Starting phenix.real_space_refine on Thu May 22 08:07:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjy_41314/05_2025/8tjy_41314_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjy_41314/05_2025/8tjy_41314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjy_41314/05_2025/8tjy_41314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjy_41314/05_2025/8tjy_41314.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjy_41314/05_2025/8tjy_41314_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjy_41314/05_2025/8tjy_41314_neut.cif" } resolution = 2.79 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= 0.022 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 64 5.16 5 C 14584 2.51 5 N 3748 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22692 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: 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: "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: 13.40, per 1000 atoms: 0.59 Number of scatterers: 22692 At special positions: 0 Unit cell: (164.64, 191.52, 110.88, 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 64 16.00 O 4296 8.00 N 3748 7.00 C 14584 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: 4.14 Conformation dependent library (CDL) restraints added in 2.6 seconds 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 20 sheets defined 49.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 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: 4.000A 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: 3.642A 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: 3.559A 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: 4.012A 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: 3.534A 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: 3.576A 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: 6.715A 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: 4.196A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.022A 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: 3.751A 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: 5.504A 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: 3.708A 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: 4.393A 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: 3.670A 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: 3.541A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.632A pdb=" N SER C 357 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.560A 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: 3.649A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 528 removed outlier: 3.578A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.716A 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: 3.624A 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: 5.504A pdb=" N ASP D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.504A 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: 4.392A 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: 3.672A 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: 3.643A pdb=" N LEU E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 326 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 removed outlier: 4.625A pdb=" N SER E 357 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.558A pdb=" N LYS E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.016A 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: 3.705A pdb=" N THR E 419 " --> pdb=" O HIS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.864A 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: 3.530A pdb=" N GLY E 502 " --> pdb=" O GLY E 498 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.783A 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: 3.536A 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 '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: 4.627A pdb=" N SER G 357 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.559A pdb=" N LYS G 364 " --> pdb=" O LYS G 360 " (cutoff:3.500A) removed outlier: 4.205A 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: 3.706A pdb=" N THR G 419 " --> pdb=" O HIS G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 456 removed outlier: 3.869A 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: 3.534A 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: 7.657A pdb=" N GLU G 522 " --> pdb=" O SER G 518 " (cutoff:3.500A) removed outlier: 6.714A 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: 4.195A 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: 3.625A 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: 3.678A 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: 4.395A 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: 6.728A pdb=" N LYS A 16 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS A 9 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 7.049A 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: 6.751A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.356A 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: 10.379A 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: 4.043A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.906A 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: 7.668A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.926A 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: 3.510A 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: 8.330A 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: 8.019A 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: 3.903A 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: 7.101A pdb=" N LYS C 9 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.052A 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: 6.708A pdb=" N ASN C 20 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN C 5 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.546A 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: 4.353A 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: 4.270A 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: 10.378A 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: 4.040A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.905A 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: 6.977A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.352A 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: 7.233A 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: 6.483A 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: 3.572A 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: 6.728A 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: 7.051A 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: 6.706A 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: 3.544A 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: 4.354A 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: 4.266A pdb=" N ILE E 8 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.771A 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: 4.042A 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: 4.906A pdb=" N SER E 128 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 7.278A 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: 7.907A 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: 7.668A 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: 3.507A 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: 7.234A 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: 6.335A pdb=" N VAL F 15 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 222 " --> pdb=" O THR F 16 " (cutoff:3.500A) Processing sheet with id=AB7, 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: 6.102A pdb=" N ASN G 5 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 2 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 6.760A 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: 6.636A pdb=" N ILE G 72 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 4.263A 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: 3.514A 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: 5.804A pdb=" N GLU G 129 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 4.041A 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: 4.903A pdb=" N SER G 128 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 149 through 154 removed outlier: 6.977A pdb=" N LYS G 24 " --> pdb=" O ARG G 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE G 334 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 26 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL G 336 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE G 28 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 403 through 407 Processing sheet with id=AC1, first strand: chain 'G' and resid 435 through 437 removed outlier: 3.505A pdb=" N ILE G 465 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 69 through 72 removed outlier: 6.733A 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: 7.235A pdb=" N VAL H 47 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.904A 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: 6.284A 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) 1023 hydrogen bonds defined for protein. 2901 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: 8.45 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7272 1.34 - 1.46: 4315 1.46 - 1.58: 11409 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 23104 Sorted by residual: bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 23099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 29568 0.97 - 1.94: 1204 1.94 - 2.90: 178 2.90 - 3.87: 62 3.87 - 4.84: 16 Bond angle restraints: 31028 Sorted by residual: angle pdb=" N TRP C 126 " pdb=" CA TRP C 126 " pdb=" CB TRP C 126 " ideal model delta sigma weight residual 111.05 115.89 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N TRP E 126 " pdb=" CA TRP E 126 " pdb=" CB TRP E 126 " ideal model delta sigma weight residual 111.05 115.89 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N TRP G 126 " pdb=" CA TRP G 126 " pdb=" CB TRP G 126 " ideal model delta sigma weight residual 111.05 115.89 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N TRP A 126 " pdb=" CA TRP A 126 " pdb=" CB TRP A 126 " ideal model delta sigma weight residual 111.05 115.81 -4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C TRP G 126 " pdb=" CA TRP G 126 " pdb=" CB TRP G 126 " ideal model delta sigma weight residual 110.24 105.69 4.55 1.88e+00 2.83e-01 5.85e+00 ... (remaining 31023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 12315 16.23 - 32.47: 1322 32.47 - 48.70: 325 48.70 - 64.93: 26 64.93 - 81.16: 16 Dihedral angle restraints: 14004 sinusoidal: 5844 harmonic: 8160 Sorted by residual: dihedral pdb=" CA LYS A 125 " pdb=" C LYS A 125 " pdb=" N TRP A 126 " pdb=" CA TRP A 126 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+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 dihedral pdb=" CA LYS C 125 " pdb=" C LYS C 125 " pdb=" N TRP C 126 " pdb=" CA TRP C 126 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2148 0.029 - 0.058: 830 0.058 - 0.087: 183 0.087 - 0.116: 155 0.116 - 0.145: 80 Chirality restraints: 3396 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL G 93 " pdb=" N VAL G 93 " pdb=" C VAL G 93 " pdb=" CB VAL G 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL E 93 " pdb=" N VAL E 93 " pdb=" C VAL E 93 " pdb=" CB VAL E 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 3393 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 126 " -0.036 2.00e-02 2.50e+03 3.23e-02 2.60e+01 pdb=" CG TRP A 126 " 0.086 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 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 126 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 126 " 0.036 2.00e-02 2.50e+03 3.21e-02 2.58e+01 pdb=" CG TRP C 126 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP C 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 126 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 126 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 126 " 0.001 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 G 126 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.57e+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 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 126 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 126 " 0.003 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 3949 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 174 2.60 - 3.18: 18334 3.18 - 3.75: 31678 3.75 - 4.33: 49626 4.33 - 4.90: 82827 Nonbonded interactions: 182639 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 G 393 " pdb=" OG1 THR G 554 " model vdw 2.039 3.040 nonbonded pdb=" OE2 GLU C 393 " pdb=" OG1 THR C 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 182634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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: 2.940 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: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.030 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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:16.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 0.033 23104 Z= 0.117 Angle : 0.469 4.841 31028 Z= 0.257 Chirality : 0.041 0.145 3396 Planarity : 0.003 0.051 3952 Dihedral : 13.842 81.163 8764 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2756 helix: 0.46 (0.15), residues: 1088 sheet: 0.52 (0.22), residues: 540 loop : -0.80 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.010 TRP A 126 HIS 0.003 0.001 HIS A 427 PHE 0.012 0.001 PHE A 315 TYR 0.013 0.001 TYR G 272 ARG 0.006 0.000 ARG C 332 Details of bonding type rmsd hydrogen bonds : bond 0.20018 ( 1023) hydrogen bonds : angle 6.71070 ( 2901) covalent geometry : bond 0.00268 (23104) covalent geometry : angle 0.46863 (31028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASN cc_start: 0.7878 (m-40) cc_final: 0.7678 (m110) REVERT: A 484 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 538 GLN cc_start: 0.8286 (mt0) cc_final: 0.7983 (mt0) REVERT: B 29 SER cc_start: 0.7250 (m) cc_final: 0.6913 (m) REVERT: B 55 LYS cc_start: 0.7438 (tppp) cc_final: 0.7236 (mmmm) REVERT: B 180 ASP cc_start: 0.7298 (m-30) cc_final: 0.7005 (m-30) REVERT: C 1 MET cc_start: 0.7255 (tpt) cc_final: 0.6977 (tpt) REVERT: C 481 ARG cc_start: 0.7225 (tpp-160) cc_final: 0.6880 (mtt-85) REVERT: C 483 ASN cc_start: 0.7962 (m-40) cc_final: 0.7529 (m-40) REVERT: C 489 ILE cc_start: 0.8220 (mm) cc_final: 0.7986 (mp) REVERT: C 510 ILE cc_start: 0.8104 (mt) cc_final: 0.7690 (mt) REVERT: C 538 GLN cc_start: 0.8499 (mt0) cc_final: 0.8150 (mt0) REVERT: D 107 PHE cc_start: 0.6320 (t80) cc_final: 0.5748 (t80) REVERT: D 176 MET cc_start: 0.8291 (mmp) cc_final: 0.7706 (mmt) REVERT: D 180 ASP cc_start: 0.7348 (m-30) cc_final: 0.7032 (m-30) REVERT: D 208 ASN cc_start: 0.7921 (m-40) cc_final: 0.7712 (m-40) REVERT: E 56 ASN cc_start: 0.7882 (m-40) cc_final: 0.7672 (m110) REVERT: E 92 VAL cc_start: 0.8735 (t) cc_final: 0.8534 (m) REVERT: E 466 THR cc_start: 0.8335 (m) cc_final: 0.8106 (p) REVERT: E 484 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6829 (mm-30) REVERT: E 489 ILE cc_start: 0.7803 (mm) cc_final: 0.7554 (mp) REVERT: E 538 GLN cc_start: 0.8412 (mt0) cc_final: 0.8126 (mt0) REVERT: F 29 SER cc_start: 0.7769 (m) cc_final: 0.7481 (m) REVERT: F 34 ASP cc_start: 0.7739 (m-30) cc_final: 0.7488 (m-30) REVERT: F 212 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6815 (mp0) REVERT: G 56 ASN cc_start: 0.8047 (m-40) cc_final: 0.7826 (m110) REVERT: G 466 THR cc_start: 0.8258 (m) cc_final: 0.8020 (p) REVERT: G 481 ARG cc_start: 0.7069 (tpp-160) cc_final: 0.6823 (mtt-85) REVERT: G 538 GLN cc_start: 0.8385 (mt0) cc_final: 0.8015 (mt0) REVERT: H 29 SER cc_start: 0.7527 (m) cc_final: 0.7210 (m) REVERT: H 34 ASP cc_start: 0.7624 (m-30) cc_final: 0.7409 (m-30) REVERT: H 176 MET cc_start: 0.8183 (mmp) cc_final: 0.7862 (mmp) REVERT: H 180 ASP cc_start: 0.7284 (m-30) cc_final: 0.7038 (m-30) outliers start: 0 outliers final: 3 residues processed: 551 average time/residue: 1.4771 time to fit residues: 913.7944 Evaluate side-chains 455 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 452 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain D residue 93 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 131 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 147 ASN A 155 ASN B 38 ASN B 173 ASN B 213 ASN C 147 ASN D 38 ASN D 181 GLN D 213 ASN E 147 ASN E 155 ASN G 147 ASN G 155 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.110634 restraints weight = 32055.766| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.03 r_work: 0.3256 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23104 Z= 0.150 Angle : 0.545 6.919 31028 Z= 0.299 Chirality : 0.043 0.156 3396 Planarity : 0.003 0.032 3952 Dihedral : 4.525 31.311 3018 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.99 % Allowed : 10.61 % Favored : 87.40 % 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: -0.15 (0.15), residues: 2756 helix: 0.38 (0.15), residues: 1132 sheet: 0.84 (0.23), residues: 540 loop : -1.04 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP E 126 HIS 0.004 0.001 HIS H 41 PHE 0.017 0.002 PHE B 157 TYR 0.026 0.001 TYR A 272 ARG 0.005 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 1023) hydrogen bonds : angle 5.09418 ( 2901) covalent geometry : bond 0.00358 (23104) covalent geometry : angle 0.54523 (31028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 470 time to evaluate : 2.547 Fit side-chains REVERT: A 50 ILE cc_start: 0.8505 (mm) cc_final: 0.8293 (mp) REVERT: A 56 ASN cc_start: 0.8280 (m-40) cc_final: 0.8012 (m110) REVERT: A 117 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 130 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 304 LYS cc_start: 0.8594 (tttt) cc_final: 0.8386 (tttt) REVERT: A 395 GLU cc_start: 0.7698 (tp30) cc_final: 0.7336 (tm-30) REVERT: A 484 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 491 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8108 (ttmt) REVERT: A 538 GLN cc_start: 0.8572 (mt0) cc_final: 0.8309 (mt0) REVERT: B 29 SER cc_start: 0.8047 (m) cc_final: 0.7752 (m) REVERT: C 1 MET cc_start: 0.7152 (tpt) cc_final: 0.6820 (tpt) REVERT: C 50 ILE cc_start: 0.8564 (mm) cc_final: 0.8345 (mp) REVERT: C 56 ASN cc_start: 0.8381 (m-40) cc_final: 0.8116 (m110) REVERT: C 103 ASP cc_start: 0.8127 (p0) cc_final: 0.7877 (p0) REVERT: C 129 GLU cc_start: 0.7812 (mp0) cc_final: 0.7580 (mp0) REVERT: C 130 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8430 (tp) REVERT: C 393 GLU cc_start: 0.7921 (tp30) cc_final: 0.7523 (mp0) REVERT: C 481 ARG cc_start: 0.8149 (tpp-160) cc_final: 0.7949 (mtt-85) REVERT: C 538 GLN cc_start: 0.8729 (mt0) cc_final: 0.8425 (mt0) REVERT: C 559 ASP cc_start: 0.8065 (m-30) cc_final: 0.7846 (m-30) REVERT: D 29 SER cc_start: 0.7891 (m) cc_final: 0.7500 (p) REVERT: D 107 PHE cc_start: 0.7118 (t80) cc_final: 0.6728 (t80) REVERT: D 185 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8297 (mmtt) REVERT: D 191 ASP cc_start: 0.7187 (t0) cc_final: 0.6599 (p0) REVERT: E 2 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8715 (mtpp) REVERT: E 50 ILE cc_start: 0.8577 (mm) cc_final: 0.8374 (mp) REVERT: E 56 ASN cc_start: 0.8288 (m-40) cc_final: 0.8039 (m110) REVERT: E 92 VAL cc_start: 0.8666 (t) cc_final: 0.8440 (m) REVERT: E 456 LEU cc_start: 0.8655 (mt) cc_final: 0.8410 (mp) REVERT: E 484 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7624 (mm-30) REVERT: E 492 GLN cc_start: 0.8070 (tt0) cc_final: 0.7849 (tt0) REVERT: E 531 GLU cc_start: 0.4418 (mp0) cc_final: 0.4120 (mp0) REVERT: E 538 GLN cc_start: 0.8528 (mt0) cc_final: 0.8301 (mt0) REVERT: F 29 SER cc_start: 0.8327 (m) cc_final: 0.8051 (m) REVERT: F 34 ASP cc_start: 0.7944 (m-30) cc_final: 0.7705 (m-30) REVERT: F 88 ASP cc_start: 0.8163 (t70) cc_final: 0.7868 (t0) REVERT: F 180 ASP cc_start: 0.8056 (m-30) cc_final: 0.7825 (m-30) REVERT: G 56 ASN cc_start: 0.8381 (m-40) cc_final: 0.8111 (m110) REVERT: G 117 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7814 (mm-30) REVERT: G 129 GLU cc_start: 0.7786 (mp0) cc_final: 0.7503 (mp0) REVERT: G 130 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (tp) REVERT: G 399 GLU cc_start: 0.8114 (tt0) cc_final: 0.7895 (tt0) REVERT: G 434 ASP cc_start: 0.7609 (m-30) cc_final: 0.7365 (m-30) REVERT: G 480 GLU cc_start: 0.7511 (pt0) cc_final: 0.7269 (pt0) REVERT: G 526 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7583 (ttm110) REVERT: G 538 GLN cc_start: 0.8631 (mt0) cc_final: 0.8377 (mt0) REVERT: H 29 SER cc_start: 0.8208 (m) cc_final: 0.7930 (m) REVERT: H 34 ASP cc_start: 0.7902 (m-30) cc_final: 0.7675 (m-30) REVERT: H 191 ASP cc_start: 0.7130 (t0) cc_final: 0.6892 (t0) REVERT: H 208 ASN cc_start: 0.8154 (m-40) cc_final: 0.7850 (m110) outliers start: 50 outliers final: 21 residues processed: 488 average time/residue: 1.4661 time to fit residues: 805.7978 Evaluate side-chains 479 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 453 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain G residue 40 TYR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 489 ILE Chi-restraints excluded: chain G residue 501 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 163 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 214 optimal weight: 0.0970 chunk 267 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 147 ASN A 155 ASN B 121 ASN B 213 ASN C 147 ASN C 350 ASN D 208 ASN D 213 ASN E 79 ASN E 147 ASN E 155 ASN F 121 ASN F 181 GLN G 79 ASN G 147 ASN G 155 ASN H 121 ASN H 173 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108823 restraints weight = 31979.067| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.01 r_work: 0.3233 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 23104 Z= 0.208 Angle : 0.581 6.848 31028 Z= 0.317 Chirality : 0.045 0.150 3396 Planarity : 0.004 0.047 3952 Dihedral : 4.555 17.647 3012 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.51 % Allowed : 13.40 % Favored : 84.09 % 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: -0.35 (0.15), residues: 2756 helix: -0.00 (0.14), residues: 1168 sheet: 1.16 (0.23), residues: 528 loop : -1.13 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 126 HIS 0.006 0.001 HIS H 41 PHE 0.021 0.002 PHE H 157 TYR 0.026 0.002 TYR A 272 ARG 0.007 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.05506 ( 1023) hydrogen bonds : angle 5.14619 ( 2901) covalent geometry : bond 0.00517 (23104) covalent geometry : angle 0.58116 (31028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 483 time to evaluate : 2.649 Fit side-chains REVERT: A 50 ILE cc_start: 0.8576 (mm) cc_final: 0.8361 (mp) REVERT: A 56 ASN cc_start: 0.8309 (m-40) cc_final: 0.8042 (m110) REVERT: A 117 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 130 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 143 ASN cc_start: 0.7820 (t0) cc_final: 0.7477 (t0) REVERT: A 393 GLU cc_start: 0.7986 (tp30) cc_final: 0.7631 (mp0) REVERT: A 456 LEU cc_start: 0.8776 (mt) cc_final: 0.8545 (mp) REVERT: A 462 LEU cc_start: 0.8488 (tp) cc_final: 0.8171 (tt) REVERT: A 480 GLU cc_start: 0.7437 (pt0) cc_final: 0.7143 (pt0) REVERT: A 484 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 491 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8174 (ttmt) REVERT: A 499 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 538 GLN cc_start: 0.8485 (mt0) cc_final: 0.8205 (mt0) REVERT: A 541 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7893 (mmpt) REVERT: B 29 SER cc_start: 0.8148 (m) cc_final: 0.7848 (m) REVERT: B 191 ASP cc_start: 0.6902 (t0) cc_final: 0.5856 (p0) REVERT: C 56 ASN cc_start: 0.8388 (m-40) cc_final: 0.8126 (m110) REVERT: C 103 ASP cc_start: 0.8059 (p0) cc_final: 0.7834 (p0) REVERT: C 117 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7694 (mm-30) REVERT: C 130 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8421 (tp) REVERT: C 264 MET cc_start: 0.6351 (mmm) cc_final: 0.5808 (mmm) REVERT: C 393 GLU cc_start: 0.8067 (tp30) cc_final: 0.7644 (mp0) REVERT: C 414 ASN cc_start: 0.8721 (m-40) cc_final: 0.8514 (m-40) REVERT: C 438 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8388 (tttm) REVERT: C 456 LEU cc_start: 0.8858 (mt) cc_final: 0.8634 (mp) REVERT: C 480 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7538 (mp0) REVERT: C 538 GLN cc_start: 0.8742 (mt0) cc_final: 0.8427 (mt0) REVERT: C 559 ASP cc_start: 0.8082 (m-30) cc_final: 0.7862 (m-30) REVERT: D 29 SER cc_start: 0.7928 (m) cc_final: 0.7610 (p) REVERT: D 180 ASP cc_start: 0.7850 (m-30) cc_final: 0.7530 (m-30) REVERT: D 191 ASP cc_start: 0.7059 (t0) cc_final: 0.6854 (t0) REVERT: E 56 ASN cc_start: 0.8271 (m-40) cc_final: 0.8018 (m110) REVERT: E 395 GLU cc_start: 0.7897 (tp30) cc_final: 0.7682 (tt0) REVERT: E 456 LEU cc_start: 0.8610 (mt) cc_final: 0.8321 (mp) REVERT: E 484 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7668 (mm-30) REVERT: E 492 GLN cc_start: 0.8179 (tt0) cc_final: 0.7922 (tt0) REVERT: E 495 ASN cc_start: 0.8782 (m-40) cc_final: 0.8539 (m-40) REVERT: E 531 GLU cc_start: 0.4171 (mp0) cc_final: 0.3821 (mp0) REVERT: E 538 GLN cc_start: 0.8555 (mt0) cc_final: 0.8347 (mt0) REVERT: F 29 SER cc_start: 0.8336 (m) cc_final: 0.8063 (m) REVERT: F 88 ASP cc_start: 0.8156 (t70) cc_final: 0.7879 (t0) REVERT: F 121 ASN cc_start: 0.7312 (t0) cc_final: 0.7027 (t0) REVERT: F 180 ASP cc_start: 0.8083 (m-30) cc_final: 0.7854 (m-30) REVERT: F 208 ASN cc_start: 0.8115 (m-40) cc_final: 0.7785 (m110) REVERT: G 56 ASN cc_start: 0.8382 (m-40) cc_final: 0.8118 (m110) REVERT: G 117 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7789 (mm-30) REVERT: G 129 GLU cc_start: 0.7764 (mp0) cc_final: 0.7474 (mp0) REVERT: G 130 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8013 (tp) REVERT: G 377 LEU cc_start: 0.8531 (mt) cc_final: 0.8317 (mp) REVERT: G 399 GLU cc_start: 0.8122 (tt0) cc_final: 0.7915 (tt0) REVERT: G 434 ASP cc_start: 0.7607 (m-30) cc_final: 0.7392 (m-30) REVERT: G 456 LEU cc_start: 0.8618 (mt) cc_final: 0.8331 (mp) REVERT: G 474 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8364 (mtmm) REVERT: G 538 GLN cc_start: 0.8617 (mt0) cc_final: 0.8382 (mt0) REVERT: G 541 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7864 (mmpt) REVERT: H 29 SER cc_start: 0.8210 (m) cc_final: 0.7930 (m) REVERT: H 96 ASP cc_start: 0.7012 (p0) cc_final: 0.6698 (p0) REVERT: H 180 ASP cc_start: 0.7928 (m-30) cc_final: 0.7716 (m-30) outliers start: 63 outliers final: 19 residues processed: 505 average time/residue: 1.4511 time to fit residues: 826.4619 Evaluate side-chains 478 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 454 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 179 optimal weight: 0.5980 chunk 186 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 258 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN C 79 ASN C 147 ASN D 121 ASN D 213 ASN E 132 ASN E 147 ASN E 155 ASN E 350 ASN G 147 ASN G 155 ASN H 208 ASN H 213 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110394 restraints weight = 32221.651| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.02 r_work: 0.3257 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23104 Z= 0.131 Angle : 0.502 6.345 31028 Z= 0.277 Chirality : 0.042 0.147 3396 Planarity : 0.003 0.037 3952 Dihedral : 4.326 18.274 3012 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.91 % Allowed : 14.51 % Favored : 82.58 % 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: 2756 helix: 0.27 (0.15), residues: 1168 sheet: 1.22 (0.23), residues: 528 loop : -1.05 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 126 HIS 0.004 0.001 HIS H 41 PHE 0.014 0.001 PHE B 157 TYR 0.025 0.001 TYR A 272 ARG 0.006 0.000 ARG G 526 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1023) hydrogen bonds : angle 4.95956 ( 2901) covalent geometry : bond 0.00313 (23104) covalent geometry : angle 0.50229 (31028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 447 time to evaluate : 2.482 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8508 (mm) cc_final: 0.8286 (mp) REVERT: A 56 ASN cc_start: 0.8284 (m-40) cc_final: 0.8025 (m110) REVERT: A 81 GLU cc_start: 0.6903 (mp0) cc_final: 0.6692 (mp0) REVERT: A 117 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 130 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 143 ASN cc_start: 0.7602 (t0) cc_final: 0.7334 (t0) REVERT: A 304 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (tttt) REVERT: A 348 MET cc_start: 0.8815 (tpt) cc_final: 0.8598 (tpt) REVERT: A 393 GLU cc_start: 0.7996 (tp30) cc_final: 0.7654 (mp0) REVERT: A 456 LEU cc_start: 0.8743 (mt) cc_final: 0.8514 (mp) REVERT: A 462 LEU cc_start: 0.8430 (tp) cc_final: 0.8096 (tt) REVERT: A 538 GLN cc_start: 0.8438 (mt0) cc_final: 0.8233 (mt0) REVERT: A 555 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7763 (tmtm) REVERT: B 29 SER cc_start: 0.8172 (m) cc_final: 0.7870 (m) REVERT: B 191 ASP cc_start: 0.6857 (t0) cc_final: 0.6583 (t70) REVERT: C 56 ASN cc_start: 0.8365 (m-40) cc_final: 0.8121 (m110) REVERT: C 103 ASP cc_start: 0.8011 (p0) cc_final: 0.7808 (p0) REVERT: C 117 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 130 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 264 MET cc_start: 0.6387 (mmm) cc_final: 0.5828 (mmm) REVERT: C 456 LEU cc_start: 0.8827 (mt) cc_final: 0.8608 (mp) REVERT: C 459 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7695 (mtt180) REVERT: C 538 GLN cc_start: 0.8696 (mt0) cc_final: 0.8403 (mt0) REVERT: C 559 ASP cc_start: 0.8041 (m-30) cc_final: 0.7769 (m-30) REVERT: D 29 SER cc_start: 0.7917 (m) cc_final: 0.7592 (p) REVERT: D 180 ASP cc_start: 0.7826 (m-30) cc_final: 0.7582 (m-30) REVERT: E 56 ASN cc_start: 0.8196 (m-40) cc_final: 0.7947 (m110) REVERT: E 456 LEU cc_start: 0.8574 (mt) cc_final: 0.8310 (mp) REVERT: F 29 SER cc_start: 0.8355 (m) cc_final: 0.8078 (m) REVERT: F 121 ASN cc_start: 0.7347 (t0) cc_final: 0.7081 (t0) REVERT: F 162 ASP cc_start: 0.7380 (p0) cc_final: 0.7167 (p0) REVERT: F 191 ASP cc_start: 0.7232 (t0) cc_final: 0.6675 (p0) REVERT: F 208 ASN cc_start: 0.8002 (m-40) cc_final: 0.7661 (m110) REVERT: G 56 ASN cc_start: 0.8334 (m-40) cc_final: 0.8087 (m110) REVERT: G 117 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7750 (mm-30) REVERT: G 130 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7992 (tp) REVERT: G 348 MET cc_start: 0.8767 (tpt) cc_final: 0.8443 (tpt) REVERT: G 393 GLU cc_start: 0.8147 (tp30) cc_final: 0.7896 (mm-30) REVERT: G 432 ASP cc_start: 0.8332 (p0) cc_final: 0.8122 (p0) REVERT: G 434 ASP cc_start: 0.7602 (m-30) cc_final: 0.7195 (m-30) REVERT: G 456 LEU cc_start: 0.8600 (mt) cc_final: 0.8324 (mp) REVERT: G 474 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8216 (mtmm) REVERT: G 480 GLU cc_start: 0.7490 (mp0) cc_final: 0.7207 (mp0) REVERT: G 538 GLN cc_start: 0.8597 (mt0) cc_final: 0.8370 (mt0) REVERT: G 541 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7843 (mmpt) REVERT: H 29 SER cc_start: 0.8232 (m) cc_final: 0.7948 (m) outliers start: 73 outliers final: 25 residues processed: 481 average time/residue: 1.4655 time to fit residues: 795.7491 Evaluate side-chains 481 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 448 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 252 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 251 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN C 147 ASN D 213 ASN E 147 ASN E 155 ASN F 181 GLN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109778 restraints weight = 32281.286| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.01 r_work: 0.3248 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23104 Z= 0.156 Angle : 0.529 8.968 31028 Z= 0.287 Chirality : 0.043 0.150 3396 Planarity : 0.003 0.040 3952 Dihedral : 4.380 18.457 3012 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.95 % Allowed : 15.39 % Favored : 81.66 % 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: -0.11 (0.15), residues: 2756 helix: 0.26 (0.14), residues: 1164 sheet: 1.23 (0.23), residues: 528 loop : -1.05 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 126 HIS 0.004 0.001 HIS H 41 PHE 0.017 0.002 PHE B 157 TYR 0.025 0.001 TYR A 272 ARG 0.008 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 1023) hydrogen bonds : angle 4.99037 ( 2901) covalent geometry : bond 0.00383 (23104) covalent geometry : angle 0.52881 (31028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 460 time to evaluate : 2.751 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8570 (mm) cc_final: 0.8341 (mp) REVERT: A 56 ASN cc_start: 0.8292 (m-40) cc_final: 0.8027 (m110) REVERT: A 116 LYS cc_start: 0.8135 (tttp) cc_final: 0.7858 (tptp) REVERT: A 117 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 130 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8223 (tp) REVERT: A 143 ASN cc_start: 0.7628 (t0) cc_final: 0.7362 (t0) REVERT: A 393 GLU cc_start: 0.8009 (tp30) cc_final: 0.7602 (mp0) REVERT: A 456 LEU cc_start: 0.8753 (mt) cc_final: 0.8532 (mp) REVERT: A 459 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7814 (ptt180) REVERT: A 462 LEU cc_start: 0.8445 (tp) cc_final: 0.8088 (tt) REVERT: A 538 GLN cc_start: 0.8432 (mt0) cc_final: 0.8209 (mt0) REVERT: A 541 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7859 (mmpt) REVERT: A 555 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7747 (tmtm) REVERT: B 29 SER cc_start: 0.8172 (m) cc_final: 0.7873 (m) REVERT: B 158 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8399 (ttmm) REVERT: B 180 ASP cc_start: 0.7857 (m-30) cc_final: 0.7612 (m-30) REVERT: C 56 ASN cc_start: 0.8360 (m-40) cc_final: 0.8114 (m110) REVERT: C 103 ASP cc_start: 0.7959 (p0) cc_final: 0.7735 (p0) REVERT: C 117 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 130 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8383 (tp) REVERT: C 264 MET cc_start: 0.6379 (mmm) cc_final: 0.5795 (mmm) REVERT: C 393 GLU cc_start: 0.8075 (tp30) cc_final: 0.7710 (mp0) REVERT: C 456 LEU cc_start: 0.8855 (mt) cc_final: 0.8641 (mp) REVERT: C 459 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7755 (mtt180) REVERT: C 538 GLN cc_start: 0.8678 (mt0) cc_final: 0.8406 (mt0) REVERT: C 559 ASP cc_start: 0.8070 (m-30) cc_final: 0.7798 (m-30) REVERT: D 29 SER cc_start: 0.7934 (m) cc_final: 0.7640 (p) REVERT: D 180 ASP cc_start: 0.7839 (m-30) cc_final: 0.7610 (m-30) REVERT: E 56 ASN cc_start: 0.8180 (m-40) cc_final: 0.7940 (m-40) REVERT: E 130 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8108 (tp) REVERT: E 456 LEU cc_start: 0.8587 (mt) cc_final: 0.8297 (mp) REVERT: E 459 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6942 (mtp85) REVERT: E 541 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8123 (mmpt) REVERT: F 29 SER cc_start: 0.8366 (m) cc_final: 0.8101 (m) REVERT: F 88 ASP cc_start: 0.8160 (t70) cc_final: 0.7860 (t0) REVERT: F 121 ASN cc_start: 0.7285 (t0) cc_final: 0.7025 (t0) REVERT: F 180 ASP cc_start: 0.8024 (m-30) cc_final: 0.7789 (m-30) REVERT: G 56 ASN cc_start: 0.8338 (m-40) cc_final: 0.8084 (m110) REVERT: G 117 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7743 (mm-30) REVERT: G 129 GLU cc_start: 0.7769 (mp0) cc_final: 0.7483 (mp0) REVERT: G 130 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8001 (tp) REVERT: G 264 MET cc_start: 0.6445 (mmm) cc_final: 0.5921 (mmm) REVERT: G 434 ASP cc_start: 0.7607 (m-30) cc_final: 0.7376 (m-30) REVERT: G 456 LEU cc_start: 0.8608 (mt) cc_final: 0.8322 (mp) REVERT: G 474 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8316 (mtmm) REVERT: G 526 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7695 (ttm110) REVERT: G 541 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7842 (mmpt) REVERT: H 29 SER cc_start: 0.8241 (m) cc_final: 0.7958 (m) outliers start: 74 outliers final: 32 residues processed: 489 average time/residue: 1.4355 time to fit residues: 791.5338 Evaluate side-chains 488 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 445 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 12 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN C 147 ASN E 132 ASN E 147 ASN E 155 ASN G 147 ASN G 155 ASN G 350 ASN G 461 ASN H 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110243 restraints weight = 32018.438| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.00 r_work: 0.3252 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23104 Z= 0.142 Angle : 0.513 7.480 31028 Z= 0.280 Chirality : 0.042 0.148 3396 Planarity : 0.003 0.047 3952 Dihedral : 4.343 18.458 3012 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.87 % Allowed : 15.99 % Favored : 81.14 % 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: -0.03 (0.15), residues: 2756 helix: 0.34 (0.14), residues: 1168 sheet: 1.23 (0.23), residues: 528 loop : -1.01 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 126 HIS 0.004 0.001 HIS H 41 PHE 0.016 0.001 PHE A 500 TYR 0.025 0.001 TYR E 272 ARG 0.009 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 1023) hydrogen bonds : angle 4.94249 ( 2901) covalent geometry : bond 0.00344 (23104) covalent geometry : angle 0.51273 (31028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 447 time to evaluate : 2.530 Fit side-chains REVERT: A 50 ILE cc_start: 0.8536 (mm) cc_final: 0.8322 (mp) REVERT: A 56 ASN cc_start: 0.8300 (m-40) cc_final: 0.8035 (m110) REVERT: A 116 LYS cc_start: 0.8265 (tttp) cc_final: 0.8038 (tptp) REVERT: A 117 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 130 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (tp) REVERT: A 143 ASN cc_start: 0.7579 (t0) cc_final: 0.7342 (t0) REVERT: A 324 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8697 (mt) REVERT: A 393 GLU cc_start: 0.7994 (tp30) cc_final: 0.7579 (mp0) REVERT: A 456 LEU cc_start: 0.8750 (mt) cc_final: 0.8533 (mp) REVERT: A 462 LEU cc_start: 0.8402 (tp) cc_final: 0.8048 (tt) REVERT: A 538 GLN cc_start: 0.8436 (mt0) cc_final: 0.8183 (mt0) REVERT: A 541 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7881 (mmpt) REVERT: A 555 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7743 (tmtm) REVERT: B 29 SER cc_start: 0.8192 (m) cc_final: 0.7893 (m) REVERT: C 56 ASN cc_start: 0.8371 (m-40) cc_final: 0.8118 (m110) REVERT: C 103 ASP cc_start: 0.7994 (p0) cc_final: 0.7773 (p0) REVERT: C 117 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7739 (mm-30) REVERT: C 130 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8344 (tp) REVERT: C 264 MET cc_start: 0.6452 (mmm) cc_final: 0.5854 (mmm) REVERT: C 393 GLU cc_start: 0.8053 (tp30) cc_final: 0.7615 (mp0) REVERT: C 456 LEU cc_start: 0.8846 (mt) cc_final: 0.8631 (mp) REVERT: C 480 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7293 (mp0) REVERT: C 538 GLN cc_start: 0.8703 (mt0) cc_final: 0.8401 (mt0) REVERT: C 559 ASP cc_start: 0.8036 (m-30) cc_final: 0.7752 (m-30) REVERT: D 29 SER cc_start: 0.7947 (m) cc_final: 0.7656 (p) REVERT: D 191 ASP cc_start: 0.7102 (t0) cc_final: 0.6841 (p0) REVERT: E 56 ASN cc_start: 0.8171 (m-40) cc_final: 0.7936 (m-40) REVERT: E 130 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (tp) REVERT: E 148 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8039 (m) REVERT: E 456 LEU cc_start: 0.8582 (mt) cc_final: 0.8300 (mp) REVERT: E 541 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8102 (mmpt) REVERT: E 571 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: F 29 SER cc_start: 0.8383 (m) cc_final: 0.8118 (m) REVERT: F 121 ASN cc_start: 0.7293 (t0) cc_final: 0.7022 (t0) REVERT: F 191 ASP cc_start: 0.7204 (t0) cc_final: 0.6735 (p0) REVERT: G 56 ASN cc_start: 0.8334 (m-40) cc_final: 0.8088 (m110) REVERT: G 117 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7725 (mm-30) REVERT: G 129 GLU cc_start: 0.7755 (mp0) cc_final: 0.7473 (mp0) REVERT: G 130 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8013 (tp) REVERT: G 264 MET cc_start: 0.6532 (mmm) cc_final: 0.5992 (mmm) REVERT: G 348 MET cc_start: 0.8746 (tpt) cc_final: 0.8470 (tpt) REVERT: G 434 ASP cc_start: 0.7597 (m-30) cc_final: 0.7309 (m-30) REVERT: G 456 LEU cc_start: 0.8611 (mt) cc_final: 0.8329 (mp) REVERT: G 459 ARG cc_start: 0.8144 (mpt-90) cc_final: 0.7829 (mtt180) REVERT: G 480 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7435 (mp0) REVERT: G 499 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7903 (mt-10) REVERT: G 541 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7851 (mmpt) REVERT: H 29 SER cc_start: 0.8252 (m) cc_final: 0.7971 (m) outliers start: 72 outliers final: 41 residues processed: 485 average time/residue: 1.4577 time to fit residues: 795.9575 Evaluate side-chains 506 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 454 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 264 optimal weight: 6.9990 chunk 117 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 247 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 151 optimal weight: 0.3980 chunk 177 optimal weight: 0.7980 chunk 265 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN A 350 ASN A 461 ASN C 147 ASN C 461 ASN E 5 ASN E 18 ASN E 132 ASN E 147 ASN E 155 ASN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112080 restraints weight = 32156.367| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.01 r_work: 0.3277 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23104 Z= 0.106 Angle : 0.479 6.065 31028 Z= 0.262 Chirality : 0.041 0.147 3396 Planarity : 0.003 0.050 3952 Dihedral : 4.178 18.679 3012 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.51 % Allowed : 16.75 % Favored : 80.74 % 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: 0.24 (0.16), residues: 2756 helix: 0.69 (0.15), residues: 1144 sheet: 1.20 (0.23), residues: 532 loop : -0.91 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 126 HIS 0.003 0.001 HIS H 41 PHE 0.018 0.001 PHE A 500 TYR 0.025 0.001 TYR E 272 ARG 0.010 0.000 ARG G 526 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1023) hydrogen bonds : angle 4.81208 ( 2901) covalent geometry : bond 0.00244 (23104) covalent geometry : angle 0.47859 (31028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 486 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8532 (mm) cc_final: 0.8294 (mp) REVERT: A 56 ASN cc_start: 0.8265 (m-40) cc_final: 0.8009 (m110) REVERT: A 116 LYS cc_start: 0.8231 (tttp) cc_final: 0.7989 (tptp) REVERT: A 117 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 130 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8146 (tp) REVERT: A 143 ASN cc_start: 0.7514 (t0) cc_final: 0.7313 (t0) REVERT: A 393 GLU cc_start: 0.7972 (tp30) cc_final: 0.7552 (mp0) REVERT: A 438 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8493 (mttm) REVERT: A 456 LEU cc_start: 0.8743 (mt) cc_final: 0.8524 (mp) REVERT: A 462 LEU cc_start: 0.8382 (tp) cc_final: 0.8022 (tt) REVERT: A 526 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7588 (ttm110) REVERT: A 538 GLN cc_start: 0.8411 (mt0) cc_final: 0.8162 (mt0) REVERT: A 541 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7850 (mmpt) REVERT: A 555 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7149 (tmtm) REVERT: A 559 ASP cc_start: 0.8159 (m-30) cc_final: 0.7699 (m-30) REVERT: B 29 SER cc_start: 0.8192 (m) cc_final: 0.7899 (m) REVERT: C 56 ASN cc_start: 0.8324 (m-40) cc_final: 0.8084 (m110) REVERT: C 117 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7686 (mm-30) REVERT: C 264 MET cc_start: 0.6416 (mmm) cc_final: 0.5809 (mmm) REVERT: C 324 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8599 (mt) REVERT: C 360 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7955 (mmtt) REVERT: C 393 GLU cc_start: 0.8054 (tp30) cc_final: 0.7599 (mp0) REVERT: C 456 LEU cc_start: 0.8829 (mt) cc_final: 0.8619 (mp) REVERT: C 538 GLN cc_start: 0.8631 (mt0) cc_final: 0.8394 (mt0) REVERT: C 559 ASP cc_start: 0.8072 (m-30) cc_final: 0.7758 (m-30) REVERT: D 29 SER cc_start: 0.7956 (m) cc_final: 0.7656 (p) REVERT: D 191 ASP cc_start: 0.7199 (t0) cc_final: 0.6796 (p0) REVERT: E 56 ASN cc_start: 0.8137 (m-40) cc_final: 0.7914 (m110) REVERT: E 117 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7689 (mm-30) REVERT: E 130 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8086 (tp) REVERT: E 393 GLU cc_start: 0.8064 (tp30) cc_final: 0.7729 (mp0) REVERT: E 397 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7775 (mm-30) REVERT: E 456 LEU cc_start: 0.8577 (mt) cc_final: 0.8316 (mp) REVERT: F 29 SER cc_start: 0.8380 (m) cc_final: 0.8132 (m) REVERT: F 88 ASP cc_start: 0.8141 (t70) cc_final: 0.7835 (t0) REVERT: F 121 ASN cc_start: 0.7328 (t0) cc_final: 0.6679 (t0) REVERT: F 180 ASP cc_start: 0.7974 (m-30) cc_final: 0.7750 (m-30) REVERT: G 56 ASN cc_start: 0.8305 (m-40) cc_final: 0.8078 (m110) REVERT: G 117 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7659 (mm-30) REVERT: G 129 GLU cc_start: 0.7728 (mp0) cc_final: 0.7420 (mp0) REVERT: G 130 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7928 (tp) REVERT: G 264 MET cc_start: 0.6496 (mmm) cc_final: 0.5925 (mmm) REVERT: G 434 ASP cc_start: 0.7550 (m-30) cc_final: 0.7293 (m-30) REVERT: G 456 LEU cc_start: 0.8621 (mt) cc_final: 0.8337 (mp) REVERT: G 459 ARG cc_start: 0.8201 (mpt-90) cc_final: 0.7780 (mtt180) REVERT: G 474 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8173 (mmmm) REVERT: G 526 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7529 (ttm110) REVERT: G 541 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7836 (mmpt) REVERT: G 555 LYS cc_start: 0.8152 (tptp) cc_final: 0.7860 (tptp) REVERT: H 29 SER cc_start: 0.8266 (m) cc_final: 0.7991 (m) outliers start: 63 outliers final: 35 residues processed: 515 average time/residue: 1.4079 time to fit residues: 823.5696 Evaluate side-chains 499 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 455 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 106 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 247 optimal weight: 0.4980 chunk 243 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 272 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 173 ASN C 147 ASN E 5 ASN E 147 ASN E 155 ASN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111153 restraints weight = 32095.211| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.02 r_work: 0.3270 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23104 Z= 0.122 Angle : 0.501 6.963 31028 Z= 0.274 Chirality : 0.042 0.148 3396 Planarity : 0.003 0.042 3952 Dihedral : 4.204 18.532 3012 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.71 % Allowed : 17.30 % Favored : 79.98 % 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: 0.27 (0.16), residues: 2756 helix: 0.73 (0.15), residues: 1140 sheet: 1.17 (0.22), residues: 540 loop : -0.89 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 126 HIS 0.003 0.001 HIS H 41 PHE 0.020 0.001 PHE A 500 TYR 0.025 0.001 TYR E 272 ARG 0.008 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1023) hydrogen bonds : angle 4.80107 ( 2901) covalent geometry : bond 0.00291 (23104) covalent geometry : angle 0.50141 (31028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 459 time to evaluate : 2.696 Fit side-chains REVERT: A 50 ILE cc_start: 0.8538 (mm) cc_final: 0.8302 (mp) REVERT: A 56 ASN cc_start: 0.8279 (m-40) cc_final: 0.8014 (m110) REVERT: A 116 LYS cc_start: 0.8254 (tttp) cc_final: 0.8010 (tptp) REVERT: A 117 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 130 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 143 ASN cc_start: 0.7529 (t0) cc_final: 0.7309 (t0) REVERT: A 324 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8709 (mt) REVERT: A 393 GLU cc_start: 0.7977 (tp30) cc_final: 0.7566 (mp0) REVERT: A 438 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8493 (mttm) REVERT: A 456 LEU cc_start: 0.8748 (mt) cc_final: 0.8524 (mp) REVERT: A 462 LEU cc_start: 0.8398 (tp) cc_final: 0.8048 (tt) REVERT: A 538 GLN cc_start: 0.8407 (mt0) cc_final: 0.8149 (mt0) REVERT: A 541 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7839 (mmpt) REVERT: A 555 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7735 (tmtm) REVERT: A 571 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: B 29 SER cc_start: 0.8202 (m) cc_final: 0.7917 (m) REVERT: B 219 LYS cc_start: 0.8771 (mttp) cc_final: 0.8459 (mmtp) REVERT: C 56 ASN cc_start: 0.8342 (m-40) cc_final: 0.8092 (m110) REVERT: C 117 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 264 MET cc_start: 0.6485 (mmm) cc_final: 0.5852 (mmm) REVERT: C 324 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8625 (mt) REVERT: C 393 GLU cc_start: 0.8060 (tp30) cc_final: 0.7590 (mp0) REVERT: C 456 LEU cc_start: 0.8862 (mt) cc_final: 0.8651 (mp) REVERT: C 459 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7857 (ptt180) REVERT: C 538 GLN cc_start: 0.8657 (mt0) cc_final: 0.8396 (mt0) REVERT: C 559 ASP cc_start: 0.8062 (m-30) cc_final: 0.7754 (m-30) REVERT: D 29 SER cc_start: 0.7969 (m) cc_final: 0.7687 (p) REVERT: D 191 ASP cc_start: 0.7186 (t0) cc_final: 0.6817 (p0) REVERT: E 56 ASN cc_start: 0.8140 (m-40) cc_final: 0.7906 (m110) REVERT: E 101 ASN cc_start: 0.8107 (m-40) cc_final: 0.7755 (m-40) REVERT: E 117 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7613 (mm-30) REVERT: E 279 GLU cc_start: 0.8201 (tp30) cc_final: 0.8001 (tp30) REVERT: E 393 GLU cc_start: 0.8057 (tp30) cc_final: 0.7745 (mp0) REVERT: E 397 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7786 (mt-10) REVERT: E 456 LEU cc_start: 0.8546 (mt) cc_final: 0.8275 (mp) REVERT: E 459 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7036 (mtp85) REVERT: E 571 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: F 29 SER cc_start: 0.8376 (m) cc_final: 0.8125 (m) REVERT: F 121 ASN cc_start: 0.7316 (t0) cc_final: 0.7060 (t0) REVERT: F 191 ASP cc_start: 0.7179 (t0) cc_final: 0.6750 (p0) REVERT: G 56 ASN cc_start: 0.8316 (m-40) cc_final: 0.8048 (m110) REVERT: G 117 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7669 (mm-30) REVERT: G 129 GLU cc_start: 0.7728 (mp0) cc_final: 0.7438 (mp0) REVERT: G 130 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7937 (tp) REVERT: G 264 MET cc_start: 0.6574 (mmm) cc_final: 0.5985 (mmm) REVERT: G 434 ASP cc_start: 0.7569 (m-30) cc_final: 0.7256 (m-30) REVERT: G 456 LEU cc_start: 0.8610 (mt) cc_final: 0.8329 (mp) REVERT: G 474 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8226 (mmmm) REVERT: G 526 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7565 (ttm110) REVERT: G 541 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7824 (mmpt) REVERT: H 29 SER cc_start: 0.8276 (m) cc_final: 0.8013 (m) REVERT: H 131 LYS cc_start: 0.5766 (pptt) cc_final: 0.5216 (pptt) outliers start: 68 outliers final: 41 residues processed: 490 average time/residue: 1.4925 time to fit residues: 824.0258 Evaluate side-chains 509 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 456 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 179 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 168 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 115 optimal weight: 0.0870 chunk 136 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN B 173 ASN C 147 ASN E 132 ASN E 147 ASN E 155 ASN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111362 restraints weight = 32103.815| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.01 r_work: 0.3271 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23104 Z= 0.120 Angle : 0.499 6.166 31028 Z= 0.273 Chirality : 0.042 0.146 3396 Planarity : 0.003 0.040 3952 Dihedral : 4.199 18.348 3012 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.55 % Allowed : 17.38 % Favored : 80.06 % 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: 0.24 (0.16), residues: 2756 helix: 0.64 (0.15), residues: 1164 sheet: 1.11 (0.22), residues: 544 loop : -0.85 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 126 HIS 0.003 0.001 HIS H 41 PHE 0.022 0.001 PHE A 500 TYR 0.025 0.001 TYR E 272 ARG 0.009 0.000 ARG E 526 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1023) hydrogen bonds : angle 4.78093 ( 2901) covalent geometry : bond 0.00286 (23104) covalent geometry : angle 0.49856 (31028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 461 time to evaluate : 2.734 Fit side-chains revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8538 (mm) cc_final: 0.8304 (mp) REVERT: A 56 ASN cc_start: 0.8256 (m-40) cc_final: 0.7992 (m110) REVERT: A 116 LYS cc_start: 0.8252 (tttp) cc_final: 0.7994 (tptp) REVERT: A 117 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 130 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8130 (tp) REVERT: A 143 ASN cc_start: 0.7497 (t0) cc_final: 0.7290 (t0) REVERT: A 324 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8705 (mt) REVERT: A 393 GLU cc_start: 0.7991 (tp30) cc_final: 0.7579 (mp0) REVERT: A 438 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8536 (mttt) REVERT: A 456 LEU cc_start: 0.8755 (mt) cc_final: 0.8537 (mp) REVERT: A 462 LEU cc_start: 0.8398 (tp) cc_final: 0.8041 (tt) REVERT: A 526 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7647 (ttm110) REVERT: A 538 GLN cc_start: 0.8424 (mt0) cc_final: 0.8148 (mt0) REVERT: A 541 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7821 (mmpt) REVERT: A 555 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7725 (tmtm) REVERT: A 571 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: B 29 SER cc_start: 0.8202 (m) cc_final: 0.7911 (m) REVERT: B 219 LYS cc_start: 0.8783 (mttp) cc_final: 0.8468 (mmtp) REVERT: C 56 ASN cc_start: 0.8346 (m-40) cc_final: 0.8104 (m110) REVERT: C 103 ASP cc_start: 0.8050 (p0) cc_final: 0.7726 (OUTLIER) REVERT: C 117 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7691 (mm-30) REVERT: C 264 MET cc_start: 0.6448 (mmm) cc_final: 0.5814 (mmm) REVERT: C 324 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8624 (mt) REVERT: C 393 GLU cc_start: 0.8046 (tp30) cc_final: 0.7585 (mp0) REVERT: C 456 LEU cc_start: 0.8844 (mt) cc_final: 0.8636 (mp) REVERT: C 459 ARG cc_start: 0.7976 (mtt180) cc_final: 0.7668 (ptp-170) REVERT: C 538 GLN cc_start: 0.8641 (mt0) cc_final: 0.8414 (mt0) REVERT: C 559 ASP cc_start: 0.8080 (m-30) cc_final: 0.7761 (m-30) REVERT: D 29 SER cc_start: 0.7973 (m) cc_final: 0.7684 (p) REVERT: D 191 ASP cc_start: 0.7183 (t0) cc_final: 0.6774 (p0) REVERT: E 56 ASN cc_start: 0.8126 (m-40) cc_final: 0.7893 (m110) REVERT: E 101 ASN cc_start: 0.8113 (m-40) cc_final: 0.7787 (m-40) REVERT: E 117 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 393 GLU cc_start: 0.8091 (tp30) cc_final: 0.7774 (mp0) REVERT: E 456 LEU cc_start: 0.8546 (mt) cc_final: 0.8281 (mp) REVERT: F 29 SER cc_start: 0.8378 (m) cc_final: 0.8119 (m) REVERT: F 61 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7897 (mp) REVERT: F 88 ASP cc_start: 0.8152 (t70) cc_final: 0.7855 (t0) REVERT: F 121 ASN cc_start: 0.7267 (t0) cc_final: 0.6626 (t0) REVERT: F 191 ASP cc_start: 0.7165 (t0) cc_final: 0.6618 (p0) REVERT: G 56 ASN cc_start: 0.8268 (m-40) cc_final: 0.8045 (m110) REVERT: G 117 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7658 (mm-30) REVERT: G 129 GLU cc_start: 0.7742 (mp0) cc_final: 0.7461 (mp0) REVERT: G 264 MET cc_start: 0.6506 (mmm) cc_final: 0.5898 (mmm) REVERT: G 432 ASP cc_start: 0.8315 (p0) cc_final: 0.7848 (p0) REVERT: G 434 ASP cc_start: 0.7585 (m-30) cc_final: 0.7045 (m-30) REVERT: G 456 LEU cc_start: 0.8604 (mt) cc_final: 0.8314 (mp) REVERT: G 474 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8180 (mmmm) REVERT: G 526 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7593 (ttm110) REVERT: G 541 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7830 (mmpt) REVERT: H 29 SER cc_start: 0.8282 (m) cc_final: 0.8019 (m) outliers start: 64 outliers final: 40 residues processed: 493 average time/residue: 1.4429 time to fit residues: 802.0966 Evaluate side-chains 500 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 451 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 126 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 250 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 173 ASN C 147 ASN E 147 ASN E 155 ASN F 38 ASN G 147 ASN G 155 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110584 restraints weight = 32187.665| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.99 r_work: 0.3252 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23104 Z= 0.160 Angle : 0.538 6.306 31028 Z= 0.293 Chirality : 0.043 0.150 3396 Planarity : 0.003 0.042 3952 Dihedral : 4.353 18.881 3012 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.15 % Allowed : 18.06 % Favored : 79.78 % 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: 0.11 (0.16), residues: 2756 helix: 0.52 (0.15), residues: 1164 sheet: 1.09 (0.23), residues: 544 loop : -0.92 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 126 HIS 0.004 0.001 HIS H 41 PHE 0.028 0.002 PHE A 500 TYR 0.025 0.001 TYR E 272 ARG 0.007 0.000 ARG G 526 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 1023) hydrogen bonds : angle 4.88740 ( 2901) covalent geometry : bond 0.00395 (23104) covalent geometry : angle 0.53782 (31028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 457 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.8587 (mm) cc_final: 0.8358 (mp) REVERT: A 56 ASN cc_start: 0.8215 (m-40) cc_final: 0.7951 (m110) REVERT: A 116 LYS cc_start: 0.8276 (tttp) cc_final: 0.8003 (tptp) REVERT: A 117 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 130 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8177 (tp) REVERT: A 143 ASN cc_start: 0.7525 (t0) cc_final: 0.7264 (t0) REVERT: A 324 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 393 GLU cc_start: 0.7955 (tp30) cc_final: 0.7505 (mp0) REVERT: A 456 LEU cc_start: 0.8786 (mt) cc_final: 0.8566 (mp) REVERT: A 462 LEU cc_start: 0.8440 (tp) cc_final: 0.8084 (tt) REVERT: A 538 GLN cc_start: 0.8422 (mt0) cc_final: 0.8122 (mt0) REVERT: A 541 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7819 (mmpt) REVERT: A 555 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7729 (tmtm) REVERT: B 29 SER cc_start: 0.8232 (m) cc_final: 0.7946 (m) REVERT: B 39 LYS cc_start: 0.8176 (mttm) cc_final: 0.7949 (mttt) REVERT: C 56 ASN cc_start: 0.8309 (m-40) cc_final: 0.8054 (m110) REVERT: C 103 ASP cc_start: 0.8029 (p0) cc_final: 0.7722 (p0) REVERT: C 117 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 264 MET cc_start: 0.6442 (mmm) cc_final: 0.5792 (mmm) REVERT: C 324 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8701 (mt) REVERT: C 393 GLU cc_start: 0.8081 (tp30) cc_final: 0.7624 (mp0) REVERT: C 456 LEU cc_start: 0.8871 (mt) cc_final: 0.8651 (mp) REVERT: C 459 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7661 (ptp-170) REVERT: C 538 GLN cc_start: 0.8688 (mt0) cc_final: 0.8381 (mt0) REVERT: C 559 ASP cc_start: 0.8058 (m-30) cc_final: 0.7784 (m-30) REVERT: D 29 SER cc_start: 0.7989 (m) cc_final: 0.7711 (p) REVERT: D 36 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7854 (ttpp) REVERT: D 191 ASP cc_start: 0.7176 (t0) cc_final: 0.6781 (p0) REVERT: E 56 ASN cc_start: 0.8121 (m-40) cc_final: 0.7883 (m110) REVERT: E 101 ASN cc_start: 0.8124 (m-40) cc_final: 0.7791 (m-40) REVERT: E 117 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7597 (mm-30) REVERT: E 393 GLU cc_start: 0.8115 (tp30) cc_final: 0.7807 (mp0) REVERT: E 456 LEU cc_start: 0.8566 (mt) cc_final: 0.8300 (mp) REVERT: E 571 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: F 29 SER cc_start: 0.8386 (m) cc_final: 0.8139 (m) REVERT: F 121 ASN cc_start: 0.7234 (t0) cc_final: 0.5807 (t0) REVERT: F 191 ASP cc_start: 0.7205 (t0) cc_final: 0.6752 (p0) REVERT: G 56 ASN cc_start: 0.8245 (m-40) cc_final: 0.8015 (m110) REVERT: G 117 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7661 (mm-30) REVERT: G 129 GLU cc_start: 0.7732 (mp0) cc_final: 0.7432 (mp0) REVERT: G 264 MET cc_start: 0.6511 (mmm) cc_final: 0.5886 (mmm) REVERT: G 432 ASP cc_start: 0.8333 (p0) cc_final: 0.7838 (p0) REVERT: G 434 ASP cc_start: 0.7594 (m-30) cc_final: 0.7127 (m-30) REVERT: G 456 LEU cc_start: 0.8629 (mt) cc_final: 0.8348 (mp) REVERT: G 474 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8173 (mmmm) REVERT: G 541 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7809 (mmpt) REVERT: H 29 SER cc_start: 0.8284 (m) cc_final: 0.8026 (m) REVERT: H 121 ASN cc_start: 0.7379 (t0) cc_final: 0.6013 (t0) outliers start: 54 outliers final: 34 residues processed: 486 average time/residue: 1.4647 time to fit residues: 803.1316 Evaluate side-chains 498 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 456 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 41 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 121 optimal weight: 0.0270 chunk 116 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 272 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN B 173 ASN C 147 ASN E 132 ASN E 147 ASN E 155 ASN F 38 ASN G 147 ASN G 155 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111440 restraints weight = 31796.651| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.97 r_work: 0.3266 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23104 Z= 0.128 Angle : 0.509 6.081 31028 Z= 0.279 Chirality : 0.042 0.146 3396 Planarity : 0.003 0.038 3952 Dihedral : 4.273 18.984 3012 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.95 % Allowed : 18.58 % Favored : 79.47 % 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: 0.19 (0.16), residues: 2756 helix: 0.62 (0.15), residues: 1164 sheet: 1.03 (0.22), residues: 552 loop : -0.86 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 126 HIS 0.005 0.001 HIS F 41 PHE 0.025 0.001 PHE A 500 TYR 0.025 0.001 TYR C 272 ARG 0.005 0.000 ARG G 526 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 1023) hydrogen bonds : angle 4.84450 ( 2901) covalent geometry : bond 0.00308 (23104) covalent geometry : angle 0.50927 (31028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19217.96 seconds wall clock time: 330 minutes 57.58 seconds (19857.58 seconds total)