Starting phenix.real_space_refine on Tue Jul 23 13:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjy_41314/07_2024/8tjy_41314_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjy_41314/07_2024/8tjy_41314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjy_41314/07_2024/8tjy_41314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjy_41314/07_2024/8tjy_41314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjy_41314/07_2024/8tjy_41314_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjy_41314/07_2024/8tjy_41314_neut.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 14584 2.51 5 N 3748 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 22692 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "E" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "G" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3892 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1781 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 12.00, per 1000 atoms: 0.53 Number of scatterers: 22692 At special positions: 0 Unit cell: (164.64, 191.52, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 4296 8.00 N 3748 7.00 C 14584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.75 Conformation dependent library (CDL) restraints added in 4.2 seconds 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 20 sheets defined 49.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 310 through 313 removed outlier: 4.000A pdb=" N LYS A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.642A pdb=" N LEU A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 removed outlier: 4.632A pdb=" N SER A 357 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.559A pdb=" N LYS A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.869A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 493 Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.534A pdb=" N GLY A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.576A pdb=" N ASP A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 553 through 562 Processing helix chain 'A' and resid 566 through 573 removed outlier: 4.196A pdb=" N LYS A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.022A pdb=" N ILE B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.751A pdb=" N VAL B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 90 removed outlier: 5.764A pdb=" N LYS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.708A pdb=" N LEU B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 195 through 201 removed outlier: 4.393A pdb=" N TRP B 199 " --> pdb=" O ILE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'C' and resid 33 through 47 removed outlier: 3.670A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 84 through 91 Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 310 through 313 removed outlier: 3.997A pdb=" N LYS C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 310 through 313' Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.643A pdb=" N LEU C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 326 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.632A pdb=" N SER C 357 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.560A pdb=" N LYS C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.870A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 493 Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.539A pdb=" N GLY C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 503 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 528 removed outlier: 3.578A pdb=" N ASP C 515 " --> pdb=" O ASP C 511 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 540 through 550 Processing helix chain 'C' and resid 553 through 562 Processing helix chain 'C' and resid 566 through 573 removed outlier: 4.196A pdb=" N LYS C 570 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 removed outlier: 4.022A pdb=" N ILE D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 38 Processing helix chain 'D' and resid 50 through 62 Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.749A pdb=" N VAL D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 90 removed outlier: 5.764A pdb=" N LYS D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 3.598A pdb=" N GLY D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.681A pdb=" N LEU D 139 " --> pdb=" O PHE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 182 Processing helix chain 'D' and resid 195 through 201 removed outlier: 4.392A pdb=" N TRP D 199 " --> pdb=" O ILE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'E' and resid 33 through 47 removed outlier: 3.672A pdb=" N LEU E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 84 through 91 Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 310 through 313 removed outlier: 3.999A pdb=" N LYS E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 310 through 313' Processing helix chain 'E' and resid 321 through 326 removed outlier: 3.643A pdb=" N LEU E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 326 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 removed outlier: 4.625A pdb=" N SER E 357 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.558A pdb=" N LYS E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 368 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 395 Processing helix chain 'E' and resid 413 through 424 removed outlier: 3.705A pdb=" N THR E 419 " --> pdb=" O HIS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.864A pdb=" N LEU E 456 " --> pdb=" O ARG E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 493 Processing helix chain 'E' and resid 493 through 503 removed outlier: 3.530A pdb=" N GLY E 502 " --> pdb=" O GLY E 498 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 503 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 528 removed outlier: 3.577A pdb=" N ASP E 515 " --> pdb=" O ASP E 511 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU E 522 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER E 523 " --> pdb=" O ALA E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 538 Processing helix chain 'E' and resid 540 through 550 removed outlier: 3.556A pdb=" N MET E 545 " --> pdb=" O LYS E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 562 Processing helix chain 'E' and resid 566 through 573 removed outlier: 4.200A pdb=" N LYS E 570 " --> pdb=" O PHE E 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.063A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 38 Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 73 through 81 removed outlier: 3.752A pdb=" N VAL F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 90 removed outlier: 5.766A pdb=" N LYS F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP F 88 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O PHE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 3.536A pdb=" N GLY F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.681A pdb=" N LEU F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.575A pdb=" N ARG F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 168 through 182 Processing helix chain 'F' and resid 195 through 201 removed outlier: 4.391A pdb=" N TRP F 199 " --> pdb=" O ILE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'G' and resid 33 through 47 removed outlier: 3.671A pdb=" N LEU G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 52 Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 310 through 313 removed outlier: 3.998A pdb=" N LYS G 313 " --> pdb=" O SER G 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 310 through 313' Processing helix chain 'G' and resid 321 through 326 removed outlier: 3.644A pdb=" N LEU G 324 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 326 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 357 removed outlier: 4.627A pdb=" N SER G 357 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 removed outlier: 3.559A pdb=" N LYS G 364 " --> pdb=" O LYS G 360 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER G 368 " --> pdb=" O LYS G 364 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA G 369 " --> pdb=" O ALA G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 395 Processing helix chain 'G' and resid 413 through 424 removed outlier: 3.706A pdb=" N THR G 419 " --> pdb=" O HIS G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 456 removed outlier: 3.869A pdb=" N LEU G 456 " --> pdb=" O ARG G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 493 Processing helix chain 'G' and resid 493 through 503 removed outlier: 3.534A pdb=" N GLY G 502 " --> pdb=" O GLY G 498 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 503 " --> pdb=" O GLU G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 528 removed outlier: 3.578A pdb=" N ASP G 515 " --> pdb=" O ASP G 511 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU G 522 " --> pdb=" O SER G 518 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER G 523 " --> pdb=" O ALA G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 538 Processing helix chain 'G' and resid 540 through 550 Processing helix chain 'G' and resid 553 through 562 Processing helix chain 'G' and resid 566 through 573 removed outlier: 4.195A pdb=" N LYS G 570 " --> pdb=" O PHE G 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 removed outlier: 4.026A pdb=" N ILE H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 50 through 62 Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.748A pdb=" N VAL H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 5.766A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP H 88 " --> pdb=" O PRO H 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 89 " --> pdb=" O PHE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 119 removed outlier: 3.581A pdb=" N GLY H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 143 removed outlier: 3.678A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.574A pdb=" N ARG H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'H' and resid 168 through 182 Processing helix chain 'H' and resid 195 through 201 removed outlier: 4.395A pdb=" N TRP H 199 " --> pdb=" O ILE H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.728A pdb=" N LYS A 16 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS A 9 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A 18 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR A 7 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN A 20 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN A 5 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 2 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 74 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 6 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 72 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE A 8 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A 70 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 105 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL A 104 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU A 129 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 112 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 121 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER A 128 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 6.976A pdb=" N LYS A 24 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 334 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 26 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL A 336 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 28 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.510A pdb=" N ILE A 465 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.730A pdb=" N SER B 43 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N PHE B 160 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 45 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP B 162 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL B 47 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B 185 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 13 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY B 190 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 15 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 222 " --> pdb=" O THR B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 20 removed outlier: 6.727A pdb=" N LYS C 16 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS C 9 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN C 18 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C 7 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN C 20 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN C 5 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 2 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 74 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE C 6 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 72 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE C 8 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU C 70 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 105 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 10.378A pdb=" N VAL C 104 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU C 129 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS C 112 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN C 121 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER C 128 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.977A pdb=" N LYS C 24 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 334 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 26 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 336 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 28 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 403 through 407 Processing sheet with id=AA9, first strand: chain 'C' and resid 435 through 437 removed outlier: 3.512A pdb=" N ILE C 465 " --> pdb=" O TYR C 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER D 43 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE D 160 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA D 45 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP D 162 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL D 47 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 185 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 13 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY D 190 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 15 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 222 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.728A pdb=" N LYS E 16 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS E 9 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN E 18 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR E 7 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN E 20 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN E 5 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS E 2 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR E 74 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE E 6 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 72 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 8 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU E 70 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE E 105 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL E 104 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU E 129 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 112 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN E 121 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER E 128 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 154 removed outlier: 6.976A pdb=" N LYS E 24 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE E 334 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL E 26 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL E 336 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE E 28 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 403 through 407 Processing sheet with id=AB5, first strand: chain 'E' and resid 435 through 437 removed outlier: 3.507A pdb=" N ILE E 465 " --> pdb=" O TYR E 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 69 through 72 removed outlier: 6.732A pdb=" N SER F 43 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE F 160 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA F 45 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP F 162 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL F 47 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS F 185 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 13 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY F 190 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL F 15 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 222 " --> pdb=" O THR F 16 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 14 through 20 removed outlier: 6.730A pdb=" N LYS G 16 " --> pdb=" O LYS G 9 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS G 9 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN G 18 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR G 7 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN G 20 " --> pdb=" O ASN G 5 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN G 5 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 2 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR G 74 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE G 6 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE G 72 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE G 8 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU G 70 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE G 105 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL G 104 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU G 129 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS G 112 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN G 121 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER G 128 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 149 through 154 removed outlier: 6.977A pdb=" N LYS G 24 " --> pdb=" O ARG G 332 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE G 334 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 26 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL G 336 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE G 28 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 403 through 407 Processing sheet with id=AC1, first strand: chain 'G' and resid 435 through 437 removed outlier: 3.505A pdb=" N ILE G 465 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 69 through 72 removed outlier: 6.733A pdb=" N SER H 43 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE H 160 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA H 45 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP H 162 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL H 47 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS H 185 " --> pdb=" O PHE H 157 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE H 13 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY H 190 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL H 15 " --> pdb=" O GLY H 190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 222 " --> pdb=" O THR H 16 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 8.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7272 1.34 - 1.46: 4315 1.46 - 1.58: 11409 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 23104 Sorted by residual: bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 23099 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 403 107.34 - 113.99: 12977 113.99 - 120.65: 9645 120.65 - 127.31: 7892 127.31 - 133.96: 111 Bond angle restraints: 31028 Sorted by residual: angle pdb=" N TRP C 126 " pdb=" CA TRP C 126 " pdb=" CB TRP C 126 " ideal model delta sigma weight residual 111.05 115.89 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N TRP E 126 " pdb=" CA TRP E 126 " pdb=" CB TRP E 126 " ideal model delta sigma weight residual 111.05 115.89 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N TRP G 126 " pdb=" CA TRP G 126 " pdb=" CB TRP G 126 " ideal model delta sigma weight residual 111.05 115.89 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N TRP A 126 " pdb=" CA TRP A 126 " pdb=" CB TRP A 126 " ideal model delta sigma weight residual 111.05 115.81 -4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C TRP G 126 " pdb=" CA TRP G 126 " pdb=" CB TRP G 126 " ideal model delta sigma weight residual 110.24 105.69 4.55 1.88e+00 2.83e-01 5.85e+00 ... (remaining 31023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 12315 16.23 - 32.47: 1322 32.47 - 48.70: 325 48.70 - 64.93: 26 64.93 - 81.16: 16 Dihedral angle restraints: 14004 sinusoidal: 5844 harmonic: 8160 Sorted by residual: dihedral pdb=" CA LYS A 125 " pdb=" C LYS A 125 " pdb=" N TRP A 126 " pdb=" CA TRP A 126 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LYS G 125 " pdb=" C LYS G 125 " pdb=" N TRP G 126 " pdb=" CA TRP G 126 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LYS C 125 " pdb=" C LYS C 125 " pdb=" N TRP C 126 " pdb=" CA TRP C 126 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2148 0.029 - 0.058: 830 0.058 - 0.087: 183 0.087 - 0.116: 155 0.116 - 0.145: 80 Chirality restraints: 3396 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL G 93 " pdb=" N VAL G 93 " pdb=" C VAL G 93 " pdb=" CB VAL G 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL E 93 " pdb=" N VAL E 93 " pdb=" C VAL E 93 " pdb=" CB VAL E 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 3393 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 126 " -0.036 2.00e-02 2.50e+03 3.23e-02 2.60e+01 pdb=" CG TRP A 126 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP A 126 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 126 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 126 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 126 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 126 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 126 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 126 " 0.036 2.00e-02 2.50e+03 3.21e-02 2.58e+01 pdb=" CG TRP C 126 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP C 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C 126 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 126 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 126 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 126 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 126 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 126 " 0.036 2.00e-02 2.50e+03 3.20e-02 2.57e+01 pdb=" CG TRP G 126 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP G 126 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP G 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 126 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 126 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 126 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 126 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 126 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 126 " 0.005 2.00e-02 2.50e+03 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 174 2.60 - 3.18: 18334 3.18 - 3.75: 31678 3.75 - 4.33: 49626 4.33 - 4.90: 82827 Nonbonded interactions: 182639 Sorted by model distance: nonbonded pdb=" OE2 GLU E 393 " pdb=" OG1 THR E 554 " model vdw 2.031 2.440 nonbonded pdb=" OE2 GLU A 393 " pdb=" OG1 THR A 554 " model vdw 2.036 2.440 nonbonded pdb=" OE2 GLU G 393 " pdb=" OG1 THR G 554 " model vdw 2.039 2.440 nonbonded pdb=" OE2 GLU C 393 " pdb=" OG1 THR C 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 182634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 59.430 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23104 Z= 0.171 Angle : 0.469 4.841 31028 Z= 0.257 Chirality : 0.041 0.145 3396 Planarity : 0.003 0.051 3952 Dihedral : 13.842 81.163 8764 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2756 helix: 0.46 (0.15), residues: 1088 sheet: 0.52 (0.22), residues: 540 loop : -0.80 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.010 TRP A 126 HIS 0.003 0.001 HIS A 427 PHE 0.012 0.001 PHE A 315 TYR 0.013 0.001 TYR G 272 ARG 0.006 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ASN cc_start: 0.7878 (m-40) cc_final: 0.7678 (m110) REVERT: A 484 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6852 (mm-30) REVERT: A 538 GLN cc_start: 0.8286 (mt0) cc_final: 0.7983 (mt0) REVERT: B 29 SER cc_start: 0.7250 (m) cc_final: 0.6913 (m) REVERT: B 55 LYS cc_start: 0.7438 (tppp) cc_final: 0.7236 (mmmm) REVERT: B 180 ASP cc_start: 0.7298 (m-30) cc_final: 0.7005 (m-30) REVERT: C 1 MET cc_start: 0.7255 (tpt) cc_final: 0.6977 (tpt) REVERT: C 481 ARG cc_start: 0.7225 (tpp-160) cc_final: 0.6880 (mtt-85) REVERT: C 483 ASN cc_start: 0.7962 (m-40) cc_final: 0.7529 (m-40) REVERT: C 489 ILE cc_start: 0.8220 (mm) cc_final: 0.7986 (mp) REVERT: C 510 ILE cc_start: 0.8104 (mt) cc_final: 0.7690 (mt) REVERT: C 538 GLN cc_start: 0.8499 (mt0) cc_final: 0.8150 (mt0) REVERT: D 107 PHE cc_start: 0.6320 (t80) cc_final: 0.5748 (t80) REVERT: D 176 MET cc_start: 0.8291 (mmp) cc_final: 0.7706 (mmt) REVERT: D 180 ASP cc_start: 0.7348 (m-30) cc_final: 0.7032 (m-30) REVERT: D 208 ASN cc_start: 0.7921 (m-40) cc_final: 0.7712 (m-40) REVERT: E 56 ASN cc_start: 0.7882 (m-40) cc_final: 0.7672 (m110) REVERT: E 92 VAL cc_start: 0.8735 (t) cc_final: 0.8534 (m) REVERT: E 466 THR cc_start: 0.8335 (m) cc_final: 0.8106 (p) REVERT: E 484 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6829 (mm-30) REVERT: E 489 ILE cc_start: 0.7803 (mm) cc_final: 0.7554 (mp) REVERT: E 538 GLN cc_start: 0.8412 (mt0) cc_final: 0.8126 (mt0) REVERT: F 29 SER cc_start: 0.7769 (m) cc_final: 0.7481 (m) REVERT: F 34 ASP cc_start: 0.7739 (m-30) cc_final: 0.7488 (m-30) REVERT: F 212 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6815 (mp0) REVERT: G 56 ASN cc_start: 0.8047 (m-40) cc_final: 0.7826 (m110) REVERT: G 466 THR cc_start: 0.8258 (m) cc_final: 0.8020 (p) REVERT: G 481 ARG cc_start: 0.7069 (tpp-160) cc_final: 0.6823 (mtt-85) REVERT: G 538 GLN cc_start: 0.8385 (mt0) cc_final: 0.8015 (mt0) REVERT: H 29 SER cc_start: 0.7527 (m) cc_final: 0.7210 (m) REVERT: H 34 ASP cc_start: 0.7624 (m-30) cc_final: 0.7409 (m-30) REVERT: H 176 MET cc_start: 0.8183 (mmp) cc_final: 0.7862 (mmp) REVERT: H 180 ASP cc_start: 0.7284 (m-30) cc_final: 0.7038 (m-30) outliers start: 0 outliers final: 3 residues processed: 551 average time/residue: 1.5517 time to fit residues: 957.2282 Evaluate side-chains 455 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 452 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain D residue 93 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 147 ASN A 155 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN B 213 ASN C 147 ASN ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 213 ASN E 147 ASN E 155 ASN G 147 ASN G 155 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23104 Z= 0.249 Angle : 0.541 7.033 31028 Z= 0.297 Chirality : 0.043 0.155 3396 Planarity : 0.003 0.033 3952 Dihedral : 4.453 21.182 3018 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.83 % Allowed : 11.12 % Favored : 87.04 % 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: 2756 helix: 0.40 (0.15), residues: 1128 sheet: 0.85 (0.23), residues: 540 loop : -0.99 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP E 126 HIS 0.004 0.001 HIS F 41 PHE 0.018 0.002 PHE B 157 TYR 0.024 0.001 TYR E 272 ARG 0.005 0.000 ARG E 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 453 time to evaluate : 2.547 Fit side-chains REVERT: A 56 ASN cc_start: 0.7913 (m-40) cc_final: 0.7699 (m-40) REVERT: A 130 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8189 (tp) REVERT: A 484 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6822 (mm-30) REVERT: A 491 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7777 (ttmt) REVERT: A 538 GLN cc_start: 0.8387 (mt0) cc_final: 0.8070 (mt0) REVERT: B 29 SER cc_start: 0.7461 (m) cc_final: 0.7097 (m) REVERT: B 55 LYS cc_start: 0.7460 (tppp) cc_final: 0.7249 (mmmm) REVERT: C 1 MET cc_start: 0.7413 (tpt) cc_final: 0.7133 (tpt) REVERT: C 56 ASN cc_start: 0.7976 (m-40) cc_final: 0.7749 (m110) REVERT: C 130 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8258 (tp) REVERT: C 438 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8226 (tttp) REVERT: C 481 ARG cc_start: 0.7440 (tpp-160) cc_final: 0.7183 (mtt-85) REVERT: C 512 LEU cc_start: 0.8727 (tp) cc_final: 0.8501 (tp) REVERT: C 538 GLN cc_start: 0.8585 (mt0) cc_final: 0.8242 (mt0) REVERT: D 107 PHE cc_start: 0.6413 (t80) cc_final: 0.6066 (t80) REVERT: D 176 MET cc_start: 0.8355 (mmp) cc_final: 0.8130 (mmt) REVERT: D 185 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (mmtt) REVERT: D 191 ASP cc_start: 0.6679 (t0) cc_final: 0.5974 (p0) REVERT: E 50 ILE cc_start: 0.8429 (mm) cc_final: 0.8227 (mp) REVERT: E 56 ASN cc_start: 0.7866 (m-40) cc_final: 0.7665 (m110) REVERT: E 481 ARG cc_start: 0.7586 (tpp-160) cc_final: 0.7365 (mtt90) REVERT: E 484 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6853 (mm-30) REVERT: E 492 GLN cc_start: 0.7799 (tt0) cc_final: 0.7572 (tt0) REVERT: E 538 GLN cc_start: 0.8387 (mt0) cc_final: 0.8162 (mt0) REVERT: F 29 SER cc_start: 0.7828 (m) cc_final: 0.7500 (m) REVERT: F 34 ASP cc_start: 0.7723 (m-30) cc_final: 0.7435 (m-30) REVERT: F 180 ASP cc_start: 0.7535 (m-30) cc_final: 0.7289 (m-30) REVERT: G 56 ASN cc_start: 0.8023 (m-40) cc_final: 0.7802 (m110) REVERT: G 130 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8117 (tp) REVERT: G 434 ASP cc_start: 0.7080 (m-30) cc_final: 0.6735 (m-30) REVERT: G 480 GLU cc_start: 0.6837 (pt0) cc_final: 0.6539 (pt0) REVERT: G 489 ILE cc_start: 0.7919 (mm) cc_final: 0.7693 (mp) REVERT: G 538 GLN cc_start: 0.8417 (mt0) cc_final: 0.8083 (mt0) REVERT: H 29 SER cc_start: 0.7599 (m) cc_final: 0.7266 (m) REVERT: H 34 ASP cc_start: 0.7689 (m-30) cc_final: 0.7422 (m-30) REVERT: H 208 ASN cc_start: 0.7709 (m-40) cc_final: 0.7475 (m-40) outliers start: 46 outliers final: 24 residues processed: 469 average time/residue: 1.4866 time to fit residues: 783.5949 Evaluate side-chains 475 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 447 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 TYR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain C residue 40 TYR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain E residue 40 TYR Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain G residue 40 TYR Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 501 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 248 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 201 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 38 ASN B 213 ASN C 147 ASN C 350 ASN D 38 ASN D 208 ASN D 213 ASN E 79 ASN E 147 ASN E 155 ASN F 121 ASN F 181 GLN G 79 ASN G 147 ASN G 155 ASN H 173 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23104 Z= 0.272 Angle : 0.537 6.707 31028 Z= 0.294 Chirality : 0.043 0.150 3396 Planarity : 0.003 0.040 3952 Dihedral : 4.400 16.004 3012 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.99 % Allowed : 12.84 % Favored : 84.17 % 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: -0.16 (0.15), residues: 2756 helix: 0.26 (0.15), residues: 1144 sheet: 1.00 (0.23), residues: 540 loop : -1.01 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 126 HIS 0.005 0.001 HIS H 41 PHE 0.018 0.002 PHE B 157 TYR 0.025 0.001 TYR A 272 ARG 0.005 0.000 ARG G 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 464 time to evaluate : 2.610 Fit side-chains REVERT: A 56 ASN cc_start: 0.7945 (m-40) cc_final: 0.7743 (m110) REVERT: A 130 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 438 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8512 (ttmm) REVERT: A 459 ARG cc_start: 0.7772 (mpp-170) cc_final: 0.7381 (mtt180) REVERT: A 491 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7800 (ttmt) REVERT: A 529 GLU cc_start: 0.7069 (pm20) cc_final: 0.6617 (pm20) REVERT: A 538 GLN cc_start: 0.8357 (mt0) cc_final: 0.8085 (mt0) REVERT: A 555 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7491 (tmtm) REVERT: B 29 SER cc_start: 0.7542 (m) cc_final: 0.7190 (m) REVERT: B 55 LYS cc_start: 0.7495 (tppp) cc_final: 0.7294 (mmmm) REVERT: B 213 ASN cc_start: 0.7213 (m-40) cc_final: 0.6997 (m-40) REVERT: C 1 MET cc_start: 0.7300 (tpt) cc_final: 0.6987 (tpt) REVERT: C 56 ASN cc_start: 0.7973 (m-40) cc_final: 0.7766 (m110) REVERT: C 130 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8282 (tp) REVERT: C 264 MET cc_start: 0.6159 (mmm) cc_final: 0.5637 (mmm) REVERT: C 432 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7674 (p0) REVERT: C 434 ASP cc_start: 0.7143 (m-30) cc_final: 0.6698 (m-30) REVERT: C 438 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8377 (tttp) REVERT: C 480 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6678 (mp0) REVERT: C 481 ARG cc_start: 0.7417 (tpp-160) cc_final: 0.7181 (mtt90) REVERT: C 538 GLN cc_start: 0.8592 (mt0) cc_final: 0.8257 (mt0) REVERT: D 29 SER cc_start: 0.7426 (m) cc_final: 0.6949 (p) REVERT: D 176 MET cc_start: 0.8315 (mmp) cc_final: 0.7861 (mmt) REVERT: D 180 ASP cc_start: 0.7454 (m-30) cc_final: 0.7146 (m-30) REVERT: D 191 ASP cc_start: 0.6604 (t0) cc_final: 0.6345 (t0) REVERT: E 393 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: E 438 LYS cc_start: 0.8277 (tttp) cc_final: 0.8063 (tttp) REVERT: E 484 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6852 (mm-30) REVERT: E 492 GLN cc_start: 0.7854 (tt0) cc_final: 0.7639 (tt0) REVERT: E 538 GLN cc_start: 0.8347 (mt0) cc_final: 0.8130 (mt0) REVERT: E 541 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7779 (mmpt) REVERT: F 29 SER cc_start: 0.7846 (m) cc_final: 0.7520 (m) REVERT: F 180 ASP cc_start: 0.7554 (m-30) cc_final: 0.7298 (m-30) REVERT: F 208 ASN cc_start: 0.7455 (m-40) cc_final: 0.7251 (m110) REVERT: G 56 ASN cc_start: 0.8015 (m-40) cc_final: 0.7809 (m110) REVERT: G 130 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8085 (tp) REVERT: G 434 ASP cc_start: 0.7080 (m-30) cc_final: 0.6805 (m-30) REVERT: G 438 LYS cc_start: 0.8425 (tttp) cc_final: 0.8196 (tttp) REVERT: G 480 GLU cc_start: 0.6858 (pt0) cc_final: 0.6562 (pt0) REVERT: G 538 GLN cc_start: 0.8419 (mt0) cc_final: 0.8140 (mt0) REVERT: G 541 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7364 (mmpt) REVERT: H 29 SER cc_start: 0.7617 (m) cc_final: 0.7293 (m) REVERT: H 121 ASN cc_start: 0.7048 (t0) cc_final: 0.6581 (t0) outliers start: 75 outliers final: 27 residues processed: 493 average time/residue: 1.4292 time to fit residues: 794.5325 Evaluate side-chains 484 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 448 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 238 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN A 350 ASN C 147 ASN D 213 ASN E 132 ASN E 147 ASN E 155 ASN E 350 ASN G 147 ASN G 155 ASN H 208 ASN H 213 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23104 Z= 0.246 Angle : 0.517 8.629 31028 Z= 0.283 Chirality : 0.043 0.149 3396 Planarity : 0.003 0.039 3952 Dihedral : 4.357 15.888 3012 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.27 % Allowed : 14.31 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2756 helix: 0.18 (0.14), residues: 1168 sheet: 1.24 (0.23), residues: 528 loop : -1.04 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 126 HIS 0.004 0.001 HIS H 41 PHE 0.017 0.002 PHE B 157 TYR 0.024 0.001 TYR A 272 ARG 0.007 0.000 ARG G 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 452 time to evaluate : 2.772 Fit side-chains REVERT: A 130 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8173 (tp) REVERT: A 459 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7495 (mtt180) REVERT: A 491 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7790 (ttmt) REVERT: A 538 GLN cc_start: 0.8357 (mt0) cc_final: 0.8089 (mt0) REVERT: A 541 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7466 (mmpt) REVERT: A 555 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7493 (tmtm) REVERT: B 29 SER cc_start: 0.7597 (m) cc_final: 0.7217 (m) REVERT: B 55 LYS cc_start: 0.7495 (tppp) cc_final: 0.7287 (mmmm) REVERT: C 1 MET cc_start: 0.7330 (tpt) cc_final: 0.7026 (tpt) REVERT: C 264 MET cc_start: 0.6212 (mmm) cc_final: 0.5678 (mmm) REVERT: C 393 GLU cc_start: 0.7502 (tp30) cc_final: 0.7177 (mp0) REVERT: C 432 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7670 (p0) REVERT: C 434 ASP cc_start: 0.7121 (m-30) cc_final: 0.6580 (m-30) REVERT: C 480 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6606 (mp0) REVERT: C 481 ARG cc_start: 0.7386 (tpp-160) cc_final: 0.7173 (mtt90) REVERT: C 538 GLN cc_start: 0.8560 (mt0) cc_final: 0.8194 (mt0) REVERT: D 29 SER cc_start: 0.7429 (m) cc_final: 0.6969 (p) REVERT: D 180 ASP cc_start: 0.7467 (m-30) cc_final: 0.7261 (m-30) REVERT: D 191 ASP cc_start: 0.6616 (t0) cc_final: 0.6363 (t0) REVERT: E 393 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: E 492 GLN cc_start: 0.7835 (tt0) cc_final: 0.7634 (tt0) REVERT: E 538 GLN cc_start: 0.8351 (mt0) cc_final: 0.8128 (mt0) REVERT: E 541 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7778 (mmpt) REVERT: F 29 SER cc_start: 0.7836 (m) cc_final: 0.7516 (m) REVERT: F 121 ASN cc_start: 0.6976 (t160) cc_final: 0.6464 (t0) REVERT: F 180 ASP cc_start: 0.7537 (m-30) cc_final: 0.7281 (m-30) REVERT: G 56 ASN cc_start: 0.8012 (m-40) cc_final: 0.7810 (m110) REVERT: G 130 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (tp) REVERT: G 432 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7717 (p0) REVERT: G 434 ASP cc_start: 0.7127 (m-30) cc_final: 0.6635 (m-30) REVERT: G 438 LYS cc_start: 0.8434 (tttp) cc_final: 0.8184 (tttp) REVERT: G 538 GLN cc_start: 0.8430 (mt0) cc_final: 0.8146 (mt0) REVERT: G 541 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7357 (mmpt) REVERT: H 29 SER cc_start: 0.7631 (m) cc_final: 0.7310 (m) REVERT: H 121 ASN cc_start: 0.7029 (t0) cc_final: 0.6600 (t0) outliers start: 82 outliers final: 45 residues processed: 488 average time/residue: 1.4201 time to fit residues: 781.5961 Evaluate side-chains 498 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 443 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 384 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 541 LYS Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN C 461 ASN E 132 ASN E 147 ASN E 155 ASN F 181 GLN F 208 ASN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 23104 Z= 0.503 Angle : 0.660 8.369 31028 Z= 0.353 Chirality : 0.048 0.156 3396 Planarity : 0.004 0.061 3952 Dihedral : 4.811 18.269 3012 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.91 % Allowed : 15.27 % Favored : 80.82 % 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: -0.49 (0.15), residues: 2756 helix: -0.14 (0.14), residues: 1132 sheet: 1.15 (0.23), residues: 532 loop : -1.19 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 126 HIS 0.006 0.001 HIS H 41 PHE 0.026 0.003 PHE F 157 TYR 0.023 0.002 TYR G 272 ARG 0.009 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 457 time to evaluate : 2.540 Fit side-chains REVERT: A 130 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8245 (tp) REVERT: A 499 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6784 (mt-10) REVERT: A 538 GLN cc_start: 0.8348 (mt0) cc_final: 0.8025 (mt0) REVERT: A 541 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7429 (mmpt) REVERT: A 555 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7530 (tmtm) REVERT: B 29 SER cc_start: 0.7630 (m) cc_final: 0.7276 (m) REVERT: B 180 ASP cc_start: 0.7499 (m-30) cc_final: 0.7236 (m-30) REVERT: C 264 MET cc_start: 0.6261 (mmm) cc_final: 0.5671 (mmm) REVERT: C 393 GLU cc_start: 0.7527 (tp30) cc_final: 0.7082 (mp0) REVERT: C 432 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7728 (p0) REVERT: C 434 ASP cc_start: 0.7142 (m-30) cc_final: 0.6679 (m-30) REVERT: C 480 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6731 (mp0) REVERT: C 481 ARG cc_start: 0.7507 (tpp-160) cc_final: 0.7263 (mtt90) REVERT: C 538 GLN cc_start: 0.8571 (mt0) cc_final: 0.8221 (mt0) REVERT: D 29 SER cc_start: 0.7462 (m) cc_final: 0.7058 (p) REVERT: D 180 ASP cc_start: 0.7546 (m-30) cc_final: 0.7337 (m-30) REVERT: D 191 ASP cc_start: 0.6626 (t0) cc_final: 0.6376 (t0) REVERT: E 148 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7880 (m) REVERT: E 393 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: E 432 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (p0) REVERT: E 434 ASP cc_start: 0.7182 (m-30) cc_final: 0.6962 (m-30) REVERT: E 495 ASN cc_start: 0.8709 (m-40) cc_final: 0.8456 (m-40) REVERT: E 538 GLN cc_start: 0.8405 (mt0) cc_final: 0.8142 (mt0) REVERT: E 571 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: F 29 SER cc_start: 0.7845 (m) cc_final: 0.7515 (m) REVERT: F 121 ASN cc_start: 0.6881 (t160) cc_final: 0.6310 (t0) REVERT: F 191 ASP cc_start: 0.6832 (t0) cc_final: 0.6449 (p0) REVERT: G 56 ASN cc_start: 0.8043 (m-40) cc_final: 0.7833 (m110) REVERT: G 130 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8115 (tp) REVERT: G 393 GLU cc_start: 0.7601 (tp30) cc_final: 0.7310 (mp0) REVERT: G 432 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7650 (p0) REVERT: G 434 ASP cc_start: 0.7106 (m-30) cc_final: 0.6744 (m-30) REVERT: G 438 LYS cc_start: 0.8434 (tttp) cc_final: 0.8144 (tttp) REVERT: G 480 GLU cc_start: 0.7054 (mp0) cc_final: 0.6767 (mp0) REVERT: G 538 GLN cc_start: 0.8443 (mt0) cc_final: 0.8128 (mt0) REVERT: H 29 SER cc_start: 0.7635 (m) cc_final: 0.7298 (m) REVERT: H 121 ASN cc_start: 0.6972 (t0) cc_final: 0.6368 (t0) outliers start: 98 outliers final: 47 residues processed: 502 average time/residue: 1.4254 time to fit residues: 808.6440 Evaluate side-chains 503 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 446 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 185 LYS Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 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 147 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN E 132 ASN E 147 ASN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23104 Z= 0.228 Angle : 0.512 6.411 31028 Z= 0.281 Chirality : 0.043 0.148 3396 Planarity : 0.003 0.046 3952 Dihedral : 4.467 17.890 3012 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.59 % Allowed : 16.71 % Favored : 79.70 % 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: -0.17 (0.15), residues: 2756 helix: 0.20 (0.14), residues: 1144 sheet: 1.15 (0.22), residues: 540 loop : -1.05 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 126 HIS 0.004 0.001 HIS H 41 PHE 0.017 0.001 PHE B 157 TYR 0.024 0.001 TYR G 272 ARG 0.009 0.000 ARG G 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 453 time to evaluate : 2.747 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8161 (tp) REVERT: A 499 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6874 (mt-10) REVERT: A 538 GLN cc_start: 0.8315 (mt0) cc_final: 0.8033 (mt0) REVERT: A 541 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7433 (mmpt) REVERT: A 555 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7485 (tmtm) REVERT: B 29 SER cc_start: 0.7604 (m) cc_final: 0.7248 (m) REVERT: B 158 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8210 (ttmm) REVERT: C 264 MET cc_start: 0.6304 (mmm) cc_final: 0.5711 (mmm) REVERT: C 324 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8681 (mt) REVERT: C 393 GLU cc_start: 0.7522 (tp30) cc_final: 0.7105 (mp0) REVERT: C 432 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7753 (p0) REVERT: C 434 ASP cc_start: 0.7128 (m-30) cc_final: 0.6640 (m-30) REVERT: C 438 LYS cc_start: 0.8569 (tttm) cc_final: 0.8170 (ttmm) REVERT: C 538 GLN cc_start: 0.8578 (mt0) cc_final: 0.8179 (mt0) REVERT: D 29 SER cc_start: 0.7452 (m) cc_final: 0.7010 (p) REVERT: D 191 ASP cc_start: 0.6686 (t0) cc_final: 0.6431 (t0) REVERT: E 348 MET cc_start: 0.8639 (tpt) cc_final: 0.8346 (tpt) REVERT: E 393 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: E 432 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7894 (p0) REVERT: E 434 ASP cc_start: 0.7160 (m-30) cc_final: 0.6911 (m-30) REVERT: E 492 GLN cc_start: 0.7820 (tt0) cc_final: 0.7601 (tt0) REVERT: E 538 GLN cc_start: 0.8350 (mt0) cc_final: 0.8131 (mt0) REVERT: E 571 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: F 29 SER cc_start: 0.7855 (m) cc_final: 0.7541 (m) REVERT: F 121 ASN cc_start: 0.6939 (t160) cc_final: 0.6460 (t0) REVERT: F 191 ASP cc_start: 0.6870 (t0) cc_final: 0.6203 (p0) REVERT: G 264 MET cc_start: 0.6403 (mmm) cc_final: 0.6110 (mmt) REVERT: G 432 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7756 (p0) REVERT: G 434 ASP cc_start: 0.7097 (m-30) cc_final: 0.6747 (m-30) REVERT: G 438 LYS cc_start: 0.8435 (tttp) cc_final: 0.8157 (tttp) REVERT: G 480 GLU cc_start: 0.6821 (mp0) cc_final: 0.6545 (mp0) REVERT: G 526 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7439 (ttm110) REVERT: G 538 GLN cc_start: 0.8413 (mt0) cc_final: 0.8109 (mt0) REVERT: H 29 SER cc_start: 0.7653 (m) cc_final: 0.7326 (m) REVERT: H 121 ASN cc_start: 0.6995 (t0) cc_final: 0.6523 (t0) outliers start: 90 outliers final: 48 residues processed: 493 average time/residue: 1.4470 time to fit residues: 804.7825 Evaluate side-chains 511 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 453 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 432 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 224 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 166 optimal weight: 0.0270 chunk 162 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN E 132 ASN E 147 ASN E 155 ASN F 181 GLN G 147 ASN G 155 ASN G 350 ASN H 213 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23104 Z= 0.220 Angle : 0.509 6.450 31028 Z= 0.278 Chirality : 0.042 0.148 3396 Planarity : 0.003 0.050 3952 Dihedral : 4.373 17.704 3012 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.11 % Allowed : 17.50 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 2756 helix: 0.39 (0.14), residues: 1144 sheet: 1.08 (0.23), residues: 548 loop : -1.00 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 126 HIS 0.004 0.001 HIS H 41 PHE 0.015 0.001 PHE B 157 TYR 0.025 0.001 TYR E 272 ARG 0.010 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 461 time to evaluate : 2.572 Fit side-chains revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7752 (ttmp) REVERT: A 526 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7313 (ttm110) REVERT: A 538 GLN cc_start: 0.8281 (mt0) cc_final: 0.8019 (mt0) REVERT: A 541 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7434 (mmpt) REVERT: A 555 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7447 (tmtm) REVERT: A 571 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: B 29 SER cc_start: 0.7607 (m) cc_final: 0.7246 (m) REVERT: B 107 PHE cc_start: 0.6603 (m-80) cc_final: 0.6257 (m-80) REVERT: C 264 MET cc_start: 0.6362 (mmm) cc_final: 0.5766 (mmm) REVERT: C 324 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8677 (mt) REVERT: C 393 GLU cc_start: 0.7528 (tp30) cc_final: 0.7195 (mp0) REVERT: C 432 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7779 (p0) REVERT: C 434 ASP cc_start: 0.7147 (m-30) cc_final: 0.6690 (m-30) REVERT: C 438 LYS cc_start: 0.8570 (tttm) cc_final: 0.8217 (ttmm) REVERT: C 538 GLN cc_start: 0.8545 (mt0) cc_final: 0.8190 (mt0) REVERT: D 29 SER cc_start: 0.7500 (m) cc_final: 0.7084 (p) REVERT: D 191 ASP cc_start: 0.6694 (t0) cc_final: 0.6426 (t0) REVERT: E 150 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8043 (tmtm) REVERT: E 348 MET cc_start: 0.8605 (tpt) cc_final: 0.8289 (tpt) REVERT: E 393 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: E 492 GLN cc_start: 0.7846 (tt0) cc_final: 0.7628 (tt0) REVERT: E 504 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8171 (mtt180) REVERT: E 538 GLN cc_start: 0.8319 (mt0) cc_final: 0.8099 (mt0) REVERT: E 564 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6558 (mm-30) REVERT: F 29 SER cc_start: 0.7882 (m) cc_final: 0.7580 (m) REVERT: F 121 ASN cc_start: 0.6955 (t160) cc_final: 0.6473 (t0) REVERT: F 191 ASP cc_start: 0.6871 (t0) cc_final: 0.6187 (p0) REVERT: G 264 MET cc_start: 0.6407 (mmm) cc_final: 0.6111 (mmt) REVERT: G 434 ASP cc_start: 0.7104 (m-30) cc_final: 0.6628 (m-30) REVERT: G 538 GLN cc_start: 0.8422 (mt0) cc_final: 0.8130 (mt0) REVERT: H 29 SER cc_start: 0.7661 (m) cc_final: 0.7328 (m) REVERT: H 121 ASN cc_start: 0.7010 (t0) cc_final: 0.6537 (t0) outliers start: 78 outliers final: 48 residues processed: 503 average time/residue: 1.4679 time to fit residues: 830.8630 Evaluate side-chains 512 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 457 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 chunk 209 optimal weight: 2.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 147 ASN E 132 ASN E 155 ASN G 147 ASN G 155 ASN H 213 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23104 Z= 0.280 Angle : 0.541 6.523 31028 Z= 0.294 Chirality : 0.044 0.150 3396 Planarity : 0.004 0.054 3952 Dihedral : 4.455 19.487 3012 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.31 % Allowed : 18.06 % Favored : 78.63 % 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: -0.09 (0.15), residues: 2756 helix: 0.32 (0.14), residues: 1144 sheet: 1.07 (0.22), residues: 548 loop : -1.01 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 126 HIS 0.004 0.001 HIS H 41 PHE 0.019 0.002 PHE B 157 TYR 0.024 0.001 TYR E 272 ARG 0.013 0.000 ARG G 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 458 time to evaluate : 2.739 Fit side-chains revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7794 (ttmt) REVERT: A 538 GLN cc_start: 0.8333 (mt0) cc_final: 0.7991 (mt0) REVERT: A 541 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7428 (mmpt) REVERT: A 555 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7473 (tmtm) REVERT: A 571 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: B 29 SER cc_start: 0.7613 (m) cc_final: 0.7246 (m) REVERT: B 107 PHE cc_start: 0.6580 (m-80) cc_final: 0.6235 (m-80) REVERT: B 158 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7906 (ttpt) REVERT: C 264 MET cc_start: 0.6390 (mmm) cc_final: 0.5789 (mmm) REVERT: C 324 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8692 (mt) REVERT: C 393 GLU cc_start: 0.7543 (tp30) cc_final: 0.7096 (mp0) REVERT: C 432 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7770 (p0) REVERT: C 434 ASP cc_start: 0.7130 (m-30) cc_final: 0.6656 (m-30) REVERT: C 438 LYS cc_start: 0.8576 (tttm) cc_final: 0.7934 (ttmt) REVERT: C 480 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: C 538 GLN cc_start: 0.8577 (mt0) cc_final: 0.8190 (mt0) REVERT: D 29 SER cc_start: 0.7500 (m) cc_final: 0.7092 (p) REVERT: D 191 ASP cc_start: 0.6671 (t0) cc_final: 0.6410 (t0) REVERT: E 150 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8032 (tmtm) REVERT: E 348 MET cc_start: 0.8628 (tpt) cc_final: 0.8360 (tpt) REVERT: E 393 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: E 504 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8161 (mtt180) REVERT: E 571 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: F 29 SER cc_start: 0.7869 (m) cc_final: 0.7555 (m) REVERT: F 61 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7787 (mp) REVERT: F 121 ASN cc_start: 0.6942 (t160) cc_final: 0.6471 (t0) REVERT: F 191 ASP cc_start: 0.6869 (t0) cc_final: 0.6217 (p0) REVERT: G 264 MET cc_start: 0.6428 (mmm) cc_final: 0.6119 (mmt) REVERT: G 393 GLU cc_start: 0.7609 (tp30) cc_final: 0.7379 (mm-30) REVERT: G 434 ASP cc_start: 0.7094 (m-30) cc_final: 0.6613 (m-30) REVERT: G 438 LYS cc_start: 0.8389 (tttp) cc_final: 0.8179 (tttp) REVERT: G 526 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7416 (ttm110) REVERT: G 538 GLN cc_start: 0.8417 (mt0) cc_final: 0.8110 (mt0) REVERT: H 29 SER cc_start: 0.7664 (m) cc_final: 0.7335 (m) REVERT: H 121 ASN cc_start: 0.7021 (t0) cc_final: 0.6515 (t0) outliers start: 83 outliers final: 54 residues processed: 500 average time/residue: 1.4497 time to fit residues: 815.6974 Evaluate side-chains 520 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 455 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 232 optimal weight: 0.2980 chunk 247 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 194 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 224 optimal weight: 0.0370 chunk 234 optimal weight: 2.9990 chunk 162 optimal weight: 0.0570 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN E 5 ASN E 18 ASN E 132 ASN E 538 GLN G 147 ASN G 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23104 Z= 0.124 Angle : 0.467 5.918 31028 Z= 0.255 Chirality : 0.041 0.149 3396 Planarity : 0.003 0.062 3952 Dihedral : 4.135 19.188 3012 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.83 % Allowed : 19.94 % Favored : 78.23 % 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: 0.34 (0.16), residues: 2756 helix: 0.79 (0.15), residues: 1144 sheet: 1.20 (0.23), residues: 540 loop : -0.87 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 126 HIS 0.002 0.000 HIS H 41 PHE 0.009 0.001 PHE A 500 TYR 0.025 0.001 TYR E 272 ARG 0.013 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 469 time to evaluate : 2.584 Fit side-chains revert: symmetry clash REVERT: A 491 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7662 (ttmt) REVERT: A 526 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7310 (ttm110) REVERT: A 538 GLN cc_start: 0.8226 (mt0) cc_final: 0.7945 (mt0) REVERT: A 555 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7431 (tmtm) REVERT: B 29 SER cc_start: 0.7615 (m) cc_final: 0.7260 (m) REVERT: B 158 LYS cc_start: 0.8441 (tppt) cc_final: 0.8227 (ttmm) REVERT: B 180 ASP cc_start: 0.7343 (m-30) cc_final: 0.7065 (m-30) REVERT: C 264 MET cc_start: 0.6392 (mmm) cc_final: 0.5782 (mmm) REVERT: C 393 GLU cc_start: 0.7545 (tp30) cc_final: 0.7216 (mp0) REVERT: C 432 ASP cc_start: 0.8049 (p0) cc_final: 0.7779 (p0) REVERT: C 434 ASP cc_start: 0.7125 (m-30) cc_final: 0.6628 (m-30) REVERT: C 438 LYS cc_start: 0.8591 (tttm) cc_final: 0.8123 (ttmt) REVERT: C 480 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: C 538 GLN cc_start: 0.8515 (mt0) cc_final: 0.8202 (mt0) REVERT: D 29 SER cc_start: 0.7505 (m) cc_final: 0.7071 (p) REVERT: D 191 ASP cc_start: 0.6725 (t0) cc_final: 0.6438 (t0) REVERT: E 348 MET cc_start: 0.8554 (tpt) cc_final: 0.8129 (tpt) REVERT: E 393 GLU cc_start: 0.7490 (tp30) cc_final: 0.7153 (mp0) REVERT: E 504 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8165 (mtt90) REVERT: F 29 SER cc_start: 0.7877 (m) cc_final: 0.7574 (m) REVERT: F 61 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7704 (mp) REVERT: F 121 ASN cc_start: 0.7006 (t160) cc_final: 0.6780 (t0) REVERT: F 191 ASP cc_start: 0.6855 (t0) cc_final: 0.6101 (p0) REVERT: G 264 MET cc_start: 0.6439 (mmm) cc_final: 0.6122 (mmt) REVERT: G 526 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7229 (ttm110) REVERT: G 538 GLN cc_start: 0.8385 (mt0) cc_final: 0.8113 (mt0) REVERT: H 29 SER cc_start: 0.7664 (m) cc_final: 0.7357 (m) REVERT: H 121 ASN cc_start: 0.6973 (t0) cc_final: 0.6588 (t0) outliers start: 46 outliers final: 25 residues processed: 492 average time/residue: 1.4635 time to fit residues: 816.1377 Evaluate side-chains 487 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 459 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 219 LYS Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 431 THR Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN C 147 ASN D 173 ASN E 5 ASN E 18 ASN E 56 ASN E 132 ASN E 155 ASN E 538 GLN G 18 ASN G 147 ASN G 155 ASN G 305 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23104 Z= 0.241 Angle : 0.530 7.641 31028 Z= 0.287 Chirality : 0.043 0.149 3396 Planarity : 0.003 0.062 3952 Dihedral : 4.306 19.012 3012 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.52 % Allowed : 20.57 % Favored : 77.91 % 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: 0.20 (0.16), residues: 2756 helix: 0.65 (0.15), residues: 1144 sheet: 1.14 (0.23), residues: 548 loop : -0.92 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 126 HIS 0.004 0.001 HIS H 41 PHE 0.020 0.002 PHE A 500 TYR 0.024 0.001 TYR E 272 ARG 0.012 0.000 ARG A 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 468 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 SER cc_start: 0.8088 (p) cc_final: 0.7871 (t) REVERT: A 491 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7759 (ttmt) REVERT: A 526 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7346 (ttm110) REVERT: A 538 GLN cc_start: 0.8257 (mt0) cc_final: 0.7953 (mt0) REVERT: A 555 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7455 (tmtm) REVERT: B 29 SER cc_start: 0.7645 (m) cc_final: 0.7299 (m) REVERT: B 107 PHE cc_start: 0.6565 (m-80) cc_final: 0.6264 (m-80) REVERT: B 158 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8201 (ttmm) REVERT: B 180 ASP cc_start: 0.7395 (m-30) cc_final: 0.7097 (m-30) REVERT: C 264 MET cc_start: 0.6426 (mmm) cc_final: 0.5801 (mmm) REVERT: C 324 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 393 GLU cc_start: 0.7544 (tp30) cc_final: 0.7206 (mp0) REVERT: C 438 LYS cc_start: 0.8566 (tttm) cc_final: 0.8056 (ttmt) REVERT: C 480 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: C 481 ARG cc_start: 0.7305 (mtt180) cc_final: 0.7094 (mtt180) REVERT: C 538 GLN cc_start: 0.8571 (mt0) cc_final: 0.8216 (mt0) REVERT: D 29 SER cc_start: 0.7509 (m) cc_final: 0.7106 (p) REVERT: D 191 ASP cc_start: 0.6692 (t0) cc_final: 0.6426 (t0) REVERT: E 348 MET cc_start: 0.8610 (tpt) cc_final: 0.8290 (tpt) REVERT: E 393 GLU cc_start: 0.7498 (tp30) cc_final: 0.7171 (mp0) REVERT: E 504 ARG cc_start: 0.8381 (mtt90) cc_final: 0.8162 (mtt90) REVERT: F 29 SER cc_start: 0.7873 (m) cc_final: 0.7569 (m) REVERT: F 61 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7809 (mp) REVERT: F 121 ASN cc_start: 0.6985 (t160) cc_final: 0.6745 (t0) REVERT: F 191 ASP cc_start: 0.6855 (t0) cc_final: 0.6172 (p0) REVERT: G 264 MET cc_start: 0.6475 (mmm) cc_final: 0.6139 (mmt) REVERT: G 393 GLU cc_start: 0.7587 (tp30) cc_final: 0.7351 (mm-30) REVERT: G 434 ASP cc_start: 0.7055 (m-30) cc_final: 0.6804 (m-30) REVERT: G 526 ARG cc_start: 0.7804 (mtm110) cc_final: 0.7314 (ttm110) REVERT: G 538 GLN cc_start: 0.8415 (mt0) cc_final: 0.8126 (mt0) REVERT: H 29 SER cc_start: 0.7686 (m) cc_final: 0.7362 (m) REVERT: H 121 ASN cc_start: 0.6966 (t0) cc_final: 0.6529 (t0) outliers start: 38 outliers final: 26 residues processed: 487 average time/residue: 1.4999 time to fit residues: 822.8063 Evaluate side-chains 492 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 461 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 154 SER Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 155 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN C 147 ASN E 132 ASN E 155 ASN E 538 GLN G 147 ASN G 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111127 restraints weight = 31679.968| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.96 r_work: 0.3268 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23104 Z= 0.209 Angle : 0.515 7.740 31028 Z= 0.280 Chirality : 0.042 0.148 3396 Planarity : 0.003 0.058 3952 Dihedral : 4.290 21.596 3012 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.71 % Allowed : 20.37 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2756 helix: 0.70 (0.15), residues: 1144 sheet: 1.14 (0.23), residues: 548 loop : -0.91 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 126 HIS 0.003 0.001 HIS H 41 PHE 0.019 0.001 PHE A 500 TYR 0.024 0.001 TYR E 272 ARG 0.012 0.000 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11370.95 seconds wall clock time: 198 minutes 1.82 seconds (11881.82 seconds total)