 (m-30) cc_final: 0.6972 (m-30) REVERT: A 559 ASP cc_start: 0.7089 (m-30) cc_final: 0.6841 (m-30) REVERT: C 465 ILE cc_start: 0.8054 (pt) cc_final: 0.7768 (pp) REVERT: C 489 ILE cc_start: 0.8480 (mm) cc_final: 0.8225 (mt) REVERT: D 88 ASP cc_start: 0.7664 (t70) cc_final: 0.7255 (t0) REVERT: D 176 MET cc_start: 0.7047 (mmp) cc_final: 0.6747 (mmm) REVERT: E 392 ASP cc_start: 0.7742 (t70) cc_final: 0.7542 (t0) REVERT: E 480 GLU cc_start: 0.6725 (pt0) cc_final: 0.6479 (pt0) REVERT: E 555 LYS cc_start: 0.7056 (tptp) cc_final: 0.6548 (mmmt) REVERT: E 559 ASP cc_start: 0.7008 (m-30) cc_final: 0.6679 (m-30) REVERT: F 34 ASP cc_start: 0.7379 (m-30) cc_final: 0.6867 (m-30) REVERT: F 42 TYR cc_start: 0.8119 (m-80) cc_final: 0.7903 (m-80) REVERT: F 74 ASP cc_start: 0.7149 (m-30) cc_final: 0.6817 (m-30) REVERT: F 88 ASP cc_start: 0.7406 (t70) cc_final: 0.6883 (t0) REVERT: F 107 PHE cc_start: 0.6866 (m-80) cc_final: 0.6462 (m-80) REVERT: F 116 VAL cc_start: 0.4787 (t) cc_final: 0.4578 (t) REVERT: F 121 ASN cc_start: 0.7590 (t160) cc_final: 0.7337 (t0) REVERT: F 176 MET cc_start: 0.8435 (mmp) cc_final: 0.7705 (mmt) REVERT: F 180 ASP cc_start: 0.6916 (m-30) cc_final: 0.6644 (m-30) REVERT: F 216 ASP cc_start: 0.7301 (p0) cc_final: 0.7075 (OUTLIER) REVERT: G 471 GLU cc_start: 0.5710 (tm-30) cc_final: 0.5306 (tp30) REVERT: G 473 ILE cc_start: 0.7737 (pt) cc_final: 0.7395 (pt) outliers start: 2 outliers final: 5 residues processed: 601 average time/residue: 1.4945 time to fit residues: 1013.5259 Evaluate side-chains 493 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 489 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 228 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN A 455 ASN A 538 GLN C 18 ASN C 155 ASN C 492 GLN C 538 GLN C 551 ASN D 38 ASN D 68 ASN E 492 GLN E 538 GLN F 213 ASN F 454 HIS G 18 ASN G 455 ASN H 221 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119094 restraints weight = 33702.526| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.21 r_work: 0.3299 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23845 Z= 0.157 Angle : 0.566 8.605 32025 Z= 0.309 Chirality : 0.044 0.154 3517 Planarity : 0.003 0.047 4075 Dihedral : 4.615 75.442 3110 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.77 % Allowed : 11.23 % Favored : 87.00 % 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: 0.04 (0.15), residues: 2837 helix: 0.58 (0.15), residues: 1157 sheet: 0.82 (0.22), residues: 554 loop : -0.89 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP G 126 HIS 0.005 0.001 HIS H 221 PHE 0.017 0.002 PHE H 153 TYR 0.026 0.001 TYR G 272 ARG 0.006 0.001 ARG G 504 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 1039) hydrogen bonds : angle 5.10027 ( 2940) covalent geometry : bond 0.00369 (23845) covalent geometry : angle 0.56627 (32025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 493 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5733 (tpt) cc_final: 0.5199 (ttp) REVERT: A 48 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8214 (pttp) REVERT: A 132 ASN cc_start: 0.7889 (t0) cc_final: 0.7470 (t0) REVERT: A 480 GLU cc_start: 0.7341 (pp20) cc_final: 0.7108 (pp20) REVERT: A 488 GLU cc_start: 0.8430 (tp30) cc_final: 0.8142 (tt0) REVERT: A 542 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 545 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7995 (tpt) REVERT: A 556 ASP cc_start: 0.7619 (m-30) cc_final: 0.7310 (m-30) REVERT: A 559 ASP cc_start: 0.7897 (m-30) cc_final: 0.7527 (m-30) REVERT: B 176 MET cc_start: 0.6244 (mmp) cc_final: 0.5722 (mmp) REVERT: C 48 LYS cc_start: 0.8310 (ptmt) cc_final: 0.8047 (ptmm) REVERT: C 103 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7533 (p0) REVERT: C 132 ASN cc_start: 0.7454 (t0) cc_final: 0.7214 (t0) REVERT: C 383 GLU cc_start: 0.8049 (mp0) cc_final: 0.7641 (mp0) REVERT: C 388 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: C 438 LYS cc_start: 0.8732 (tttt) cc_final: 0.8400 (tttm) REVERT: C 444 VAL cc_start: 0.8505 (m) cc_final: 0.8264 (p) REVERT: C 477 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7462 (mmmm) REVERT: C 480 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7148 (tp30) REVERT: C 493 TYR cc_start: 0.7850 (m-80) cc_final: 0.7602 (m-80) REVERT: D 107 PHE cc_start: 0.7129 (t80) cc_final: 0.6870 (t80) REVERT: D 176 MET cc_start: 0.7756 (mmp) cc_final: 0.7527 (tpp) REVERT: D 212 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6962 (mp0) REVERT: E 70 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8069 (mt-10) REVERT: E 116 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7754 (ttpp) REVERT: E 117 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7100 (mm-30) REVERT: E 360 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8219 (mmmm) REVERT: E 392 ASP cc_start: 0.8284 (t70) cc_final: 0.8066 (t0) REVERT: E 406 LEU cc_start: 0.8418 (tp) cc_final: 0.8199 (tt) REVERT: E 445 TYR cc_start: 0.8523 (m-80) cc_final: 0.8063 (m-80) REVERT: E 484 GLU cc_start: 0.8016 (tp30) cc_final: 0.7320 (tp30) REVERT: F 42 TYR cc_start: 0.8402 (m-80) cc_final: 0.7701 (m-80) REVERT: F 49 PHE cc_start: 0.8447 (m-80) cc_final: 0.8188 (m-80) REVERT: F 74 ASP cc_start: 0.7964 (m-30) cc_final: 0.7579 (m-30) REVERT: F 88 ASP cc_start: 0.7985 (t70) cc_final: 0.7533 (t0) REVERT: F 121 ASN cc_start: 0.7731 (t0) cc_final: 0.7353 (t0) REVERT: F 131 LYS cc_start: 0.7091 (tttm) cc_final: 0.6836 (tttm) REVERT: F 177 TYR cc_start: 0.8173 (t80) cc_final: 0.7968 (t80) REVERT: G 83 ASP cc_start: 0.6695 (t0) cc_final: 0.6449 (t0) REVERT: G 117 GLU cc_start: 0.8023 (tp30) cc_final: 0.7807 (tp30) REVERT: G 279 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7354 (tp30) REVERT: G 444 VAL cc_start: 0.8194 (m) cc_final: 0.7936 (p) REVERT: G 471 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6527 (tp30) REVERT: G 473 ILE cc_start: 0.8065 (pt) cc_final: 0.7839 (pt) REVERT: G 474 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8069 (mppt) REVERT: G 480 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7099 (tm-30) REVERT: G 484 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7820 (mt-10) REVERT: G 559 ASP cc_start: 0.7984 (m-30) cc_final: 0.7761 (m-30) REVERT: H 36 LYS cc_start: 0.8226 (tttt) cc_final: 0.7881 (tppp) REVERT: H 180 ASP cc_start: 0.6820 (m-30) cc_final: 0.6597 (m-30) outliers start: 46 outliers final: 14 residues processed: 511 average time/residue: 1.5125 time to fit residues: 874.4351 Evaluate side-chains 488 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 468 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 55 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 213 optimal weight: 50.0000 chunk 120 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN A 538 GLN C 56 ASN C 492 GLN C 538 GLN E 492 GLN E 538 GLN F 121 ASN H 121 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116625 restraints weight = 33536.142| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.20 r_work: 0.3276 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23845 Z= 0.192 Angle : 0.563 9.198 32025 Z= 0.307 Chirality : 0.044 0.151 3517 Planarity : 0.003 0.064 4075 Dihedral : 4.489 39.463 3107 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.97 % Allowed : 14.20 % Favored : 83.83 % 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: 0.01 (0.15), residues: 2837 helix: 0.49 (0.15), residues: 1161 sheet: 0.95 (0.22), residues: 546 loop : -0.91 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 126 HIS 0.006 0.001 HIS A 61 PHE 0.020 0.002 PHE A 315 TYR 0.026 0.002 TYR E 272 ARG 0.007 0.001 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 1039) hydrogen bonds : angle 5.00030 ( 2940) covalent geometry : bond 0.00469 (23845) covalent geometry : angle 0.56313 (32025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 510 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASN cc_start: 0.7923 (t0) cc_final: 0.7691 (t0) REVERT: A 48 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8147 (pttp) REVERT: A 132 ASN cc_start: 0.8250 (t0) cc_final: 0.7768 (t0) REVERT: A 351 VAL cc_start: 0.8533 (t) cc_final: 0.8180 (p) REVERT: A 488 GLU cc_start: 0.8449 (tp30) cc_final: 0.8090 (tp30) REVERT: A 508 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8544 (p) REVERT: A 511 ASP cc_start: 0.8116 (m-30) cc_final: 0.7797 (m-30) REVERT: A 542 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 545 MET cc_start: 0.8332 (tpp) cc_final: 0.7932 (tpt) REVERT: A 556 ASP cc_start: 0.7474 (m-30) cc_final: 0.7157 (m-30) REVERT: A 559 ASP cc_start: 0.7790 (m-30) cc_final: 0.7444 (m-30) REVERT: A 562 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7755 (mp0) REVERT: B 92 ASN cc_start: 0.6709 (m-40) cc_final: 0.6427 (t0) REVERT: B 155 LYS cc_start: 0.6312 (tptt) cc_final: 0.6044 (tttt) REVERT: B 176 MET cc_start: 0.6288 (mmp) cc_final: 0.5717 (mmp) REVERT: C 114 ASP cc_start: 0.7607 (t0) cc_final: 0.7388 (t0) REVERT: C 132 ASN cc_start: 0.7667 (t0) cc_final: 0.7392 (t0) REVERT: C 355 TYR cc_start: 0.8512 (m-80) cc_final: 0.8270 (m-10) REVERT: C 383 GLU cc_start: 0.7996 (mp0) cc_final: 0.7653 (mp0) REVERT: C 395 GLU cc_start: 0.7552 (tp30) cc_final: 0.7273 (tt0) REVERT: C 431 THR cc_start: 0.8293 (m) cc_final: 0.8088 (t) REVERT: C 438 LYS cc_start: 0.8767 (tttt) cc_final: 0.8496 (tttm) REVERT: C 480 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7309 (tp30) REVERT: C 493 TYR cc_start: 0.8078 (m-80) cc_final: 0.7721 (m-80) REVERT: D 78 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7207 (mm-30) REVERT: D 107 PHE cc_start: 0.7313 (t80) cc_final: 0.7017 (t80) REVERT: D 176 MET cc_start: 0.7842 (mmp) cc_final: 0.7580 (mmm) REVERT: D 212 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6945 (mp0) REVERT: E 15 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 16 LYS cc_start: 0.8421 (ttpt) cc_final: 0.8131 (ttpp) REVERT: E 65 THR cc_start: 0.8627 (p) cc_final: 0.8371 (p) REVERT: E 70 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8083 (mt-10) REVERT: E 116 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7720 (ttpp) REVERT: E 117 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6971 (mm-30) REVERT: E 132 ASN cc_start: 0.7709 (t0) cc_final: 0.7380 (t0) REVERT: E 361 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8021 (ttpt) REVERT: E 392 ASP cc_start: 0.8277 (t70) cc_final: 0.8047 (t0) REVERT: E 406 LEU cc_start: 0.8408 (tp) cc_final: 0.8165 (tt) REVERT: E 445 TYR cc_start: 0.8538 (m-80) cc_final: 0.8052 (m-80) REVERT: E 484 GLU cc_start: 0.8076 (tp30) cc_final: 0.7795 (mm-30) REVERT: E 488 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7701 (mm-30) REVERT: E 510 ILE cc_start: 0.8517 (mt) cc_final: 0.8188 (mt) REVERT: E 526 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8116 (ttp80) REVERT: E 551 ASN cc_start: 0.8652 (m-40) cc_final: 0.8445 (m-40) REVERT: F 42 TYR cc_start: 0.8455 (m-80) cc_final: 0.8037 (m-80) REVERT: F 49 PHE cc_start: 0.8483 (m-80) cc_final: 0.8195 (m-80) REVERT: F 55 LYS cc_start: 0.7656 (tppp) cc_final: 0.7341 (tppp) REVERT: F 88 ASP cc_start: 0.8072 (t70) cc_final: 0.7564 (t0) REVERT: F 121 ASN cc_start: 0.7733 (t0) cc_final: 0.7403 (t0) REVERT: F 177 TYR cc_start: 0.8230 (t80) cc_final: 0.8026 (t80) REVERT: F 469 MET cc_start: 0.2602 (tpp) cc_final: 0.2293 (tpp) REVERT: G 3 PHE cc_start: 0.8597 (m-80) cc_final: 0.8375 (m-10) REVERT: G 117 GLU cc_start: 0.8024 (tp30) cc_final: 0.7592 (tp30) REVERT: G 373 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7946 (mt-10) REVERT: G 393 GLU cc_start: 0.7818 (tp30) cc_final: 0.7491 (mm-30) REVERT: G 444 VAL cc_start: 0.8400 (m) cc_final: 0.8179 (p) REVERT: G 447 LEU cc_start: 0.8333 (mp) cc_final: 0.8133 (mt) REVERT: G 471 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6928 (tp30) REVERT: G 480 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7260 (tm-30) REVERT: G 559 ASP cc_start: 0.8022 (m-30) cc_final: 0.7775 (m-30) REVERT: H 36 LYS cc_start: 0.8222 (tttt) cc_final: 0.7825 (ttmm) REVERT: H 55 LYS cc_start: 0.7527 (mmmm) cc_final: 0.7160 (mmmm) REVERT: H 68 ASN cc_start: 0.8460 (m-40) cc_final: 0.8224 (m-40) REVERT: H 93 ASP cc_start: 0.8491 (p0) cc_final: 0.8291 (p0) REVERT: H 111 ASP cc_start: 0.5663 (m-30) cc_final: 0.5079 (p0) REVERT: H 121 ASN cc_start: 0.8004 (t0) cc_final: 0.7718 (t160) REVERT: H 143 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8522 (mttt) REVERT: H 179 LYS cc_start: 0.8287 (ttpp) cc_final: 0.8078 (ttpp) outliers start: 51 outliers final: 15 residues processed: 533 average time/residue: 1.5018 time to fit residues: 905.5286 Evaluate side-chains 501 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 481 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain H residue 143 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 249 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 461 ASN A 538 GLN B 121 ASN C 56 ASN C 79 ASN C 101 ASN C 155 ASN C 492 GLN C 538 GLN E 143 ASN E 350 ASN E 538 GLN F 213 ASN G 5 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117196 restraints weight = 33791.641| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.21 r_work: 0.3279 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23845 Z= 0.156 Angle : 0.531 10.523 32025 Z= 0.288 Chirality : 0.043 0.144 3517 Planarity : 0.003 0.056 4075 Dihedral : 4.301 23.840 3105 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.12 % Allowed : 15.90 % Favored : 81.98 % 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: 0.14 (0.15), residues: 2837 helix: 0.66 (0.15), residues: 1145 sheet: 0.90 (0.22), residues: 558 loop : -0.85 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 126 HIS 0.004 0.001 HIS A 61 PHE 0.017 0.001 PHE A 315 TYR 0.026 0.001 TYR E 272 ARG 0.006 0.000 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1039) hydrogen bonds : angle 4.88305 ( 2940) covalent geometry : bond 0.00377 (23845) covalent geometry : angle 0.53087 (32025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 481 time to evaluate : 2.475 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.8221 (t0) cc_final: 0.7771 (t0) REVERT: A 480 GLU cc_start: 0.7035 (pp20) cc_final: 0.6803 (pp20) REVERT: A 488 GLU cc_start: 0.8434 (tp30) cc_final: 0.8019 (tp30) REVERT: A 542 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8244 (mt) REVERT: A 545 MET cc_start: 0.8284 (tpp) cc_final: 0.7975 (tpt) REVERT: A 556 ASP cc_start: 0.7370 (m-30) cc_final: 0.7046 (m-30) REVERT: A 559 ASP cc_start: 0.7811 (m-30) cc_final: 0.7554 (m-30) REVERT: A 562 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7811 (mp0) REVERT: B 155 LYS cc_start: 0.6337 (tptt) cc_final: 0.6026 (tttt) REVERT: B 176 MET cc_start: 0.6222 (mmp) cc_final: 0.5655 (mmt) REVERT: C 114 ASP cc_start: 0.7583 (t0) cc_final: 0.7362 (t0) REVERT: C 132 ASN cc_start: 0.7692 (t0) cc_final: 0.7422 (t0) REVERT: C 279 GLU cc_start: 0.8110 (tt0) cc_final: 0.7387 (tp30) REVERT: C 355 TYR cc_start: 0.8499 (m-80) cc_final: 0.8241 (m-10) REVERT: C 383 GLU cc_start: 0.8040 (mp0) cc_final: 0.7603 (mp0) REVERT: C 395 GLU cc_start: 0.7508 (tp30) cc_final: 0.7307 (tp30) REVERT: C 431 THR cc_start: 0.8317 (m) cc_final: 0.8068 (t) REVERT: C 432 ASP cc_start: 0.8158 (p0) cc_final: 0.7922 (p0) REVERT: C 438 LYS cc_start: 0.8732 (tttt) cc_final: 0.8469 (tttm) REVERT: C 455 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8322 (t0) REVERT: C 480 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7314 (tp30) REVERT: C 481 ARG cc_start: 0.8339 (ttm170) cc_final: 0.8131 (ttm110) REVERT: D 78 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7086 (mm-30) REVERT: D 107 PHE cc_start: 0.7298 (t80) cc_final: 0.6992 (t80) REVERT: D 176 MET cc_start: 0.7902 (mmp) cc_final: 0.7674 (mmm) REVERT: E 32 ASP cc_start: 0.7707 (t0) cc_final: 0.7427 (t0) REVERT: E 49 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7745 (mm-30) REVERT: E 65 THR cc_start: 0.8635 (p) cc_final: 0.8342 (p) REVERT: E 70 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8024 (mt-10) REVERT: E 116 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7745 (ttpp) REVERT: E 117 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7060 (mm-30) REVERT: E 132 ASN cc_start: 0.7677 (t0) cc_final: 0.7353 (t0) REVERT: E 361 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7968 (ttpt) REVERT: E 392 ASP cc_start: 0.8278 (t70) cc_final: 0.8043 (t0) REVERT: E 395 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: E 397 GLU cc_start: 0.7426 (mp0) cc_final: 0.7163 (mp0) REVERT: E 421 ASN cc_start: 0.8706 (t0) cc_final: 0.8228 (t0) REVERT: E 445 TYR cc_start: 0.8521 (m-80) cc_final: 0.8048 (m-80) REVERT: E 484 GLU cc_start: 0.8025 (tp30) cc_final: 0.7253 (tp30) REVERT: E 488 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7442 (mm-30) REVERT: E 526 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8193 (ttp80) REVERT: E 551 ASN cc_start: 0.8669 (m-40) cc_final: 0.8450 (m-40) REVERT: F 1 MET cc_start: 0.6198 (pmm) cc_final: 0.5724 (ptm) REVERT: F 49 PHE cc_start: 0.8499 (m-80) cc_final: 0.8237 (m-80) REVERT: F 74 ASP cc_start: 0.8173 (m-30) cc_final: 0.7943 (t0) REVERT: F 121 ASN cc_start: 0.7650 (t0) cc_final: 0.7428 (t0) REVERT: G 3 PHE cc_start: 0.8563 (m-80) cc_final: 0.8329 (m-10) REVERT: G 117 GLU cc_start: 0.8040 (tp30) cc_final: 0.7610 (tp30) REVERT: G 373 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7942 (mt-10) REVERT: G 393 GLU cc_start: 0.7801 (tp30) cc_final: 0.7522 (mm-30) REVERT: G 444 VAL cc_start: 0.8474 (m) cc_final: 0.8266 (p) REVERT: G 471 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6883 (tp30) REVERT: G 474 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8137 (mppt) REVERT: G 480 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7207 (tm-30) REVERT: G 523 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8634 (t) REVERT: G 559 ASP cc_start: 0.8057 (m-30) cc_final: 0.7814 (m-30) REVERT: H 14 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7578 (mp) REVERT: H 36 LYS cc_start: 0.8234 (tttt) cc_final: 0.7840 (ttmm) REVERT: H 55 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7168 (mmmm) REVERT: H 68 ASN cc_start: 0.8467 (m-40) cc_final: 0.8231 (m-40) REVERT: H 121 ASN cc_start: 0.8041 (t0) cc_final: 0.7760 (t0) REVERT: H 143 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8514 (mttt) outliers start: 55 outliers final: 26 residues processed: 511 average time/residue: 1.5354 time to fit residues: 896.3828 Evaluate side-chains 499 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 466 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 553 SER Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 213 optimal weight: 50.0000 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 192 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 538 GLN C 56 ASN C 101 ASN C 492 GLN C 538 GLN E 538 GLN F 213 ASN G 538 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116494 restraints weight = 33639.388| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.21 r_work: 0.3263 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23845 Z= 0.189 Angle : 0.560 10.035 32025 Z= 0.303 Chirality : 0.044 0.153 3517 Planarity : 0.003 0.059 4075 Dihedral : 4.415 24.491 3105 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.47 % Allowed : 16.74 % Favored : 80.79 % 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: 0.08 (0.15), residues: 2837 helix: 0.61 (0.15), residues: 1158 sheet: 0.88 (0.22), residues: 558 loop : -0.90 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 126 HIS 0.005 0.001 HIS A 61 PHE 0.031 0.002 PHE D 175 TYR 0.025 0.001 TYR C 272 ARG 0.006 0.001 ARG C 526 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 1039) hydrogen bonds : angle 4.89896 ( 2940) covalent geometry : bond 0.00463 (23845) covalent geometry : angle 0.56004 (32025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 487 time to evaluate : 2.737 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8103 (pttp) REVERT: A 110 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 132 ASN cc_start: 0.8276 (t0) cc_final: 0.7832 (t0) REVERT: A 289 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 345 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 488 GLU cc_start: 0.8389 (tp30) cc_final: 0.7988 (tp30) REVERT: A 545 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7988 (tpt) REVERT: A 556 ASP cc_start: 0.7335 (m-30) cc_final: 0.6978 (m-30) REVERT: A 559 ASP cc_start: 0.7786 (m-30) cc_final: 0.7531 (m-30) REVERT: A 562 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 155 LYS cc_start: 0.6329 (tptt) cc_final: 0.5970 (tttt) REVERT: B 176 MET cc_start: 0.6207 (mmp) cc_final: 0.5716 (mmt) REVERT: C 48 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8150 (ptmm) REVERT: C 49 GLU cc_start: 0.7920 (mp0) cc_final: 0.7702 (mp0) REVERT: C 114 ASP cc_start: 0.7561 (t0) cc_final: 0.7360 (t0) REVERT: C 117 GLU cc_start: 0.8045 (tp30) cc_final: 0.7525 (tp30) REVERT: C 132 ASN cc_start: 0.7747 (t0) cc_final: 0.7462 (t0) REVERT: C 383 GLU cc_start: 0.8026 (mp0) cc_final: 0.7570 (mp0) REVERT: C 438 LYS cc_start: 0.8791 (tttt) cc_final: 0.8513 (tttt) REVERT: C 479 LYS cc_start: 0.8362 (tptm) cc_final: 0.8080 (ttmm) REVERT: C 480 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7508 (tp30) REVERT: C 493 TYR cc_start: 0.7961 (m-80) cc_final: 0.7722 (m-80) REVERT: D 58 GLU cc_start: 0.7709 (tt0) cc_final: 0.7440 (tt0) REVERT: D 78 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7215 (mm-30) REVERT: D 143 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: D 176 MET cc_start: 0.7912 (mmp) cc_final: 0.7681 (mmm) REVERT: D 203 GLU cc_start: 0.7764 (mt-10) cc_final: 0.6871 (tm-30) REVERT: D 211 ILE cc_start: 0.7905 (mt) cc_final: 0.7641 (pp) REVERT: E 16 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8134 (ttpp) REVERT: E 32 ASP cc_start: 0.7706 (t0) cc_final: 0.7392 (t0) REVERT: E 65 THR cc_start: 0.8634 (p) cc_final: 0.8327 (p) REVERT: E 70 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8044 (mt-10) REVERT: E 117 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7039 (mm-30) REVERT: E 132 ASN cc_start: 0.7758 (t0) cc_final: 0.7393 (t0) REVERT: E 361 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8062 (ttpt) REVERT: E 392 ASP cc_start: 0.8157 (t70) cc_final: 0.7940 (t0) REVERT: E 395 GLU cc_start: 0.7782 (tp30) cc_final: 0.7428 (tm-30) REVERT: E 421 ASN cc_start: 0.8680 (t0) cc_final: 0.8254 (t0) REVERT: E 432 ASP cc_start: 0.8164 (p0) cc_final: 0.7924 (p0) REVERT: E 434 ASP cc_start: 0.7494 (m-30) cc_final: 0.7266 (m-30) REVERT: E 445 TYR cc_start: 0.8550 (m-80) cc_final: 0.8135 (m-80) REVERT: E 484 GLU cc_start: 0.7984 (tp30) cc_final: 0.7225 (tp30) REVERT: E 488 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 526 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8214 (ttp80) REVERT: E 551 ASN cc_start: 0.8659 (m-40) cc_final: 0.8443 (m-40) REVERT: F 1 MET cc_start: 0.6580 (pmm) cc_final: 0.6029 (ptm) REVERT: F 49 PHE cc_start: 0.8487 (m-80) cc_final: 0.8228 (m-80) REVERT: F 88 ASP cc_start: 0.8164 (t70) cc_final: 0.7659 (t0) REVERT: F 121 ASN cc_start: 0.7660 (t0) cc_final: 0.7379 (t0) REVERT: F 130 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.7051 (tptm) REVERT: F 131 LYS cc_start: 0.7552 (pptt) cc_final: 0.7233 (pptt) REVERT: F 216 ASP cc_start: 0.7289 (p0) cc_final: 0.7053 (OUTLIER) REVERT: F 217 PHE cc_start: 0.8259 (m-80) cc_final: 0.7954 (m-80) REVERT: G 117 GLU cc_start: 0.8040 (tp30) cc_final: 0.7501 (tp30) REVERT: G 279 GLU cc_start: 0.7681 (tp30) cc_final: 0.7477 (tp30) REVERT: G 373 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8001 (mt-10) REVERT: G 393 GLU cc_start: 0.7783 (tp30) cc_final: 0.7568 (mm-30) REVERT: G 471 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6872 (tp30) REVERT: G 474 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8114 (mppt) REVERT: G 523 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8634 (t) REVERT: G 559 ASP cc_start: 0.8053 (m-30) cc_final: 0.7795 (m-30) REVERT: H 14 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7682 (mp) REVERT: H 36 LYS cc_start: 0.8142 (tttt) cc_final: 0.7751 (ttmm) REVERT: H 55 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7219 (mmmm) REVERT: H 68 ASN cc_start: 0.8535 (m-40) cc_final: 0.8291 (m110) REVERT: H 121 ASN cc_start: 0.7968 (t0) cc_final: 0.7577 (t0) REVERT: H 143 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8541 (mttt) outliers start: 64 outliers final: 33 residues processed: 517 average time/residue: 1.4551 time to fit residues: 852.7116 Evaluate side-chains 513 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 471 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 465 ILE Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 553 SER Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 103 optimal weight: 2.9990 chunk 266 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 174 optimal weight: 0.0020 chunk 230 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 257 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN C 101 ASN C 155 ASN C 350 ASN C 492 GLN C 538 GLN E 538 GLN F 213 ASN G 538 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119203 restraints weight = 33361.540| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.18 r_work: 0.3293 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23845 Z= 0.124 Angle : 0.506 8.360 32025 Z= 0.275 Chirality : 0.042 0.140 3517 Planarity : 0.003 0.039 4075 Dihedral : 4.211 24.280 3105 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.01 % Allowed : 18.67 % Favored : 79.32 % 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: 0.29 (0.15), residues: 2837 helix: 0.86 (0.15), residues: 1151 sheet: 0.93 (0.22), residues: 558 loop : -0.84 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 126 HIS 0.003 0.001 HIS A 61 PHE 0.015 0.001 PHE E 500 TYR 0.025 0.001 TYR C 272 ARG 0.006 0.000 ARG C 481 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1039) hydrogen bonds : angle 4.73978 ( 2940) covalent geometry : bond 0.00294 (23845) covalent geometry : angle 0.50647 (32025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 470 time to evaluate : 2.482 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 132 ASN cc_start: 0.8204 (t0) cc_final: 0.7771 (t0) REVERT: A 289 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 480 GLU cc_start: 0.6940 (pp20) cc_final: 0.6721 (pp20) REVERT: A 488 GLU cc_start: 0.8433 (tp30) cc_final: 0.8023 (tp30) REVERT: A 545 MET cc_start: 0.8236 (tpp) cc_final: 0.7881 (tpt) REVERT: A 559 ASP cc_start: 0.7809 (m-30) cc_final: 0.7532 (m-30) REVERT: A 562 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 571 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 133 PHE cc_start: 0.7545 (t80) cc_final: 0.7013 (t80) REVERT: B 155 LYS cc_start: 0.6395 (tptt) cc_final: 0.6046 (tttt) REVERT: B 176 MET cc_start: 0.6195 (mmp) cc_final: 0.5742 (mmt) REVERT: C 49 GLU cc_start: 0.7976 (mp0) cc_final: 0.7688 (mp0) REVERT: C 117 GLU cc_start: 0.8063 (tp30) cc_final: 0.7518 (tp30) REVERT: C 132 ASN cc_start: 0.7678 (t0) cc_final: 0.7396 (t0) REVERT: C 355 TYR cc_start: 0.8479 (m-80) cc_final: 0.8256 (m-10) REVERT: C 383 GLU cc_start: 0.8066 (mp0) cc_final: 0.7667 (mp0) REVERT: C 480 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7332 (tp30) REVERT: C 493 TYR cc_start: 0.7782 (m-80) cc_final: 0.7371 (m-80) REVERT: D 58 GLU cc_start: 0.7702 (tt0) cc_final: 0.7434 (tt0) REVERT: D 78 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7188 (mm-30) REVERT: D 176 MET cc_start: 0.7990 (mmp) cc_final: 0.7741 (mmm) REVERT: D 203 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6890 (tm-30) REVERT: D 211 ILE cc_start: 0.7880 (mt) cc_final: 0.7596 (pp) REVERT: E 16 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8112 (ttpp) REVERT: E 32 ASP cc_start: 0.7677 (t0) cc_final: 0.7404 (t0) REVERT: E 65 THR cc_start: 0.8629 (p) cc_final: 0.8321 (p) REVERT: E 70 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7996 (mt-10) REVERT: E 117 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7066 (mm-30) REVERT: E 132 ASN cc_start: 0.7657 (t0) cc_final: 0.7366 (t0) REVERT: E 360 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8077 (mmmm) REVERT: E 361 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7919 (ttpt) REVERT: E 392 ASP cc_start: 0.8194 (t70) cc_final: 0.7975 (t0) REVERT: E 395 GLU cc_start: 0.7747 (tp30) cc_final: 0.7374 (tm-30) REVERT: E 421 ASN cc_start: 0.8658 (t0) cc_final: 0.8251 (t0) REVERT: E 445 TYR cc_start: 0.8513 (m-80) cc_final: 0.8117 (m-80) REVERT: E 484 GLU cc_start: 0.7927 (tp30) cc_final: 0.7008 (tp30) REVERT: E 488 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7494 (mm-30) REVERT: E 526 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8278 (ttp80) REVERT: E 551 ASN cc_start: 0.8651 (m-40) cc_final: 0.8425 (m-40) REVERT: F 1 MET cc_start: 0.6449 (pmm) cc_final: 0.5944 (ptm) REVERT: F 49 PHE cc_start: 0.8466 (m-80) cc_final: 0.8200 (m-80) REVERT: F 88 ASP cc_start: 0.8203 (t70) cc_final: 0.7754 (t0) REVERT: F 93 ASP cc_start: 0.8288 (p0) cc_final: 0.8031 (p0) REVERT: F 216 ASP cc_start: 0.7258 (p0) cc_final: 0.7026 (OUTLIER) REVERT: F 217 PHE cc_start: 0.8188 (m-80) cc_final: 0.7728 (m-80) REVERT: F 219 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (mttp) REVERT: G 110 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7332 (tm-30) REVERT: G 117 GLU cc_start: 0.8022 (tp30) cc_final: 0.7472 (tp30) REVERT: G 264 MET cc_start: 0.6358 (mmm) cc_final: 0.6083 (mmm) REVERT: G 279 GLU cc_start: 0.7710 (tp30) cc_final: 0.7381 (tp30) REVERT: G 373 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7988 (mt-10) REVERT: G 465 ILE cc_start: 0.8094 (pt) cc_final: 0.7637 (mt) REVERT: G 471 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6873 (tp30) REVERT: G 474 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8053 (mppt) REVERT: G 480 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7140 (tm-30) REVERT: G 523 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8632 (t) REVERT: G 559 ASP cc_start: 0.8046 (m-30) cc_final: 0.7807 (m-30) REVERT: H 14 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7652 (mp) REVERT: H 36 LYS cc_start: 0.8245 (tttt) cc_final: 0.7855 (ttmm) REVERT: H 55 LYS cc_start: 0.7623 (mmmm) cc_final: 0.7264 (mmmm) REVERT: H 68 ASN cc_start: 0.8468 (m-40) cc_final: 0.8217 (m110) REVERT: H 79 SER cc_start: 0.8429 (t) cc_final: 0.8211 (m) REVERT: H 121 ASN cc_start: 0.7992 (t0) cc_final: 0.7666 (t0) REVERT: H 143 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8517 (mttt) outliers start: 52 outliers final: 26 residues processed: 496 average time/residue: 1.4542 time to fit residues: 815.8765 Evaluate side-chains 497 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 465 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 179 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 229 optimal weight: 0.0060 chunk 65 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 197 optimal weight: 0.1980 chunk 227 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN C 56 ASN C 101 ASN C 492 GLN C 538 GLN E 538 GLN F 213 ASN G 538 GLN H 12 ASN H 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.153025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119331 restraints weight = 33473.545| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.19 r_work: 0.3292 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23845 Z= 0.115 Angle : 0.501 7.678 32025 Z= 0.271 Chirality : 0.042 0.160 3517 Planarity : 0.003 0.039 4075 Dihedral : 4.129 23.940 3105 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 18.79 % Favored : 79.32 % 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: 0.40 (0.16), residues: 2837 helix: 0.96 (0.15), residues: 1175 sheet: 0.98 (0.22), residues: 558 loop : -0.82 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 126 HIS 0.003 0.001 HIS A 61 PHE 0.014 0.001 PHE E 500 TYR 0.025 0.001 TYR C 272 ARG 0.009 0.000 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1039) hydrogen bonds : angle 4.65897 ( 2940) covalent geometry : bond 0.00269 (23845) covalent geometry : angle 0.50052 (32025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 466 time to evaluate : 3.673 Fit side-chains REVERT: A 132 ASN cc_start: 0.8187 (t0) cc_final: 0.7748 (t0) REVERT: A 289 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 345 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 480 GLU cc_start: 0.6966 (pp20) cc_final: 0.6740 (pp20) REVERT: A 488 GLU cc_start: 0.8398 (tp30) cc_final: 0.7992 (tp30) REVERT: A 545 MET cc_start: 0.8259 (tpp) cc_final: 0.7903 (tpt) REVERT: A 559 ASP cc_start: 0.7814 (m-30) cc_final: 0.7528 (m-30) REVERT: A 562 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 133 PHE cc_start: 0.7495 (t80) cc_final: 0.6965 (t80) REVERT: B 155 LYS cc_start: 0.6352 (tptt) cc_final: 0.5959 (tttt) REVERT: B 176 MET cc_start: 0.6162 (mmp) cc_final: 0.5803 (mmt) REVERT: C 49 GLU cc_start: 0.7990 (mp0) cc_final: 0.7696 (mp0) REVERT: C 117 GLU cc_start: 0.8039 (tp30) cc_final: 0.7574 (tp30) REVERT: C 132 ASN cc_start: 0.7643 (t0) cc_final: 0.7367 (t0) REVERT: C 279 GLU cc_start: 0.8121 (tt0) cc_final: 0.7446 (tp30) REVERT: C 311 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7930 (t) REVERT: C 355 TYR cc_start: 0.8485 (m-80) cc_final: 0.8231 (m-10) REVERT: C 383 GLU cc_start: 0.8060 (mp0) cc_final: 0.7550 (mp0) REVERT: C 438 LYS cc_start: 0.8941 (tttt) cc_final: 0.8721 (tttm) REVERT: C 481 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8116 (ttm110) REVERT: C 493 TYR cc_start: 0.7730 (m-80) cc_final: 0.7343 (m-80) REVERT: D 58 GLU cc_start: 0.7687 (tt0) cc_final: 0.7441 (tt0) REVERT: D 78 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7203 (mm-30) REVERT: D 176 MET cc_start: 0.8032 (mmp) cc_final: 0.7795 (mmm) REVERT: D 203 GLU cc_start: 0.7746 (mt-10) cc_final: 0.6953 (tm-30) REVERT: D 211 ILE cc_start: 0.7872 (mt) cc_final: 0.7569 (pp) REVERT: E 16 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8128 (ttpp) REVERT: E 32 ASP cc_start: 0.7653 (t0) cc_final: 0.7365 (t0) REVERT: E 65 THR cc_start: 0.8625 (p) cc_final: 0.8319 (p) REVERT: E 70 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7993 (mt-10) REVERT: E 110 GLU cc_start: 0.7635 (mp0) cc_final: 0.7407 (mp0) REVERT: E 117 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7028 (mm-30) REVERT: E 132 ASN cc_start: 0.7650 (t0) cc_final: 0.7345 (t0) REVERT: E 360 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8014 (mmmm) REVERT: E 392 ASP cc_start: 0.8146 (t70) cc_final: 0.7917 (t0) REVERT: E 395 GLU cc_start: 0.7703 (tp30) cc_final: 0.7326 (tm-30) REVERT: E 445 TYR cc_start: 0.8495 (m-80) cc_final: 0.8054 (m-80) REVERT: E 484 GLU cc_start: 0.7874 (tp30) cc_final: 0.7046 (tp30) REVERT: E 488 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7539 (mm-30) REVERT: E 500 PHE cc_start: 0.7979 (m-10) cc_final: 0.7556 (m-10) REVERT: E 526 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8270 (ttp80) REVERT: E 551 ASN cc_start: 0.8613 (m-40) cc_final: 0.8405 (m-40) REVERT: E 559 ASP cc_start: 0.7971 (m-30) cc_final: 0.7663 (m-30) REVERT: F 1 MET cc_start: 0.6379 (pmm) cc_final: 0.5963 (ptm) REVERT: F 49 PHE cc_start: 0.8431 (m-80) cc_final: 0.8169 (m-80) REVERT: F 88 ASP cc_start: 0.8200 (t70) cc_final: 0.7755 (t0) REVERT: F 121 ASN cc_start: 0.7559 (t0) cc_final: 0.7304 (t0) REVERT: F 131 LYS cc_start: 0.7621 (pptt) cc_final: 0.7400 (pptt) REVERT: F 216 ASP cc_start: 0.7274 (p0) cc_final: 0.7001 (OUTLIER) REVERT: F 217 PHE cc_start: 0.8080 (m-80) cc_final: 0.7700 (m-80) REVERT: F 219 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8552 (mttp) REVERT: G 110 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7304 (tm-30) REVERT: G 117 GLU cc_start: 0.7991 (tp30) cc_final: 0.7442 (tp30) REVERT: G 264 MET cc_start: 0.6521 (mmm) cc_final: 0.6191 (mmm) REVERT: G 279 GLU cc_start: 0.7708 (tp30) cc_final: 0.7311 (tp30) REVERT: G 373 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7966 (mt-10) REVERT: G 465 ILE cc_start: 0.8065 (pt) cc_final: 0.7599 (mt) REVERT: G 471 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6846 (tp30) REVERT: G 474 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7999 (mppt) REVERT: G 480 GLU cc_start: 0.7300 (tm-30) cc_final: 0.7086 (tm-30) REVERT: G 523 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8634 (t) REVERT: G 559 ASP cc_start: 0.8044 (m-30) cc_final: 0.7803 (m-30) REVERT: H 14 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7643 (mp) REVERT: H 36 LYS cc_start: 0.8219 (tttt) cc_final: 0.7827 (ttmm) REVERT: H 55 LYS cc_start: 0.7591 (mmmm) cc_final: 0.7234 (mmmm) REVERT: H 68 ASN cc_start: 0.8427 (m-40) cc_final: 0.8212 (m-40) REVERT: H 79 SER cc_start: 0.8440 (t) cc_final: 0.8207 (m) REVERT: H 121 ASN cc_start: 0.7956 (t0) cc_final: 0.7669 (t0) REVERT: H 143 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8515 (mttt) outliers start: 49 outliers final: 29 residues processed: 492 average time/residue: 2.0669 time to fit residues: 1163.1542 Evaluate side-chains 508 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 472 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 257 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 225 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 56 ASN C 20 ASN C 56 ASN C 101 ASN C 147 ASN C 155 ASN C 295 HIS C 330 ASN C 492 GLN C 538 GLN E 79 ASN E 538 GLN F 181 GLN F 213 ASN G 330 ASN G 461 ASN G 538 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117740 restraints weight = 33471.950| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.18 r_work: 0.3274 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23845 Z= 0.174 Angle : 0.558 9.488 32025 Z= 0.301 Chirality : 0.043 0.164 3517 Planarity : 0.003 0.061 4075 Dihedral : 4.282 23.932 3105 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.93 % Allowed : 19.60 % Favored : 78.47 % 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: 0.21 (0.16), residues: 2837 helix: 0.78 (0.15), residues: 1173 sheet: 0.90 (0.23), residues: 534 loop : -0.85 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 126 HIS 0.005 0.001 HIS A 61 PHE 0.019 0.002 PHE A 315 TYR 0.025 0.001 TYR E 272 ARG 0.010 0.001 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 1039) hydrogen bonds : angle 4.76369 ( 2940) covalent geometry : bond 0.00427 (23845) covalent geometry : angle 0.55837 (32025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 482 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ASN cc_start: 0.8281 (t0) cc_final: 0.7853 (t0) REVERT: A 289 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: A 345 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 480 GLU cc_start: 0.7100 (pp20) cc_final: 0.6879 (pp20) REVERT: A 488 GLU cc_start: 0.8396 (tp30) cc_final: 0.7998 (tp30) REVERT: A 545 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7948 (tpt) REVERT: A 556 ASP cc_start: 0.7314 (m-30) cc_final: 0.7001 (m-30) REVERT: A 559 ASP cc_start: 0.7788 (m-30) cc_final: 0.7525 (m-30) REVERT: A 562 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 133 PHE cc_start: 0.7562 (t80) cc_final: 0.7037 (t80) REVERT: B 155 LYS cc_start: 0.6415 (tptt) cc_final: 0.6017 (tttt) REVERT: B 176 MET cc_start: 0.6147 (mmp) cc_final: 0.5804 (mmt) REVERT: C 49 GLU cc_start: 0.7980 (mp0) cc_final: 0.7690 (mp0) REVERT: C 114 ASP cc_start: 0.7355 (t0) cc_final: 0.7147 (t70) REVERT: C 117 GLU cc_start: 0.8018 (tp30) cc_final: 0.7509 (tp30) REVERT: C 132 ASN cc_start: 0.7822 (t0) cc_final: 0.7448 (t0) REVERT: C 279 GLU cc_start: 0.8091 (tt0) cc_final: 0.7475 (tp30) REVERT: C 288 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: C 355 TYR cc_start: 0.8556 (m-80) cc_final: 0.8277 (m-10) REVERT: C 383 GLU cc_start: 0.8054 (mp0) cc_final: 0.7598 (mp0) REVERT: C 393 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7709 (mm-30) REVERT: C 434 ASP cc_start: 0.7951 (m-30) cc_final: 0.7700 (m-30) REVERT: C 493 TYR cc_start: 0.7998 (m-80) cc_final: 0.7523 (m-80) REVERT: D 9 ASP cc_start: 0.7899 (t0) cc_final: 0.7678 (t0) REVERT: D 58 GLU cc_start: 0.7713 (tt0) cc_final: 0.7464 (tt0) REVERT: D 78 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 176 MET cc_start: 0.8028 (mmp) cc_final: 0.7792 (mmm) REVERT: D 203 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7035 (tm-30) REVERT: E 16 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8136 (ttpp) REVERT: E 32 ASP cc_start: 0.7664 (t0) cc_final: 0.7381 (t0) REVERT: E 65 THR cc_start: 0.8636 (p) cc_final: 0.8330 (p) REVERT: E 70 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7997 (mt-10) REVERT: E 110 GLU cc_start: 0.7748 (mp0) cc_final: 0.7515 (mp0) REVERT: E 117 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7025 (mm-30) REVERT: E 132 ASN cc_start: 0.7749 (t0) cc_final: 0.7443 (t0) REVERT: E 316 PHE cc_start: 0.8704 (m-80) cc_final: 0.8499 (m-80) REVERT: E 392 ASP cc_start: 0.8104 (t70) cc_final: 0.7877 (t0) REVERT: E 395 GLU cc_start: 0.7792 (tp30) cc_final: 0.7429 (tm-30) REVERT: E 432 ASP cc_start: 0.8177 (p0) cc_final: 0.7884 (p0) REVERT: E 445 TYR cc_start: 0.8539 (m-80) cc_final: 0.8076 (m-80) REVERT: E 484 GLU cc_start: 0.7952 (tp30) cc_final: 0.7136 (tp30) REVERT: E 488 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7575 (mm-30) REVERT: E 526 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8269 (ttp80) REVERT: E 551 ASN cc_start: 0.8652 (m-40) cc_final: 0.8437 (m-40) REVERT: F 1 MET cc_start: 0.6602 (pmm) cc_final: 0.6218 (ptm) REVERT: F 14 LEU cc_start: 0.8485 (mp) cc_final: 0.8196 (mp) REVERT: F 49 PHE cc_start: 0.8460 (m-80) cc_final: 0.8154 (m-80) REVERT: F 73 ASN cc_start: 0.8577 (p0) cc_final: 0.8360 (p0) REVERT: F 74 ASP cc_start: 0.8164 (m-30) cc_final: 0.7723 (t0) REVERT: F 121 ASN cc_start: 0.7615 (t0) cc_final: 0.7374 (t0) REVERT: F 131 LYS cc_start: 0.7655 (pptt) cc_final: 0.7348 (pptt) REVERT: F 217 PHE cc_start: 0.8150 (m-80) cc_final: 0.7683 (m-80) REVERT: G 48 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8307 (ptmt) REVERT: G 110 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7334 (tm-30) REVERT: G 117 GLU cc_start: 0.8008 (tp30) cc_final: 0.7415 (tp30) REVERT: G 141 ASN cc_start: 0.8472 (m-40) cc_final: 0.8204 (m110) REVERT: G 264 MET cc_start: 0.6526 (mmm) cc_final: 0.6188 (mmm) REVERT: G 279 GLU cc_start: 0.7724 (tp30) cc_final: 0.7287 (tp30) REVERT: G 373 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8012 (mt-10) REVERT: G 471 GLU cc_start: 0.7257 (tm-30) cc_final: 0.7002 (tp30) REVERT: G 473 ILE cc_start: 0.8145 (pt) cc_final: 0.7847 (pp) REVERT: G 480 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7171 (tm-30) REVERT: G 559 ASP cc_start: 0.8063 (m-30) cc_final: 0.7830 (m-30) REVERT: H 14 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7707 (mt) REVERT: H 36 LYS cc_start: 0.8166 (tttt) cc_final: 0.7772 (ttmm) REVERT: H 55 LYS cc_start: 0.7727 (mmmm) cc_final: 0.7395 (mmmm) REVERT: H 68 ASN cc_start: 0.8488 (m-40) cc_final: 0.8286 (m110) REVERT: H 79 SER cc_start: 0.8462 (t) cc_final: 0.8197 (m) REVERT: H 121 ASN cc_start: 0.7947 (t0) cc_final: 0.7611 (t0) REVERT: H 143 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (mttt) outliers start: 50 outliers final: 35 residues processed: 507 average time/residue: 1.4341 time to fit residues: 823.5120 Evaluate side-chains 528 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 487 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 553 SER Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 234 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 194 optimal weight: 0.0470 chunk 255 optimal weight: 0.0970 chunk 23 optimal weight: 0.5980 chunk 123 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 250 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 455 ASN C 56 ASN C 101 ASN C 147 ASN C 492 GLN C 538 GLN E 79 ASN E 538 GLN F 213 ASN G 538 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120198 restraints weight = 33437.912| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.20 r_work: 0.3311 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23845 Z= 0.099 Angle : 0.504 7.636 32025 Z= 0.272 Chirality : 0.041 0.158 3517 Planarity : 0.003 0.039 4075 Dihedral : 4.044 25.184 3105 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.27 % Allowed : 20.49 % Favored : 78.24 % 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: 0.51 (0.16), residues: 2837 helix: 1.04 (0.15), residues: 1178 sheet: 1.08 (0.23), residues: 553 loop : -0.77 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 126 HIS 0.002 0.000 HIS C 295 PHE 0.014 0.001 PHE E 500 TYR 0.025 0.001 TYR C 272 ARG 0.008 0.000 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 1039) hydrogen bonds : angle 4.59553 ( 2940) covalent geometry : bond 0.00224 (23845) covalent geometry : angle 0.50375 (32025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 473 time to evaluate : 2.565 Fit side-chains REVERT: A 132 ASN cc_start: 0.8177 (t0) cc_final: 0.7751 (t0) REVERT: A 289 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: A 345 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8348 (p) REVERT: A 488 GLU cc_start: 0.8424 (tp30) cc_final: 0.8011 (tp30) REVERT: A 504 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8388 (mtt90) REVERT: A 545 MET cc_start: 0.8226 (tpp) cc_final: 0.7876 (tpt) REVERT: A 559 ASP cc_start: 0.7796 (m-30) cc_final: 0.7523 (m-30) REVERT: A 562 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7786 (mt-10) REVERT: B 133 PHE cc_start: 0.7498 (t80) cc_final: 0.6955 (t80) REVERT: B 153 PHE cc_start: 0.6730 (t80) cc_final: 0.6275 (t80) REVERT: B 155 LYS cc_start: 0.6428 (tptt) cc_final: 0.6021 (tttt) REVERT: B 176 MET cc_start: 0.6125 (mmp) cc_final: 0.5755 (mmt) REVERT: C 49 GLU cc_start: 0.7990 (mp0) cc_final: 0.7691 (mp0) REVERT: C 114 ASP cc_start: 0.7208 (t0) cc_final: 0.6966 (t70) REVERT: C 117 GLU cc_start: 0.8038 (tp30) cc_final: 0.7544 (tp30) REVERT: C 132 ASN cc_start: 0.7626 (t0) cc_final: 0.7336 (t0) REVERT: C 279 GLU cc_start: 0.8058 (tt0) cc_final: 0.7387 (tp30) REVERT: C 355 TYR cc_start: 0.8423 (m-80) cc_final: 0.8200 (m-10) REVERT: C 383 GLU cc_start: 0.8080 (mp0) cc_final: 0.7584 (mp0) REVERT: C 438 LYS cc_start: 0.8948 (tttt) cc_final: 0.8688 (tttm) REVERT: C 481 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7944 (ttm-80) REVERT: C 493 TYR cc_start: 0.7524 (m-80) cc_final: 0.7196 (m-80) REVERT: D 58 GLU cc_start: 0.7677 (tt0) cc_final: 0.7438 (tt0) REVERT: D 78 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7238 (mm-30) REVERT: D 203 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6989 (tm-30) REVERT: E 16 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8100 (ttpp) REVERT: E 65 THR cc_start: 0.8638 (p) cc_final: 0.8333 (p) REVERT: E 70 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7991 (mt-10) REVERT: E 106 TYR cc_start: 0.8633 (m-80) cc_final: 0.8396 (m-80) REVERT: E 110 GLU cc_start: 0.7645 (mp0) cc_final: 0.7404 (mp0) REVERT: E 117 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7002 (mm-30) REVERT: E 130 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8279 (tp) REVERT: E 132 ASN cc_start: 0.7592 (t0) cc_final: 0.7287 (t0) REVERT: E 360 LYS cc_start: 0.8203 (mttp) cc_final: 0.7977 (mmmm) REVERT: E 392 ASP cc_start: 0.8164 (t70) cc_final: 0.7935 (t0) REVERT: E 395 GLU cc_start: 0.7650 (tp30) cc_final: 0.7299 (tm-30) REVERT: E 445 TYR cc_start: 0.8471 (m-80) cc_final: 0.8041 (m-80) REVERT: E 484 GLU cc_start: 0.7831 (tp30) cc_final: 0.6954 (tp30) REVERT: E 488 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7525 (mm-30) REVERT: E 526 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8298 (ttp80) REVERT: E 539 LYS cc_start: 0.8706 (mttm) cc_final: 0.8475 (mtpp) REVERT: E 551 ASN cc_start: 0.8589 (m-40) cc_final: 0.8380 (m-40) REVERT: E 559 ASP cc_start: 0.7971 (m-30) cc_final: 0.7671 (m-30) REVERT: F 1 MET cc_start: 0.6395 (pmm) cc_final: 0.6068 (ptm) REVERT: F 49 PHE cc_start: 0.8385 (m-80) cc_final: 0.8148 (m-80) REVERT: F 88 ASP cc_start: 0.8213 (t70) cc_final: 0.7795 (t0) REVERT: F 121 ASN cc_start: 0.7584 (t0) cc_final: 0.7139 (t0) REVERT: F 131 LYS cc_start: 0.7611 (pptt) cc_final: 0.7408 (pptt) REVERT: F 216 ASP cc_start: 0.7405 (p0) cc_final: 0.7117 (p0) REVERT: F 222 LEU cc_start: 0.8230 (mt) cc_final: 0.7927 (pp) REVERT: G 48 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8340 (ptmt) REVERT: G 110 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7357 (tm-30) REVERT: G 117 GLU cc_start: 0.8009 (tp30) cc_final: 0.7420 (tp30) REVERT: G 141 ASN cc_start: 0.8356 (m-40) cc_final: 0.8057 (m110) REVERT: G 264 MET cc_start: 0.6504 (mmm) cc_final: 0.6168 (mmm) REVERT: G 279 GLU cc_start: 0.7706 (tp30) cc_final: 0.7249 (tp30) REVERT: G 283 VAL cc_start: 0.8578 (t) cc_final: 0.8348 (m) REVERT: G 465 ILE cc_start: 0.8072 (pt) cc_final: 0.7594 (mt) REVERT: G 471 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6745 (tp30) REVERT: G 474 LYS cc_start: 0.8513 (mtmm) cc_final: 0.7973 (mppt) REVERT: G 480 GLU cc_start: 0.7278 (tm-30) cc_final: 0.7029 (tm-30) REVERT: G 559 ASP cc_start: 0.8067 (m-30) cc_final: 0.7819 (m-30) REVERT: H 14 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7646 (mp) REVERT: H 36 LYS cc_start: 0.8238 (tttt) cc_final: 0.7847 (ttmm) REVERT: H 55 LYS cc_start: 0.7675 (mmmm) cc_final: 0.7329 (mmmm) REVERT: H 68 ASN cc_start: 0.8370 (m-40) cc_final: 0.8167 (m-40) REVERT: H 79 SER cc_start: 0.8421 (t) cc_final: 0.8203 (m) REVERT: H 121 ASN cc_start: 0.7992 (t0) cc_final: 0.7184 (t0) REVERT: H 143 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8529 (mttt) outliers start: 33 outliers final: 21 residues processed: 493 average time/residue: 1.4488 time to fit residues: 809.4127 Evaluate side-chains 484 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 458 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 56 ASN A 295 HIS A 455 ASN C 56 ASN C 101 ASN C 147 ASN C 155 ASN C 347 HIS C 492 GLN C 538 GLN C 551 ASN E 79 ASN E 538 GLN F 213 ASN G 79 ASN G 330 ASN G 538 GLN H 12 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115690 restraints weight = 33428.341| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.18 r_work: 0.3243 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 23845 Z= 0.307 Angle : 0.670 8.672 32025 Z= 0.358 Chirality : 0.048 0.158 3517 Planarity : 0.004 0.057 4075 Dihedral : 4.560 24.457 3105 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.31 % Allowed : 20.60 % Favored : 78.09 % 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: 0.06 (0.15), residues: 2837 helix: 0.67 (0.15), residues: 1119 sheet: 0.82 (0.22), residues: 564 loop : -0.94 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 126 HIS 0.007 0.002 HIS H 41 PHE 0.028 0.003 PHE A 315 TYR 0.025 0.002 TYR E 272 ARG 0.009 0.001 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.05823 ( 1039) hydrogen bonds : angle 4.94100 ( 2940) covalent geometry : bond 0.00765 (23845) covalent geometry : angle 0.67013 (32025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 509 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ASN cc_start: 0.8363 (t0) cc_final: 0.7951 (t0) REVERT: A 289 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 345 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 432 ASP cc_start: 0.7840 (p0) cc_final: 0.7448 (p0) REVERT: A 466 THR cc_start: 0.8557 (m) cc_final: 0.8352 (m) REVERT: A 480 GLU cc_start: 0.7403 (pp20) cc_final: 0.7155 (pp20) REVERT: A 488 GLU cc_start: 0.8396 (tp30) cc_final: 0.7997 (tp30) REVERT: A 545 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8008 (tpt) REVERT: A 559 ASP cc_start: 0.7748 (m-30) cc_final: 0.7531 (m-30) REVERT: A 562 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 153 PHE cc_start: 0.6782 (t80) cc_final: 0.6367 (t80) REVERT: B 155 LYS cc_start: 0.6376 (tptt) cc_final: 0.5974 (tttt) REVERT: B 176 MET cc_start: 0.6117 (mmp) cc_final: 0.5901 (mmp) REVERT: C 49 GLU cc_start: 0.7920 (mp0) cc_final: 0.7649 (mp0) REVERT: C 117 GLU cc_start: 0.8067 (tp30) cc_final: 0.7472 (tp30) REVERT: C 132 ASN cc_start: 0.7930 (t0) cc_final: 0.7579 (t0) REVERT: C 279 GLU cc_start: 0.8137 (tt0) cc_final: 0.7442 (tp30) REVERT: C 383 GLU cc_start: 0.8032 (mp0) cc_final: 0.7600 (mp0) REVERT: C 393 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7730 (mm-30) REVERT: C 395 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6902 (tm-30) REVERT: C 459 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.8002 (mtm-85) REVERT: C 492 GLN cc_start: 0.8268 (tt0) cc_final: 0.7969 (tt0) REVERT: C 493 TYR cc_start: 0.8173 (m-80) cc_final: 0.7539 (m-80) REVERT: D 58 GLU cc_start: 0.7731 (tt0) cc_final: 0.7464 (tt0) REVERT: D 78 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 203 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7037 (tm-30) REVERT: E 16 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8161 (ttpp) REVERT: E 32 ASP cc_start: 0.7739 (t0) cc_final: 0.7446 (t0) REVERT: E 45 LEU cc_start: 0.8700 (tp) cc_final: 0.8488 (tt) REVERT: E 65 THR cc_start: 0.8627 (p) cc_final: 0.8353 (p) REVERT: E 70 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8018 (mt-10) REVERT: E 117 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7024 (mm-30) REVERT: E 132 ASN cc_start: 0.7900 (t0) cc_final: 0.7617 (t0) REVERT: E 392 ASP cc_start: 0.8059 (t70) cc_final: 0.7809 (t0) REVERT: E 395 GLU cc_start: 0.7796 (tp30) cc_final: 0.7384 (tm-30) REVERT: E 407 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7330 (mm-30) REVERT: E 421 ASN cc_start: 0.8650 (t0) cc_final: 0.8325 (t0) REVERT: E 445 TYR cc_start: 0.8552 (m-80) cc_final: 0.8111 (m-80) REVERT: E 477 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7766 (mtpt) REVERT: E 484 GLU cc_start: 0.7980 (tp30) cc_final: 0.7174 (tp30) REVERT: E 488 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 526 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8268 (ttp80) REVERT: E 551 ASN cc_start: 0.8677 (m-40) cc_final: 0.8461 (m-40) REVERT: F 1 MET cc_start: 0.6693 (pmm) cc_final: 0.6416 (ptm) REVERT: F 49 PHE cc_start: 0.8486 (m-80) cc_final: 0.8176 (m-80) REVERT: F 88 ASP cc_start: 0.8250 (t70) cc_final: 0.7803 (t0) REVERT: F 121 ASN cc_start: 0.7523 (t0) cc_final: 0.7263 (t0) REVERT: F 216 ASP cc_start: 0.7360 (p0) cc_final: 0.7125 (p0) REVERT: G 110 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7302 (tm-30) REVERT: G 117 GLU cc_start: 0.8018 (tp30) cc_final: 0.7371 (tp30) REVERT: G 131 ASP cc_start: 0.8309 (m-30) cc_final: 0.8072 (m-30) REVERT: G 264 MET cc_start: 0.6532 (mmm) cc_final: 0.6189 (mmm) REVERT: G 279 GLU cc_start: 0.7802 (tp30) cc_final: 0.7302 (tp30) REVERT: G 343 VAL cc_start: 0.8892 (t) cc_final: 0.8625 (m) REVERT: G 471 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7063 (tp30) REVERT: G 480 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7436 (tm-30) REVERT: G 559 ASP cc_start: 0.8086 (m-30) cc_final: 0.7856 (m-30) REVERT: H 14 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7798 (mt) REVERT: H 36 LYS cc_start: 0.8172 (tttt) cc_final: 0.7775 (ttmm) REVERT: H 55 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7355 (mmmm) REVERT: H 58 GLU cc_start: 0.7196 (tp30) cc_final: 0.6974 (tp30) REVERT: H 68 ASN cc_start: 0.8573 (m-40) cc_final: 0.8314 (m110) REVERT: H 78 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7374 (mm-30) REVERT: H 79 SER cc_start: 0.8535 (t) cc_final: 0.8105 (m) REVERT: H 121 ASN cc_start: 0.7922 (t0) cc_final: 0.7542 (t0) outliers start: 34 outliers final: 23 residues processed: 526 average time/residue: 1.5136 time to fit residues: 904.2400 Evaluate side-chains 530 residues out of total 2596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 503 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 553 SER Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 115 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 283 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 243 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 274 optimal weight: 0.4980 chunk 261 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN A 455 ASN C 56 ASN C 101 ASN C 147 ASN C 538 GLN E 79 ASN E 538 GLN F 213 ASN G 538 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118381 restraints weight = 33437.149| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.19 r_work: 0.3288 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23845 Z= 0.130 Angle : 0.556 12.140 32025 Z= 0.298 Chirality : 0.042 0.146 3517 Planarity : 0.003 0.043 4075 Dihedral : 4.257 25.872 3105 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.12 % Allowed : 21.14 % Favored : 77.74 % 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: 0.28 (0.16), residues: 2837 helix: 0.78 (0.15), residues: 1160 sheet: 0.88 (0.22), residues: 565 loop : -0.74 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 126 HIS 0.003 0.001 HIS A 61 PHE 0.022 0.001 PHE H 153 TYR 0.025 0.001 TYR C 272 ARG 0.008 0.000 ARG G 481 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1039) hydrogen bonds : angle 4.70564 ( 2940) covalent geometry : bond 0.00311 (23845) covalent geometry : angle 0.55638 (32025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23708.98 seconds wall clock time: 410 minutes 32.53 seconds (24632.53 seconds total)