Starting phenix.real_space_refine on Tue Jul 23 17:48:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk1_41321/07_2024/8tk1_41321_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk1_41321/07_2024/8tk1_41321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk1_41321/07_2024/8tk1_41321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk1_41321/07_2024/8tk1_41321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk1_41321/07_2024/8tk1_41321_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk1_41321/07_2024/8tk1_41321_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 15057 2.51 5 N 3871 2.21 5 O 4429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 241": "OE1" <-> "OE2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F GLU 453": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23424 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "E" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2513 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 6, 'TRANS': 303} Chain breaks: 5 Chain: "G" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 12.27, per 1000 atoms: 0.52 Number of scatterers: 23424 At special positions: 0 Unit cell: (137.76, 163.52, 189.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 4429 8.00 N 3871 7.00 C 15057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 8.52 Conformation dependent library (CDL) restraints added in 3.9 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5416 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 21 sheets defined 48.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 310 through 313 removed outlier: 3.999A pdb=" N LYS A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.643A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 removed outlier: 4.632A pdb=" N SER A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.560A pdb=" N LYS A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.869A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.535A pdb=" N GLY A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.577A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 553 through 562 Processing helix chain 'A' and resid 566 through 573 removed outlier: 4.195A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.023A pdb=" N ILE B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.750A pdb=" N VAL B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 90 removed outlier: 5.764A pdb=" N LYS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.707A pdb=" N LEU B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 195 through 201 removed outlier: 4.392A pdb=" N TRP B 199 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'C' and resid 33 through 47 removed outlier: 3.669A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 310 through 313 removed outlier: 3.997A pdb=" N LYS C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.643A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.634A pdb=" N SER C 357 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.559A pdb=" N LYS C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.870A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.539A pdb=" N GLY C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 528 removed outlier: 3.576A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 540 through 550 Processing helix chain 'C' and resid 553 through 562 Processing helix chain 'C' and resid 566 through 573 removed outlier: 4.196A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 removed outlier: 4.022A pdb=" N ILE D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 38 Processing helix chain 'D' and resid 50 through 62 Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.749A pdb=" N VAL D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 90 removed outlier: 5.764A pdb=" N LYS D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.598A pdb=" N GLY D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.681A pdb=" N LEU D 139 " --> pdb=" O PHE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 182 Processing helix chain 'D' and resid 195 through 201 removed outlier: 4.393A pdb=" N TRP D 199 " --> pdb=" O ILE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'E' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 310 through 313 removed outlier: 3.999A pdb=" N LYS E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 321 through 326 removed outlier: 3.642A pdb=" N LEU E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 326 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 removed outlier: 4.626A pdb=" N SER E 357 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.557A pdb=" N LYS E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 395 Processing helix chain 'E' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR E 419 " --> pdb=" O HIS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.865A pdb=" N LEU E 456 " --> pdb=" O ARG E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 493 Processing helix chain 'E' and resid 493 through 503 removed outlier: 3.531A pdb=" N GLY E 502 " --> pdb=" O GLY E 498 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 503 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 528 removed outlier: 3.577A pdb=" N ASP E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU E 522 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER E 523 " --> pdb=" O ALA E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 538 Processing helix chain 'E' and resid 540 through 550 removed outlier: 3.556A pdb=" N MET E 545 " --> pdb=" O LYS E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 566 through 573 removed outlier: 4.200A pdb=" N LYS E 570 " --> pdb=" O PHE E 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.063A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 38 Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 73 through 81 removed outlier: 3.752A pdb=" N VAL F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 90 removed outlier: 5.766A pdb=" N LYS F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O PHE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 3.537A pdb=" N GLY F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.681A pdb=" N LEU F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.575A pdb=" N ARG F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 195 through 201 removed outlier: 4.391A pdb=" N TRP F 199 " --> pdb=" O ILE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 229 through 239 removed outlier: 4.131A pdb=" N PHE F 239 " --> pdb=" O TYR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 247 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 452 through 459 Processing helix chain 'G' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 52 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 310 through 313 removed outlier: 3.998A pdb=" N LYS G 313 " --> pdb=" O SER G 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 310 through 313' Processing helix chain 'G' and resid 321 through 326 removed outlier: 3.644A pdb=" N LEU G 324 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 326 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 357 removed outlier: 4.628A pdb=" N SER G 357 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.560A pdb=" N LYS G 364 " --> pdb=" O LYS G 360 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 368 " --> pdb=" O LYS G 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA G 369 " --> pdb=" O ALA G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 395 Processing helix chain 'G' and resid 413 through 424 removed outlier: 3.705A pdb=" N THR G 419 " --> pdb=" O HIS G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 456 removed outlier: 3.868A pdb=" N LEU G 456 " --> pdb=" O ARG G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 493 Processing helix chain 'G' and resid 493 through 503 removed outlier: 3.533A pdb=" N GLY G 502 " --> pdb=" O GLY G 498 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 503 " --> pdb=" O GLU G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 528 removed outlier: 3.578A pdb=" N ASP G 515 " --> pdb=" O ASP G 511 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU G 522 " --> pdb=" O SER G 518 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER G 523 " --> pdb=" O ALA G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 538 Processing helix chain 'G' and resid 540 through 550 Processing helix chain 'G' and resid 553 through 562 Processing helix chain 'G' and resid 566 through 573 removed outlier: 4.194A pdb=" N LYS G 570 " --> pdb=" O PHE G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 removed outlier: 4.026A pdb=" N ILE H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 50 through 62 Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.748A pdb=" N VAL H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 5.766A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 89 " --> pdb=" O PHE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 119 removed outlier: 3.581A pdb=" N GLY H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 143 removed outlier: 3.677A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'H' and resid 168 through 182 Processing helix chain 'H' and resid 195 through 201 removed outlier: 4.397A pdb=" N TRP H 199 " --> pdb=" O ILE H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.729A pdb=" N LYS A 16 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS A 9 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN A 18 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A 7 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 20 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN A 5 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 2 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 6 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 72 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE A 8 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A 70 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 105 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N VAL A 104 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU A 129 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A 128 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.976A pdb=" N LYS A 24 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 334 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.511A pdb=" N ILE A 465 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.730A pdb=" N SER B 43 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE B 160 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 45 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP B 162 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL B 47 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS B 185 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 13 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY B 190 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 15 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 222 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.727A pdb=" N LYS C 16 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS C 9 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN C 18 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C 7 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 20 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN C 5 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 2 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 105 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL C 104 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU C 129 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER C 128 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.978A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 403 through 407 Processing sheet with id=AA9, first strand: chain 'C' and resid 435 through 437 removed outlier: 3.512A pdb=" N ILE C 465 " --> pdb=" O TYR C 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER D 43 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE D 160 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA D 45 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP D 162 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL D 47 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 185 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 13 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY D 190 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 15 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 222 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.729A pdb=" N LYS E 16 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS E 9 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN E 18 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR E 7 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN E 20 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN E 5 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 2 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR E 74 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 6 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 72 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 8 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU E 70 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 105 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL E 104 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU E 129 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 112 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 121 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER E 128 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 154 removed outlier: 6.976A pdb=" N LYS E 24 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 334 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL E 26 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL E 336 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE E 28 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 403 through 407 Processing sheet with id=AB5, first strand: chain 'E' and resid 435 through 437 removed outlier: 3.506A pdb=" N ILE E 465 " --> pdb=" O TYR E 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER F 43 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE F 160 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA F 45 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP F 162 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL F 47 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS F 185 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 13 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY F 190 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL F 15 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 222 " --> pdb=" O THR F 16 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 256 through 259 removed outlier: 6.533A pdb=" N ILE F 257 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN F 434 " --> pdb=" O LYS F 464 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE F 466 " --> pdb=" O ASN F 434 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL F 436 " --> pdb=" O ILE F 466 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE F 468 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE F 438 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE F 287 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE F 310 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR F 424 " --> pdb=" O ILE F 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 14 through 20 removed outlier: 6.730A pdb=" N LYS G 16 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS G 9 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN G 18 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR G 7 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN G 20 " --> pdb=" O ASN G 5 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASN G 5 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 2 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR G 74 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE G 6 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE G 72 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE G 8 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU G 70 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE G 105 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL G 104 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU G 129 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS G 112 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN G 121 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER G 128 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 149 through 154 removed outlier: 6.979A pdb=" N LYS G 24 " --> pdb=" O ARG G 332 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE G 334 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL G 26 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL G 336 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE G 28 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 403 through 407 Processing sheet with id=AC2, first strand: chain 'G' and resid 435 through 437 removed outlier: 3.506A pdb=" N ILE G 465 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER H 43 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE H 160 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA H 45 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP H 162 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL H 47 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS H 185 " --> pdb=" O PHE H 157 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE H 13 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY H 190 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL H 15 " --> pdb=" O GLY H 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 222 " --> pdb=" O THR H 16 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.67 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7366 1.34 - 1.46: 3981 1.46 - 1.58: 12386 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 23845 Sorted by residual: bond pdb=" N SER F 224 " pdb=" CA SER F 224 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.26e-02 6.30e+03 1.03e+01 bond pdb=" N ASN F 225 " pdb=" CA ASN F 225 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N CYS F 229 " pdb=" CA CYS F 229 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.32e-02 5.74e+03 7.61e+00 bond pdb=" N THR F 223 " pdb=" CA THR F 223 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 6.96e+00 bond pdb=" ND1 HIS F 426 " pdb=" CE1 HIS F 426 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.43e+00 ... (remaining 23840 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 423 107.34 - 114.00: 13423 114.00 - 120.67: 10037 120.67 - 127.33: 8032 127.33 - 134.00: 110 Bond angle restraints: 32025 Sorted by residual: angle pdb=" CB HIS F 426 " pdb=" CG HIS F 426 " pdb=" CD2 HIS F 426 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 angle pdb=" OE1 GLN F 314 " pdb=" CD GLN F 314 " pdb=" NE2 GLN F 314 " ideal model delta sigma weight residual 122.60 118.14 4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CB HIS F 454 " pdb=" CG HIS F 454 " pdb=" CD2 HIS F 454 " ideal model delta sigma weight residual 131.20 125.67 5.53 1.30e+00 5.92e-01 1.81e+01 angle pdb=" OE1 GLN F 254 " pdb=" CD GLN F 254 " pdb=" NE2 GLN F 254 " ideal model delta sigma weight residual 122.60 118.60 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" OD1 ASN F 240 " pdb=" CG ASN F 240 " pdb=" ND2 ASN F 240 " ideal model delta sigma weight residual 122.60 118.71 3.89 1.00e+00 1.00e+00 1.52e+01 ... (remaining 32020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 12725 16.24 - 32.49: 1352 32.49 - 48.73: 329 48.73 - 64.98: 27 64.98 - 81.22: 18 Dihedral angle restraints: 14451 sinusoidal: 6027 harmonic: 8424 Sorted by residual: dihedral pdb=" CA PHE F 423 " pdb=" C PHE F 423 " pdb=" N THR F 424 " pdb=" CA THR F 424 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER F 224 " pdb=" C SER F 224 " pdb=" N ASN F 225 " pdb=" CA ASN F 225 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LYS G 125 " pdb=" C LYS G 125 " pdb=" N TRP G 126 " pdb=" CA TRP G 126 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 14448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3022 0.057 - 0.115: 390 0.115 - 0.172: 102 0.172 - 0.230: 2 0.230 - 0.287: 1 Chirality restraints: 3517 Sorted by residual: chirality pdb=" CA THR F 243 " pdb=" N THR F 243 " pdb=" C THR F 243 " pdb=" CB THR F 243 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA VAL F 253 " pdb=" N VAL F 253 " pdb=" C VAL F 253 " pdb=" CB VAL F 253 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA GLU F 432 " pdb=" N GLU F 432 " pdb=" C GLU F 432 " pdb=" CB GLU F 432 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 3514 not shown) Planarity restraints: 4075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 126 " 0.036 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP C 126 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP C 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 126 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 126 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 126 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 126 " -0.035 2.00e-02 2.50e+03 3.21e-02 2.57e+01 pdb=" CG TRP A 126 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A 126 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 126 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 126 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 126 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 126 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 126 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.56e+01 pdb=" CG TRP G 126 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP G 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP G 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 126 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 126 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 126 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 126 " 0.005 2.00e-02 2.50e+03 ... (remaining 4072 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 176 2.60 - 3.18: 18899 3.18 - 3.75: 32696 3.75 - 4.33: 51116 4.33 - 4.90: 85193 Nonbonded interactions: 188080 Sorted by model distance: nonbonded pdb=" OE2 GLU E 393 " pdb=" OG1 THR E 554 " model vdw 2.031 2.440 nonbonded pdb=" OE2 GLU A 393 " pdb=" OG1 THR A 554 " model vdw 2.036 2.440 nonbonded pdb=" OE2 GLU C 393 " pdb=" OG1 THR C 554 " model vdw 2.039 2.440 nonbonded pdb=" OE2 GLU G 393 " pdb=" OG1 THR G 554 " model vdw 2.040 2.440 nonbonded pdb=" NZ LYS A 439 " pdb=" O ILE E 527 " model vdw 2.103 2.520 ... (remaining 188075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 59.130 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23845 Z= 0.219 Angle : 0.540 5.890 32025 Z= 0.317 Chirality : 0.043 0.287 3517 Planarity : 0.004 0.147 4075 Dihedral : 13.820 81.221 9035 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2837 helix: 0.43 (0.15), residues: 1113 sheet: 0.52 (0.22), residues: 554 loop : -0.74 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.010 TRP C 126 HIS 0.012 0.001 HIS F 426 PHE 0.030 0.002 PHE F 309 TYR 0.039 0.001 TYR F 418 ARG 0.008 0.000 ARG F 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 599 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.8426 (tttt) cc_final: 0.7802 (ttpp) REVERT: A 328 MET cc_start: 0.8419 (ptt) cc_final: 0.8159 (ptp) REVERT: A 556 ASP cc_start: 0.7211 (m-30) cc_final: 0.6972 (m-30) REVERT: A 559 ASP cc_start: 0.7089 (m-30) cc_final: 0.6841 (m-30) REVERT: C 465 ILE cc_start: 0.8054 (pt) cc_final: 0.7768 (pp) REVERT: C 489 ILE cc_start: 0.8480 (mm) cc_final: 0.8225 (mt) REVERT: D 88 ASP cc_start: 0.7664 (t70) cc_final: 0.7255 (t0) REVERT: D 176 MET cc_start: 0.7047 (mmp) cc_final: 0.6747 (mmm) REVERT: E 392 ASP cc_start: 0.7742 (t70) cc_final: 0.7542 (t0) REVERT: E 480 GLU cc_start: 0.6725 (pt0) cc_final: 0.6479 (pt0) REVERT: E 555 LYS cc_start: 0.7056 (tptp) cc_final: 0.6548 (mmmt) REVERT: E 559 ASP cc_start: 0.7008 (m-30) cc_final: 0.6679 (m-30) REVERT: F 34 ASP cc_start: 0.7379 (m-30) cc_final: 0.6867 (m-30) REVERT: F 42 TYR cc_start: 0.8119 (m-80) cc_final: 0.7903 (m-80) REVERT: F 74 ASP cc_start: 0.7149 (m-30) cc_final: 0.6817 (m-30) REVERT: F 88 ASP cc_start: 0.7406 (t70) cc_final: 0.6883 (t0) REVERT: F 107 PHE cc_start: 0.6866 (m-80) cc_final: 0.6462 (m-80) REVERT: F 116 VAL cc_start: 0.4787 (t) cc_final: 0.4578 (t) REVERT: F 121 ASN cc_start: 0.7590 (t160) cc_final: 0.7337 (t0) REVERT: F 176 MET cc_start: 0.8435 (mmp) cc_final: 0.7705 (mmt) REVERT: F 180 ASP cc_start: 0.6916 (m-30) cc_final: 0.6644 (m-30) REVERT: F 216 ASP cc_start: 0.7301 (p0) cc_final: 0.7075 (OUTLIER) REVERT: G 471 GLU cc_start: 0.5710 (tm-30) cc_final: 0.5306 (tp30) REVERT: G 473 ILE cc_start: 0.7737 (pt) cc_final: 0.7395 (pt) outliers start: 2 outliers final: 5 residues processed: 601 average time/residue: 1.4938 time to fit residues: 1014.1479 Evaluate side-chains 493 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 489 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 228 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.0980 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 145 optimal weight: 0.4980 chunk 115 optimal weight: 0.0870 chunk 223 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN A 455 ASN A 538 GLN C 18 ASN C 155 ASN C 538 GLN C 551 ASN D 38 ASN D 68 ASN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 ASN E 492 GLN E 538 GLN F 213 ASN F 454 HIS G 18 ASN G 455 ASN H 221 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23845 Z= 0.148 Angle : 0.502 9.412 32025 Z= 0.274 Chirality : 0.042 0.155 3517 Planarity : 0.003 0.042 4075 Dihedral : 4.569 97.124 3110 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.54 % Allowed : 11.54 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2837 helix: 0.78 (0.15), residues: 1153 sheet: 0.89 (0.22), residues: 546 loop : -0.83 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP G 126 HIS 0.005 0.001 HIS H 221 PHE 0.018 0.001 PHE H 153 TYR 0.025 0.001 TYR G 272 ARG 0.005 0.000 ARG G 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 494 time to evaluate : 2.772 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5580 (tpt) cc_final: 0.5139 (ttp) REVERT: A 328 MET cc_start: 0.8458 (ptt) cc_final: 0.8182 (ptt) REVERT: A 542 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 559 ASP cc_start: 0.7007 (m-30) cc_final: 0.6743 (m-30) REVERT: B 176 MET cc_start: 0.5268 (mmp) cc_final: 0.4992 (mmp) REVERT: C 383 GLU cc_start: 0.7668 (mp0) cc_final: 0.7420 (mp0) REVERT: C 438 LYS cc_start: 0.8352 (tttt) cc_final: 0.7960 (tttt) REVERT: C 465 ILE cc_start: 0.8020 (pt) cc_final: 0.7645 (pp) REVERT: C 466 THR cc_start: 0.8655 (m) cc_final: 0.8309 (t) REVERT: C 477 LYS cc_start: 0.7014 (mmmm) cc_final: 0.6789 (mmmm) REVERT: C 487 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8251 (mtmm) REVERT: C 510 ILE cc_start: 0.8368 (mt) cc_final: 0.8087 (mt) REVERT: D 38 ASN cc_start: 0.7421 (t0) cc_final: 0.7202 (t0) REVERT: D 131 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5223 (tttm) REVERT: E 392 ASP cc_start: 0.7816 (t70) cc_final: 0.7605 (t0) REVERT: E 445 TYR cc_start: 0.8233 (m-80) cc_final: 0.7807 (m-80) REVERT: E 484 GLU cc_start: 0.7186 (tp30) cc_final: 0.6260 (tp30) REVERT: E 544 ASN cc_start: 0.8389 (m-40) cc_final: 0.8169 (m-40) REVERT: F 30 LYS cc_start: 0.7974 (tptp) cc_final: 0.7460 (tptm) REVERT: F 34 ASP cc_start: 0.7459 (m-30) cc_final: 0.6949 (m-30) REVERT: F 42 TYR cc_start: 0.8146 (m-80) cc_final: 0.7855 (m-80) REVERT: F 49 PHE cc_start: 0.8247 (m-80) cc_final: 0.7977 (m-80) REVERT: F 74 ASP cc_start: 0.7126 (m-30) cc_final: 0.6763 (m-30) REVERT: F 88 ASP cc_start: 0.7341 (t70) cc_final: 0.6811 (t0) REVERT: G 117 GLU cc_start: 0.7499 (tp30) cc_final: 0.7287 (tp30) REVERT: G 444 VAL cc_start: 0.8070 (m) cc_final: 0.7799 (p) REVERT: G 471 GLU cc_start: 0.5938 (tm-30) cc_final: 0.5697 (tp30) REVERT: G 474 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7394 (mppt) REVERT: G 484 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6977 (mt-10) REVERT: G 492 GLN cc_start: 0.7266 (tt0) cc_final: 0.7041 (tt0) REVERT: G 562 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: H 36 LYS cc_start: 0.8112 (tttt) cc_final: 0.7906 (ttmm) REVERT: H 121 ASN cc_start: 0.7896 (t0) cc_final: 0.7691 (t0) outliers start: 40 outliers final: 13 residues processed: 510 average time/residue: 1.4459 time to fit residues: 835.8336 Evaluate side-chains 480 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 463 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 562 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 259 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN A 538 GLN C 492 GLN C 538 GLN D 121 ASN E 492 GLN E 538 GLN H 12 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23845 Z= 0.233 Angle : 0.526 7.157 32025 Z= 0.288 Chirality : 0.043 0.159 3517 Planarity : 0.003 0.061 4075 Dihedral : 4.514 84.142 3107 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.55 % Allowed : 13.50 % Favored : 83.95 % 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: 0.22 (0.15), residues: 2837 helix: 0.73 (0.15), residues: 1166 sheet: 0.96 (0.22), residues: 546 loop : -0.83 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP G 126 HIS 0.005 0.001 HIS A 61 PHE 0.024 0.002 PHE D 107 TYR 0.025 0.001 TYR A 272 ARG 0.008 0.000 ARG G 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 486 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7917 (pttp) REVERT: A 289 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: A 488 GLU cc_start: 0.7387 (tt0) cc_final: 0.7169 (pt0) REVERT: A 559 ASP cc_start: 0.7017 (m-30) cc_final: 0.6794 (m-30) REVERT: B 176 MET cc_start: 0.5399 (mmp) cc_final: 0.5071 (mmp) REVERT: C 117 GLU cc_start: 0.7582 (tp30) cc_final: 0.7366 (tp30) REVERT: C 279 GLU cc_start: 0.7572 (tp30) cc_final: 0.7207 (tp30) REVERT: C 355 TYR cc_start: 0.8288 (m-80) cc_final: 0.8050 (m-10) REVERT: C 383 GLU cc_start: 0.7569 (mp0) cc_final: 0.7330 (mp0) REVERT: C 438 LYS cc_start: 0.8402 (tttt) cc_final: 0.8148 (tttm) REVERT: C 442 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7884 (mtmm) REVERT: C 478 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7845 (tttp) REVERT: C 480 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6754 (tp30) REVERT: C 493 TYR cc_start: 0.7670 (m-80) cc_final: 0.7458 (m-80) REVERT: C 510 ILE cc_start: 0.8406 (mt) cc_final: 0.8068 (mt) REVERT: D 14 LEU cc_start: 0.8144 (tp) cc_final: 0.7936 (tp) REVERT: D 38 ASN cc_start: 0.7401 (t0) cc_final: 0.7181 (t0) REVERT: E 392 ASP cc_start: 0.7962 (t70) cc_final: 0.7745 (t0) REVERT: E 445 TYR cc_start: 0.8256 (m-80) cc_final: 0.7748 (m-80) REVERT: E 484 GLU cc_start: 0.7283 (tp30) cc_final: 0.7037 (mm-30) REVERT: E 510 ILE cc_start: 0.8122 (mt) cc_final: 0.7689 (mt) REVERT: E 511 ASP cc_start: 0.7650 (m-30) cc_final: 0.7447 (m-30) REVERT: E 539 LYS cc_start: 0.8301 (mttm) cc_final: 0.8045 (mtpp) REVERT: E 559 ASP cc_start: 0.7051 (m-30) cc_final: 0.6762 (m-30) REVERT: F 14 LEU cc_start: 0.8052 (mp) cc_final: 0.7653 (tp) REVERT: F 49 PHE cc_start: 0.8341 (m-80) cc_final: 0.8093 (m-80) REVERT: F 55 LYS cc_start: 0.7548 (tppp) cc_final: 0.7291 (mmmm) REVERT: F 74 ASP cc_start: 0.7269 (m-30) cc_final: 0.6875 (m-30) REVERT: F 88 ASP cc_start: 0.7390 (t70) cc_final: 0.6920 (t0) REVERT: F 469 MET cc_start: 0.3758 (tpp) cc_final: 0.3221 (tpp) REVERT: G 117 GLU cc_start: 0.7552 (tp30) cc_final: 0.7215 (tp30) REVERT: G 444 VAL cc_start: 0.8330 (m) cc_final: 0.8095 (p) REVERT: G 471 GLU cc_start: 0.6375 (tm-30) cc_final: 0.6160 (tp30) REVERT: G 473 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7611 (pp) REVERT: G 474 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7463 (mppt) REVERT: G 480 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6616 (tm-30) REVERT: G 539 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7980 (mtpt) REVERT: H 36 LYS cc_start: 0.8160 (tttt) cc_final: 0.7911 (ttmm) REVERT: H 143 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8601 (mttt) outliers start: 66 outliers final: 18 residues processed: 516 average time/residue: 1.4290 time to fit residues: 836.2025 Evaluate side-chains 484 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 462 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 168 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.9990 chunk 194 optimal weight: 0.0870 chunk 134 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 246 optimal weight: 0.2980 chunk 74 optimal weight: 0.0370 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 461 ASN A 538 GLN C 56 ASN C 155 ASN C 492 GLN C 538 GLN E 132 ASN E 143 ASN E 538 GLN E 544 ASN F 213 ASN G 5 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.003 0.027 23845 Z= 0.168 Angle : 0.490 9.954 32025 Z= 0.265 Chirality : 0.042 0.144 3517 Planarity : 0.003 0.040 4075 Dihedral : 4.061 23.821 3105 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.93 % Allowed : 16.05 % Favored : 82.02 % 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: 0.42 (0.16), residues: 2837 helix: 0.93 (0.15), residues: 1170 sheet: 1.03 (0.22), residues: 546 loop : -0.74 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 126 HIS 0.003 0.001 HIS H 41 PHE 0.035 0.001 PHE D 107 TYR 0.024 0.001 TYR A 272 ARG 0.008 0.000 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 471 time to evaluate : 2.597 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7879 (pttp) REVERT: A 289 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 480 GLU cc_start: 0.6468 (pp20) cc_final: 0.6236 (pp20) REVERT: A 509 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7034 (tp30) REVERT: A 559 ASP cc_start: 0.6942 (m-30) cc_final: 0.6647 (m-30) REVERT: C 279 GLU cc_start: 0.7557 (tp30) cc_final: 0.7151 (tp30) REVERT: C 383 GLU cc_start: 0.7538 (mp0) cc_final: 0.7274 (mp0) REVERT: C 388 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: C 438 LYS cc_start: 0.8616 (tttt) cc_final: 0.8301 (tttm) REVERT: C 442 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7882 (mtmm) REVERT: C 455 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8237 (t0) REVERT: C 478 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7837 (tttp) REVERT: C 480 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6634 (tp30) REVERT: C 493 TYR cc_start: 0.7567 (m-80) cc_final: 0.7220 (m-80) REVERT: C 510 ILE cc_start: 0.8478 (mt) cc_final: 0.8190 (mt) REVERT: D 14 LEU cc_start: 0.8098 (tp) cc_final: 0.7888 (tp) REVERT: D 38 ASN cc_start: 0.7352 (t0) cc_final: 0.7123 (t0) REVERT: D 107 PHE cc_start: 0.6241 (t80) cc_final: 0.5898 (t80) REVERT: E 130 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8290 (tp) REVERT: E 392 ASP cc_start: 0.7941 (t70) cc_final: 0.7738 (t0) REVERT: E 421 ASN cc_start: 0.8625 (t0) cc_final: 0.8233 (t0) REVERT: E 445 TYR cc_start: 0.8208 (m-80) cc_final: 0.7696 (m-80) REVERT: E 510 ILE cc_start: 0.8235 (mt) cc_final: 0.7767 (mt) REVERT: E 511 ASP cc_start: 0.7686 (m-30) cc_final: 0.7477 (m-30) REVERT: F 14 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7724 (tp) REVERT: F 42 TYR cc_start: 0.8245 (m-80) cc_final: 0.7936 (m-80) REVERT: F 49 PHE cc_start: 0.8305 (m-80) cc_final: 0.8049 (m-80) REVERT: F 74 ASP cc_start: 0.7264 (m-30) cc_final: 0.6872 (m-30) REVERT: F 88 ASP cc_start: 0.7382 (t70) cc_final: 0.6909 (t0) REVERT: F 131 LYS cc_start: 0.7216 (pptt) cc_final: 0.6831 (pptt) REVERT: F 469 MET cc_start: 0.3817 (tpp) cc_final: 0.3415 (tpp) REVERT: G 117 GLU cc_start: 0.7527 (tp30) cc_final: 0.7279 (tp30) REVERT: G 444 VAL cc_start: 0.8376 (m) cc_final: 0.8159 (p) REVERT: G 474 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7387 (mppt) REVERT: G 539 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7971 (mtpt) REVERT: H 55 LYS cc_start: 0.7530 (mmmm) cc_final: 0.7141 (mmmm) outliers start: 50 outliers final: 26 residues processed: 496 average time/residue: 1.4441 time to fit residues: 810.1591 Evaluate side-chains 481 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 449 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 154 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 205 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 538 GLN C 56 ASN C 492 GLN C 538 GLN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 181 GLN F 213 ASN G 538 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23845 Z= 0.236 Angle : 0.525 9.685 32025 Z= 0.283 Chirality : 0.043 0.145 3517 Planarity : 0.003 0.052 4075 Dihedral : 4.156 24.051 3105 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.31 % Allowed : 16.78 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2837 helix: 0.89 (0.15), residues: 1160 sheet: 1.01 (0.22), residues: 550 loop : -0.80 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 126 HIS 0.004 0.001 HIS A 61 PHE 0.022 0.002 PHE D 107 TYR 0.024 0.001 TYR E 272 ARG 0.009 0.000 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 465 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7834 (pttp) REVERT: A 289 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 488 GLU cc_start: 0.7373 (tt0) cc_final: 0.7064 (pt0) REVERT: A 559 ASP cc_start: 0.6870 (m-30) cc_final: 0.6585 (m-30) REVERT: C 279 GLU cc_start: 0.7567 (tp30) cc_final: 0.7142 (tp30) REVERT: C 298 MET cc_start: 0.8160 (mtt) cc_final: 0.7937 (mtt) REVERT: C 383 GLU cc_start: 0.7562 (mp0) cc_final: 0.7322 (mp0) REVERT: C 393 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 438 LYS cc_start: 0.8630 (tttt) cc_final: 0.8414 (tttt) REVERT: C 442 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7976 (mtmm) REVERT: C 455 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8225 (t0) REVERT: C 478 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7850 (tttp) REVERT: C 480 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6689 (tp30) REVERT: C 493 TYR cc_start: 0.7719 (m-80) cc_final: 0.7224 (m-80) REVERT: D 14 LEU cc_start: 0.8118 (tp) cc_final: 0.7913 (tp) REVERT: D 107 PHE cc_start: 0.6408 (t80) cc_final: 0.6202 (t80) REVERT: E 421 ASN cc_start: 0.8613 (t0) cc_final: 0.8249 (t0) REVERT: E 445 TYR cc_start: 0.8275 (m-80) cc_final: 0.7769 (m-80) REVERT: E 484 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6522 (tp30) REVERT: E 488 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6323 (mm-30) REVERT: F 1 MET cc_start: 0.6161 (pmm) cc_final: 0.5651 (ptm) REVERT: F 14 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7763 (tp) REVERT: F 49 PHE cc_start: 0.8305 (m-80) cc_final: 0.8047 (m-80) REVERT: F 94 TYR cc_start: 0.7763 (m-80) cc_final: 0.7444 (m-80) REVERT: F 130 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6766 (tptm) REVERT: F 131 LYS cc_start: 0.7355 (pttt) cc_final: 0.6871 (pptt) REVERT: F 469 MET cc_start: 0.4140 (tpp) cc_final: 0.3687 (tpp) REVERT: G 117 GLU cc_start: 0.7544 (tp30) cc_final: 0.7208 (tp30) REVERT: G 444 VAL cc_start: 0.8438 (m) cc_final: 0.8188 (p) REVERT: G 480 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6578 (tm-30) REVERT: G 503 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7244 (mm-30) REVERT: G 539 LYS cc_start: 0.8254 (mtpp) cc_final: 0.8044 (mtpt) REVERT: H 55 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7177 (mmmm) REVERT: H 143 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8595 (mttt) outliers start: 60 outliers final: 36 residues processed: 495 average time/residue: 1.4519 time to fit residues: 814.5538 Evaluate side-chains 492 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 450 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 168 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN C 56 ASN C 79 ASN C 155 ASN C 492 GLN C 538 GLN D 38 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 105 ASN F 213 ASN G 538 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23845 Z= 0.308 Angle : 0.562 9.068 32025 Z= 0.303 Chirality : 0.044 0.152 3517 Planarity : 0.003 0.058 4075 Dihedral : 4.315 24.541 3105 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.85 % Allowed : 17.52 % Favored : 79.63 % 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: 0.23 (0.15), residues: 2837 helix: 0.78 (0.15), residues: 1160 sheet: 0.93 (0.22), residues: 550 loop : -0.84 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 126 HIS 0.005 0.001 HIS A 61 PHE 0.025 0.002 PHE D 175 TYR 0.024 0.001 TYR E 272 ARG 0.007 0.001 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 481 time to evaluate : 2.808 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (pttp) REVERT: A 289 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 488 GLU cc_start: 0.7335 (tt0) cc_final: 0.6942 (pt0) REVERT: A 559 ASP cc_start: 0.6898 (m-30) cc_final: 0.6627 (m-30) REVERT: C 114 ASP cc_start: 0.6433 (t0) cc_final: 0.6224 (t70) REVERT: C 117 GLU cc_start: 0.7506 (tp30) cc_final: 0.7280 (tp30) REVERT: C 279 GLU cc_start: 0.7580 (tp30) cc_final: 0.7151 (tp30) REVERT: C 438 LYS cc_start: 0.8596 (tttt) cc_final: 0.8301 (tttt) REVERT: C 442 LYS cc_start: 0.8263 (mtmm) cc_final: 0.8023 (mtmm) REVERT: C 478 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7811 (tttp) REVERT: C 479 LYS cc_start: 0.7919 (tptm) cc_final: 0.7595 (ttmm) REVERT: C 480 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6787 (tp30) REVERT: C 481 ARG cc_start: 0.7623 (ttm170) cc_final: 0.7412 (ttm170) REVERT: C 493 TYR cc_start: 0.7824 (m-80) cc_final: 0.7421 (m-80) REVERT: D 107 PHE cc_start: 0.6459 (t80) cc_final: 0.6239 (t80) REVERT: D 212 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6321 (mp0) REVERT: E 110 GLU cc_start: 0.7316 (mp0) cc_final: 0.7016 (mp0) REVERT: E 421 ASN cc_start: 0.8612 (t0) cc_final: 0.8260 (t0) REVERT: E 445 TYR cc_start: 0.8284 (m-80) cc_final: 0.7751 (m-80) REVERT: E 484 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6544 (tp30) REVERT: E 488 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6602 (mm-30) REVERT: E 570 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7958 (mtpp) REVERT: F 1 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.5921 (ptm) REVERT: F 14 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7741 (tp) REVERT: F 49 PHE cc_start: 0.8348 (m-80) cc_final: 0.8077 (m-80) REVERT: F 88 ASP cc_start: 0.7601 (t70) cc_final: 0.7102 (t0) REVERT: F 94 TYR cc_start: 0.7808 (m-80) cc_final: 0.7533 (m-80) REVERT: F 130 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6815 (tptm) REVERT: F 131 LYS cc_start: 0.7436 (pttt) cc_final: 0.7194 (pptt) REVERT: F 469 MET cc_start: 0.4197 (tpp) cc_final: 0.3783 (tpp) REVERT: G 98 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8077 (t) REVERT: G 117 GLU cc_start: 0.7548 (tp30) cc_final: 0.7196 (tp30) REVERT: G 444 VAL cc_start: 0.8418 (m) cc_final: 0.8191 (p) REVERT: G 471 GLU cc_start: 0.6178 (tp30) cc_final: 0.5825 (tp30) REVERT: G 474 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7240 (mppt) REVERT: G 477 LYS cc_start: 0.7425 (tppp) cc_final: 0.6954 (tppp) REVERT: G 480 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6687 (tm-30) REVERT: G 539 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8094 (mtpt) REVERT: H 55 LYS cc_start: 0.7642 (mmmm) cc_final: 0.7309 (mmmm) REVERT: H 121 ASN cc_start: 0.7905 (t0) cc_final: 0.7624 (t0) REVERT: H 143 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8588 (mttt) outliers start: 74 outliers final: 44 residues processed: 519 average time/residue: 1.4515 time to fit residues: 854.8494 Evaluate side-chains 525 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 473 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 313 LYS Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain E residue 570 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 168 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 157 optimal weight: 0.2980 chunk 201 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 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 56 ASN C 56 ASN C 492 GLN C 538 GLN D 38 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 105 ASN F 213 ASN G 538 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23845 Z= 0.223 Angle : 0.527 7.729 32025 Z= 0.285 Chirality : 0.042 0.143 3517 Planarity : 0.003 0.046 4075 Dihedral : 4.207 25.272 3105 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.51 % Allowed : 18.98 % Favored : 78.51 % 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: 0.32 (0.16), residues: 2837 helix: 0.91 (0.15), residues: 1160 sheet: 0.92 (0.22), residues: 550 loop : -0.84 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 126 HIS 0.003 0.001 HIS A 61 PHE 0.019 0.001 PHE D 175 TYR 0.024 0.001 TYR G 272 ARG 0.007 0.000 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 470 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 480 GLU cc_start: 0.6365 (pp20) cc_final: 0.6138 (pp20) REVERT: A 488 GLU cc_start: 0.7364 (tt0) cc_final: 0.6951 (pt0) REVERT: A 559 ASP cc_start: 0.6862 (m-30) cc_final: 0.6586 (m-30) REVERT: C 114 ASP cc_start: 0.6408 (t0) cc_final: 0.6194 (t70) REVERT: C 117 GLU cc_start: 0.7488 (tp30) cc_final: 0.7267 (tp30) REVERT: C 279 GLU cc_start: 0.7557 (tp30) cc_final: 0.7113 (tp30) REVERT: C 298 MET cc_start: 0.8119 (mtt) cc_final: 0.7915 (mtt) REVERT: C 311 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7861 (t) REVERT: C 383 GLU cc_start: 0.7557 (mp0) cc_final: 0.7328 (mp0) REVERT: C 438 LYS cc_start: 0.8487 (tttt) cc_final: 0.8070 (tttt) REVERT: C 455 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8239 (t0) REVERT: C 459 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: C 478 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7759 (tttp) REVERT: C 480 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6736 (tp30) REVERT: C 493 TYR cc_start: 0.7691 (m-80) cc_final: 0.7275 (m-80) REVERT: D 203 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6685 (tm-30) REVERT: E 130 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8329 (tp) REVERT: E 421 ASN cc_start: 0.8564 (t0) cc_final: 0.8211 (t0) REVERT: E 445 TYR cc_start: 0.8230 (m-80) cc_final: 0.7760 (m-80) REVERT: E 484 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6314 (tp30) REVERT: E 488 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6558 (mm-30) REVERT: F 1 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5845 (ptm) REVERT: F 14 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7801 (tp) REVERT: F 49 PHE cc_start: 0.8328 (m-80) cc_final: 0.8080 (m-80) REVERT: F 88 ASP cc_start: 0.7631 (t70) cc_final: 0.7124 (t0) REVERT: F 94 TYR cc_start: 0.7795 (m-80) cc_final: 0.7419 (m-80) REVERT: F 130 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6817 (tptm) REVERT: F 469 MET cc_start: 0.4570 (tpp) cc_final: 0.4123 (tpp) REVERT: G 117 GLU cc_start: 0.7543 (tp30) cc_final: 0.7204 (tp30) REVERT: G 444 VAL cc_start: 0.8417 (m) cc_final: 0.8210 (p) REVERT: G 480 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6637 (tm-30) REVERT: G 539 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8074 (mtpt) REVERT: H 55 LYS cc_start: 0.7686 (mmmm) cc_final: 0.7355 (mmmm) REVERT: H 143 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8578 (mttt) outliers start: 65 outliers final: 37 residues processed: 503 average time/residue: 1.4290 time to fit residues: 814.6616 Evaluate side-chains 515 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 469 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 360 LYS Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 215 optimal weight: 40.0000 chunk 249 optimal weight: 0.6980 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 56 ASN C 20 ASN C 56 ASN C 155 ASN C 492 GLN C 538 GLN D 38 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 105 ASN F 213 ASN G 538 GLN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23845 Z= 0.227 Angle : 0.540 9.162 32025 Z= 0.291 Chirality : 0.042 0.144 3517 Planarity : 0.003 0.051 4075 Dihedral : 4.192 25.257 3105 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.35 % Allowed : 19.64 % Favored : 78.01 % 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: 0.39 (0.16), residues: 2837 helix: 0.97 (0.15), residues: 1152 sheet: 0.97 (0.22), residues: 555 loop : -0.80 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 126 HIS 0.004 0.001 HIS D 172 PHE 0.021 0.001 PHE D 107 TYR 0.024 0.001 TYR E 272 ARG 0.007 0.000 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 472 time to evaluate : 2.645 Fit side-chains REVERT: A 289 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: A 480 GLU cc_start: 0.6385 (pp20) cc_final: 0.6072 (pp20) REVERT: A 488 GLU cc_start: 0.7359 (tt0) cc_final: 0.6947 (pt0) REVERT: C 114 ASP cc_start: 0.6425 (t0) cc_final: 0.6211 (t70) REVERT: C 117 GLU cc_start: 0.7503 (tp30) cc_final: 0.7279 (tp30) REVERT: C 279 GLU cc_start: 0.7560 (tp30) cc_final: 0.7123 (tp30) REVERT: C 298 MET cc_start: 0.8141 (mtt) cc_final: 0.7932 (mtt) REVERT: C 383 GLU cc_start: 0.7568 (mp0) cc_final: 0.7342 (mp0) REVERT: C 455 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8227 (t0) REVERT: C 459 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: C 478 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7741 (tttp) REVERT: C 479 LYS cc_start: 0.7842 (tptm) cc_final: 0.7517 (ttmm) REVERT: C 480 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6700 (tp30) REVERT: C 493 TYR cc_start: 0.7685 (m-80) cc_final: 0.7234 (m-80) REVERT: D 58 GLU cc_start: 0.7392 (tt0) cc_final: 0.7175 (tt0) REVERT: D 176 MET cc_start: 0.7194 (mpp) cc_final: 0.6805 (mpp) REVERT: D 203 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6678 (tm-30) REVERT: E 421 ASN cc_start: 0.8555 (t0) cc_final: 0.8210 (t0) REVERT: E 445 TYR cc_start: 0.8247 (m-80) cc_final: 0.7782 (m-80) REVERT: E 481 ARG cc_start: 0.7334 (ttm110) cc_final: 0.7129 (ttm-80) REVERT: E 484 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6280 (tp30) REVERT: E 488 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6582 (mm-30) REVERT: E 539 LYS cc_start: 0.8311 (mttm) cc_final: 0.8080 (mtpp) REVERT: E 559 ASP cc_start: 0.6896 (m-30) cc_final: 0.6610 (m-30) REVERT: F 1 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.5830 (ptm) REVERT: F 14 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7805 (tp) REVERT: F 49 PHE cc_start: 0.8326 (m-80) cc_final: 0.8077 (m-80) REVERT: F 88 ASP cc_start: 0.7641 (t70) cc_final: 0.7378 (t70) REVERT: F 94 TYR cc_start: 0.7748 (m-80) cc_final: 0.7399 (m-80) REVERT: F 130 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6874 (tptm) REVERT: F 158 LYS cc_start: 0.8476 (tttp) cc_final: 0.8120 (tttp) REVERT: F 469 MET cc_start: 0.4527 (tpp) cc_final: 0.4129 (tpp) REVERT: G 117 GLU cc_start: 0.7556 (tp30) cc_final: 0.7237 (tp30) REVERT: G 444 VAL cc_start: 0.8430 (m) cc_final: 0.8193 (p) REVERT: G 471 GLU cc_start: 0.6183 (tp30) cc_final: 0.5766 (tp30) REVERT: G 474 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7342 (mppt) REVERT: G 539 LYS cc_start: 0.8285 (mtpp) cc_final: 0.8074 (mtpt) REVERT: H 55 LYS cc_start: 0.7709 (mmmm) cc_final: 0.7396 (mmmm) REVERT: H 121 ASN cc_start: 0.7906 (t0) cc_final: 0.7273 (t0) REVERT: H 143 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8584 (mttt) outliers start: 61 outliers final: 44 residues processed: 499 average time/residue: 1.4453 time to fit residues: 817.0171 Evaluate side-chains 520 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 469 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 56 ASN A 79 ASN C 56 ASN C 147 ASN C 295 HIS C 492 GLN C 538 GLN D 38 ASN E 79 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 105 ASN F 213 ASN G 79 ASN G 538 GLN H 97 ASN ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23845 Z= 0.375 Angle : 0.617 10.530 32025 Z= 0.330 Chirality : 0.045 0.153 3517 Planarity : 0.004 0.073 4075 Dihedral : 4.446 25.815 3105 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.89 % Allowed : 19.41 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2837 helix: 0.78 (0.15), residues: 1126 sheet: 0.88 (0.22), residues: 555 loop : -0.98 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 126 HIS 0.005 0.001 HIS A 61 PHE 0.024 0.002 PHE A 315 TYR 0.024 0.002 TYR E 272 ARG 0.009 0.001 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 487 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.7807 (t80) cc_final: 0.7570 (t80) REVERT: A 289 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 480 GLU cc_start: 0.6608 (pp20) cc_final: 0.6257 (pp20) REVERT: A 488 GLU cc_start: 0.7334 (tt0) cc_final: 0.7019 (pt0) REVERT: C 117 GLU cc_start: 0.7543 (tp30) cc_final: 0.7311 (tp30) REVERT: C 279 GLU cc_start: 0.7585 (tp30) cc_final: 0.7125 (tp30) REVERT: C 383 GLU cc_start: 0.7594 (mp0) cc_final: 0.7317 (mp0) REVERT: C 459 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7596 (mtm-85) REVERT: C 478 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7826 (ttmm) REVERT: C 479 LYS cc_start: 0.7975 (tptm) cc_final: 0.7643 (ttmm) REVERT: C 480 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6800 (tp30) REVERT: D 176 MET cc_start: 0.7305 (mpp) cc_final: 0.6794 (mpp) REVERT: E 421 ASN cc_start: 0.8598 (t0) cc_final: 0.8238 (t0) REVERT: E 445 TYR cc_start: 0.8292 (m-80) cc_final: 0.7788 (m-80) REVERT: E 484 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6342 (tp30) REVERT: E 488 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6627 (mm-30) REVERT: E 539 LYS cc_start: 0.8333 (mttm) cc_final: 0.8098 (mtpp) REVERT: F 1 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.5809 (ptm) REVERT: F 14 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7782 (tp) REVERT: F 49 PHE cc_start: 0.8358 (m-80) cc_final: 0.8108 (m-80) REVERT: F 94 TYR cc_start: 0.7861 (m-80) cc_final: 0.7556 (m-80) REVERT: F 153 PHE cc_start: 0.8005 (t80) cc_final: 0.7803 (t80) REVERT: F 158 LYS cc_start: 0.8469 (tttp) cc_final: 0.8089 (tttt) REVERT: F 469 MET cc_start: 0.4534 (tpp) cc_final: 0.4158 (tpp) REVERT: G 98 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8064 (t) REVERT: G 117 GLU cc_start: 0.7559 (tp30) cc_final: 0.7224 (tp30) REVERT: G 444 VAL cc_start: 0.8451 (m) cc_final: 0.8218 (p) REVERT: G 471 GLU cc_start: 0.6298 (tp30) cc_final: 0.5844 (tp30) REVERT: G 474 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7406 (mppt) REVERT: G 480 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6795 (tm-30) REVERT: G 539 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8106 (mtpt) REVERT: H 55 LYS cc_start: 0.7717 (mmmm) cc_final: 0.7424 (mmmm) REVERT: H 79 SER cc_start: 0.8346 (t) cc_final: 0.7965 (m) REVERT: H 143 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8586 (mttt) outliers start: 75 outliers final: 48 residues processed: 526 average time/residue: 1.4745 time to fit residues: 878.1993 Evaluate side-chains 537 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 483 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 36 LYS Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 523 SER Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 226 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 79 ASN A 451 ASN A 455 ASN C 56 ASN C 147 ASN C 155 ASN C 492 GLN C 538 GLN D 38 ASN E 79 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 105 ASN F 106 GLN F 255 ASN G 538 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23845 Z= 0.233 Angle : 0.550 8.462 32025 Z= 0.297 Chirality : 0.043 0.147 3517 Planarity : 0.003 0.041 4075 Dihedral : 4.256 25.991 3105 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.24 % Allowed : 20.14 % Favored : 77.62 % 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: 2837 helix: 0.79 (0.15), residues: 1158 sheet: 0.86 (0.22), residues: 563 loop : -0.76 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 126 HIS 0.004 0.001 HIS A 61 PHE 0.020 0.001 PHE D 107 TYR 0.024 0.001 TYR E 272 ARG 0.010 0.000 ARG E 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 474 time to evaluate : 2.801 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 488 GLU cc_start: 0.7354 (tt0) cc_final: 0.6928 (pt0) REVERT: C 48 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7738 (ptmt) REVERT: C 279 GLU cc_start: 0.7536 (tp30) cc_final: 0.7143 (tp30) REVERT: C 298 MET cc_start: 0.8131 (mtt) cc_final: 0.7890 (mtt) REVERT: C 383 GLU cc_start: 0.7574 (mp0) cc_final: 0.7338 (mp0) REVERT: C 438 LYS cc_start: 0.8623 (tttt) cc_final: 0.8400 (ttmt) REVERT: C 459 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7235 (mtm-85) REVERT: C 478 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7729 (ttmm) REVERT: C 479 LYS cc_start: 0.7806 (tptm) cc_final: 0.7523 (ttmm) REVERT: C 480 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6679 (tp30) REVERT: C 493 TYR cc_start: 0.7687 (m-80) cc_final: 0.7170 (m-80) REVERT: D 58 GLU cc_start: 0.7395 (tt0) cc_final: 0.7180 (tt0) REVERT: D 212 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6292 (mp0) REVERT: E 130 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8377 (tp) REVERT: E 421 ASN cc_start: 0.8564 (t0) cc_final: 0.8213 (t0) REVERT: E 445 TYR cc_start: 0.8239 (m-80) cc_final: 0.7800 (m-80) REVERT: E 481 ARG cc_start: 0.7343 (ttm110) cc_final: 0.7131 (ttm-80) REVERT: E 484 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6240 (tp30) REVERT: E 488 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6582 (mm-30) REVERT: E 539 LYS cc_start: 0.8311 (mttm) cc_final: 0.8078 (mtpp) REVERT: E 559 ASP cc_start: 0.6894 (m-30) cc_final: 0.6624 (m-30) REVERT: F 1 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5853 (ptm) REVERT: F 14 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7814 (tp) REVERT: F 49 PHE cc_start: 0.8307 (m-80) cc_final: 0.8070 (m-80) REVERT: F 94 TYR cc_start: 0.7793 (m-80) cc_final: 0.7426 (m-80) REVERT: F 153 PHE cc_start: 0.8011 (t80) cc_final: 0.7802 (t80) REVERT: F 469 MET cc_start: 0.4514 (tpp) cc_final: 0.4161 (tpp) REVERT: G 117 GLU cc_start: 0.7560 (tp30) cc_final: 0.7214 (tp30) REVERT: G 141 ASN cc_start: 0.8296 (m-40) cc_final: 0.8093 (m110) REVERT: G 444 VAL cc_start: 0.8440 (m) cc_final: 0.8183 (p) REVERT: G 465 ILE cc_start: 0.7794 (pt) cc_final: 0.7386 (mt) REVERT: H 55 LYS cc_start: 0.7625 (mmmm) cc_final: 0.7311 (mmmm) REVERT: H 79 SER cc_start: 0.8301 (t) cc_final: 0.8009 (m) REVERT: H 143 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8582 (mttt) REVERT: H 205 GLU cc_start: 0.6305 (mp0) cc_final: 0.5955 (mp0) outliers start: 58 outliers final: 44 residues processed: 503 average time/residue: 1.5473 time to fit residues: 878.2610 Evaluate side-chains 517 residues out of total 2596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 467 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 541 LYS Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 465 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 455 ASN Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 185 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 2.9990 chunk 208 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 455 ASN A 461 ASN C 56 ASN C 147 ASN C 492 GLN C 538 GLN D 38 ASN E 79 ASN ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 GLN F 105 ASN F 213 ASN F 255 ASN G 538 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.150236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116919 restraints weight = 33399.963| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.20 r_work: 0.3269 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23845 Z= 0.324 Angle : 0.602 9.805 32025 Z= 0.323 Chirality : 0.044 0.168 3517 Planarity : 0.004 0.043 4075 Dihedral : 4.378 25.831 3105 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.43 % Allowed : 19.95 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2837 helix: 0.78 (0.15), residues: 1156 sheet: 0.81 (0.22), residues: 563 loop : -0.83 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 126 HIS 0.005 0.001 HIS C 295 PHE 0.021 0.002 PHE A 315 TYR 0.024 0.001 TYR E 272 ARG 0.010 0.001 ARG E 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11917.50 seconds wall clock time: 207 minutes 43.30 seconds (12463.30 seconds total)