Starting phenix.real_space_refine on Mon Mar 25 10:10:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vd8_43145/03_2024/8vd8_43145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vd8_43145/03_2024/8vd8_43145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vd8_43145/03_2024/8vd8_43145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vd8_43145/03_2024/8vd8_43145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vd8_43145/03_2024/8vd8_43145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vd8_43145/03_2024/8vd8_43145.pdb" } resolution = 3.2 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= 0.007 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 132 5.16 5 C 30036 2.51 5 N 8112 2.21 5 O 9600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 364": "OD1" <-> "OD2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 364": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 364": "OD1" <-> "OD2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 364": "OD1" <-> "OD2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 364": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 364": "OD1" <-> "OD2" Residue "P TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 364": "OD1" <-> "OD2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 364": "OD1" <-> "OD2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 364": "OD1" <-> "OD2" Residue "V TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 364": "OD1" <-> "OD2" Residue "X TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47880 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "B" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "C" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "D" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "E" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "F" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "G" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "H" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "I" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "J" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "K" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "M" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "N" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "O" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "P" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "Q" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "R" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "S" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "T" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "U" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "V" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "W" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3819 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 10, 'TRANS': 455} Chain: "X" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 171 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Time building chain proxies: 22.25, per 1000 atoms: 0.46 Number of scatterers: 47880 At special positions: 0 Unit cell: (179.55, 179.55, 154.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 9600 8.00 N 8112 7.00 C 30036 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: 16.06 Conformation dependent library (CDL) restraints added in 7.9 seconds 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11088 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 72 sheets defined 50.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL A 27 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR A 423 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL C 27 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG C 59 " --> pdb=" O TYR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 261 through 282 removed outlier: 3.939A pdb=" N THR C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS C 304 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 358 Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR C 423 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL C 469 " --> pdb=" O PRO C 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL E 27 " --> pdb=" O GLU E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 40 Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR E 275 " --> pdb=" O ALA E 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS E 304 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 358 Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET E 376 " --> pdb=" O SER E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR E 423 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL G 27 " --> pdb=" O GLU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA G 123 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 282 " --> pdb=" O TYR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS G 304 " --> pdb=" O ARG G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 358 Processing helix chain 'G' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET G 376 " --> pdb=" O SER G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR G 389 " --> pdb=" O GLN G 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY G 397 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR G 423 " --> pdb=" O ASP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU G 458 " --> pdb=" O THR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL G 469 " --> pdb=" O PRO G 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL I 27 " --> pdb=" O GLU I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 40 Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG I 59 " --> pdb=" O TYR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 261 through 282 removed outlier: 3.939A pdb=" N THR I 275 " --> pdb=" O ALA I 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 282 " --> pdb=" O TYR I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS I 304 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 358 Processing helix chain 'I' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET I 376 " --> pdb=" O SER I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR I 389 " --> pdb=" O GLN I 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY I 397 " --> pdb=" O LEU I 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 400 " --> pdb=" O LYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR I 423 " --> pdb=" O ASP I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 446 Processing helix chain 'I' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU I 458 " --> pdb=" O THR I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL I 469 " --> pdb=" O PRO I 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 98 Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL K 27 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 40 Processing helix chain 'K' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG K 59 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP K 143 " --> pdb=" O SER K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR K 275 " --> pdb=" O ALA K 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 282 " --> pdb=" O TYR K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS K 304 " --> pdb=" O ARG K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 358 Processing helix chain 'K' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET K 376 " --> pdb=" O SER K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY K 397 " --> pdb=" O LEU K 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR K 423 " --> pdb=" O ASP K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 446 Processing helix chain 'K' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU K 458 " --> pdb=" O THR K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL K 469 " --> pdb=" O PRO K 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS K 470 " --> pdb=" O GLU K 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL M 27 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 40 Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG M 59 " --> pdb=" O TYR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR M 97 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA M 123 " --> pdb=" O ASP M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP M 143 " --> pdb=" O SER M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 170 No H-bonds generated for 'chain 'M' and resid 168 through 170' Processing helix chain 'M' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS M 304 " --> pdb=" O ARG M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 358 Processing helix chain 'M' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET M 376 " --> pdb=" O SER M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR M 389 " --> pdb=" O GLN M 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY M 397 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG M 400 " --> pdb=" O LYS M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR M 423 " --> pdb=" O ASP M 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 446 Processing helix chain 'M' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU M 458 " --> pdb=" O THR M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL M 469 " --> pdb=" O PRO M 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS M 470 " --> pdb=" O GLU M 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 98 Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL O 27 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 40 Processing helix chain 'O' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER O 46 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG O 59 " --> pdb=" O TYR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL O 75 " --> pdb=" O THR O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR O 97 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA O 123 " --> pdb=" O ASP O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP O 143 " --> pdb=" O SER O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 170 No H-bonds generated for 'chain 'O' and resid 168 through 170' Processing helix chain 'O' and resid 261 through 282 removed outlier: 3.939A pdb=" N THR O 275 " --> pdb=" O ALA O 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU O 282 " --> pdb=" O TYR O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS O 304 " --> pdb=" O ARG O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 358 Processing helix chain 'O' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET O 376 " --> pdb=" O SER O 372 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR O 389 " --> pdb=" O GLN O 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG O 400 " --> pdb=" O LYS O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR O 423 " --> pdb=" O ASP O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 446 Processing helix chain 'O' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU O 458 " --> pdb=" O THR O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL O 469 " --> pdb=" O PRO O 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS O 470 " --> pdb=" O GLU O 466 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 98 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL Q 27 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 40 Processing helix chain 'Q' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER Q 46 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG Q 59 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR Q 97 " --> pdb=" O ASP Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA Q 123 " --> pdb=" O ASP Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP Q 143 " --> pdb=" O SER Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 170 No H-bonds generated for 'chain 'Q' and resid 168 through 170' Processing helix chain 'Q' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR Q 275 " --> pdb=" O ALA Q 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU Q 282 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS Q 304 " --> pdb=" O ARG Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 358 Processing helix chain 'Q' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET Q 376 " --> pdb=" O SER Q 372 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR Q 389 " --> pdb=" O GLN Q 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY Q 397 " --> pdb=" O LEU Q 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Q 400 " --> pdb=" O LYS Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR Q 423 " --> pdb=" O ASP Q 420 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 446 Processing helix chain 'Q' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU Q 458 " --> pdb=" O THR Q 454 " (cutoff:3.500A) Processing helix chain 'Q' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL Q 469 " --> pdb=" O PRO Q 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS Q 470 " --> pdb=" O GLU Q 466 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 98 Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL S 27 " --> pdb=" O GLU S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 40 Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.774A pdb=" N SER S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS S 47 " --> pdb=" O ASN S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG S 59 " --> pdb=" O TYR S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL S 75 " --> pdb=" O THR S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR S 97 " --> pdb=" O ASP S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA S 123 " --> pdb=" O ASP S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP S 143 " --> pdb=" O SER S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 170 No H-bonds generated for 'chain 'S' and resid 168 through 170' Processing helix chain 'S' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR S 275 " --> pdb=" O ALA S 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU S 282 " --> pdb=" O TYR S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS S 304 " --> pdb=" O ARG S 301 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 358 Processing helix chain 'S' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET S 376 " --> pdb=" O SER S 372 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR S 389 " --> pdb=" O GLN S 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG S 400 " --> pdb=" O LYS S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR S 423 " --> pdb=" O ASP S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 446 Processing helix chain 'S' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU S 458 " --> pdb=" O THR S 454 " (cutoff:3.500A) Processing helix chain 'S' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL S 469 " --> pdb=" O PRO S 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS S 470 " --> pdb=" O GLU S 466 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 98 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL U 27 " --> pdb=" O GLU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 40 Processing helix chain 'U' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER U 46 " --> pdb=" O VAL U 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS U 47 " --> pdb=" O ASN U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG U 59 " --> pdb=" O TYR U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL U 75 " --> pdb=" O THR U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR U 97 " --> pdb=" O ASP U 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 132 removed outlier: 3.942A pdb=" N ALA U 123 " --> pdb=" O ASP U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP U 143 " --> pdb=" O SER U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 170 No H-bonds generated for 'chain 'U' and resid 168 through 170' Processing helix chain 'U' and resid 261 through 282 removed outlier: 3.939A pdb=" N THR U 275 " --> pdb=" O ALA U 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU U 282 " --> pdb=" O TYR U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 305 removed outlier: 4.183A pdb=" N LYS U 304 " --> pdb=" O ARG U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 338 through 358 Processing helix chain 'U' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET U 376 " --> pdb=" O SER U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR U 389 " --> pdb=" O GLN U 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY U 397 " --> pdb=" O LEU U 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 400 " --> pdb=" O LYS U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR U 423 " --> pdb=" O ASP U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 446 Processing helix chain 'U' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU U 458 " --> pdb=" O THR U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 464 through 479 removed outlier: 3.758A pdb=" N VAL U 469 " --> pdb=" O PRO U 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS U 470 " --> pdb=" O GLU U 466 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 98 Processing helix chain 'W' and resid 16 through 21 Processing helix chain 'W' and resid 23 through 27 removed outlier: 3.736A pdb=" N VAL W 27 " --> pdb=" O GLU W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 40 Processing helix chain 'W' and resid 42 through 55 removed outlier: 3.775A pdb=" N SER W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS W 47 " --> pdb=" O ASN W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 68 removed outlier: 4.134A pdb=" N ARG W 59 " --> pdb=" O TYR W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 76 removed outlier: 3.693A pdb=" N VAL W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 108 removed outlier: 3.519A pdb=" N TYR W 97 " --> pdb=" O ASP W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 removed outlier: 3.943A pdb=" N ALA W 123 " --> pdb=" O ASP W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 148 removed outlier: 3.547A pdb=" N ASP W 143 " --> pdb=" O SER W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 170 No H-bonds generated for 'chain 'W' and resid 168 through 170' Processing helix chain 'W' and resid 261 through 282 removed outlier: 3.940A pdb=" N THR W 275 " --> pdb=" O ALA W 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU W 282 " --> pdb=" O TYR W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 305 removed outlier: 4.184A pdb=" N LYS W 304 " --> pdb=" O ARG W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 358 Processing helix chain 'W' and resid 371 through 380 removed outlier: 3.685A pdb=" N MET W 376 " --> pdb=" O SER W 372 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 411 removed outlier: 4.089A pdb=" N THR W 389 " --> pdb=" O GLN W 385 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY W 397 " --> pdb=" O LEU W 393 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG W 400 " --> pdb=" O LYS W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 424 removed outlier: 3.626A pdb=" N THR W 423 " --> pdb=" O ASP W 420 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 446 Processing helix chain 'W' and resid 451 through 458 removed outlier: 3.544A pdb=" N LEU W 458 " --> pdb=" O THR W 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 464 through 479 removed outlier: 3.757A pdb=" N VAL W 469 " --> pdb=" O PRO W 465 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS W 470 " --> pdb=" O GLU W 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 92 through 98 Processing sheet with id= 1, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR A 29 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP A 177 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 184 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER A 234 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU A 219 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU A 232 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 11.211A pdb=" N ASN A 221 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id= 3, first strand: chain 'A' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR A 151 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 285 through 291 Processing sheet with id= 5, first strand: chain 'A' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN A 294 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 315 through 317 Processing sheet with id= 7, first strand: chain 'C' and resid 29 through 31 removed outlier: 7.054A pdb=" N TYR C 29 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP C 177 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER C 184 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER C 234 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU C 219 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN C 221 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 112 through 114 Processing sheet with id= 9, first strand: chain 'C' and resid 162 through 167 removed outlier: 4.028A pdb=" N TYR C 151 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 285 through 291 Processing sheet with id= 11, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN C 294 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 315 through 317 Processing sheet with id= 13, first strand: chain 'E' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR E 29 " --> pdb=" O TYR E 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP E 177 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER E 184 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER E 234 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU E 219 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU E 232 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN E 221 " --> pdb=" O PRO E 230 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 112 through 114 Processing sheet with id= 15, first strand: chain 'E' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR E 151 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 285 through 291 Processing sheet with id= 17, first strand: chain 'E' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN E 294 " --> pdb=" O ALA F 107 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 315 through 317 Processing sheet with id= 19, first strand: chain 'G' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR G 29 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP G 177 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER G 184 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER G 234 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU G 219 " --> pdb=" O GLU G 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU G 232 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 11.211A pdb=" N ASN G 221 " --> pdb=" O PRO G 230 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 112 through 114 Processing sheet with id= 21, first strand: chain 'G' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR G 151 " --> pdb=" O SER G 167 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 285 through 291 Processing sheet with id= 23, first strand: chain 'G' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN G 294 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 315 through 317 Processing sheet with id= 25, first strand: chain 'I' and resid 29 through 31 removed outlier: 7.054A pdb=" N TYR I 29 " --> pdb=" O TYR I 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP I 177 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER I 184 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER I 234 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU I 219 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU I 232 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN I 221 " --> pdb=" O PRO I 230 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 112 through 114 Processing sheet with id= 27, first strand: chain 'I' and resid 162 through 167 removed outlier: 4.028A pdb=" N TYR I 151 " --> pdb=" O SER I 167 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'I' and resid 285 through 291 Processing sheet with id= 29, first strand: chain 'I' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN I 294 " --> pdb=" O ALA J 107 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'I' and resid 315 through 317 Processing sheet with id= 31, first strand: chain 'K' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR K 29 " --> pdb=" O TYR K 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP K 177 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER K 184 " --> pdb=" O ASP K 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER K 234 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU K 219 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU K 232 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN K 221 " --> pdb=" O PRO K 230 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 112 through 114 Processing sheet with id= 33, first strand: chain 'K' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR K 151 " --> pdb=" O SER K 167 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'K' and resid 285 through 291 Processing sheet with id= 35, first strand: chain 'K' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN K 294 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 315 through 317 Processing sheet with id= 37, first strand: chain 'M' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR M 29 " --> pdb=" O TYR M 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP M 177 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER M 184 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER M 234 " --> pdb=" O ARG M 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU M 219 " --> pdb=" O GLU M 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU M 232 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 11.211A pdb=" N ASN M 221 " --> pdb=" O PRO M 230 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 112 through 114 Processing sheet with id= 39, first strand: chain 'M' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR M 151 " --> pdb=" O SER M 167 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'M' and resid 285 through 291 Processing sheet with id= 41, first strand: chain 'M' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN M 294 " --> pdb=" O ALA N 107 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'M' and resid 315 through 317 Processing sheet with id= 43, first strand: chain 'O' and resid 29 through 31 removed outlier: 7.054A pdb=" N TYR O 29 " --> pdb=" O TYR O 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP O 177 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER O 184 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER O 234 " --> pdb=" O ARG O 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU O 219 " --> pdb=" O GLU O 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU O 232 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN O 221 " --> pdb=" O PRO O 230 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 112 through 114 Processing sheet with id= 45, first strand: chain 'O' and resid 162 through 167 removed outlier: 4.028A pdb=" N TYR O 151 " --> pdb=" O SER O 167 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'O' and resid 285 through 291 Processing sheet with id= 47, first strand: chain 'O' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN O 294 " --> pdb=" O ALA P 107 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'O' and resid 315 through 317 Processing sheet with id= 49, first strand: chain 'Q' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR Q 29 " --> pdb=" O TYR Q 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP Q 177 " --> pdb=" O SER Q 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER Q 184 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER Q 234 " --> pdb=" O ARG Q 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU Q 232 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN Q 221 " --> pdb=" O PRO Q 230 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Q' and resid 112 through 114 Processing sheet with id= 51, first strand: chain 'Q' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR Q 151 " --> pdb=" O SER Q 167 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Q' and resid 285 through 291 Processing sheet with id= 53, first strand: chain 'Q' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN Q 294 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Q' and resid 315 through 317 Processing sheet with id= 55, first strand: chain 'S' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR S 29 " --> pdb=" O TYR S 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP S 177 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER S 184 " --> pdb=" O ASP S 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER S 234 " --> pdb=" O ARG S 217 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LEU S 219 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU S 232 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 11.211A pdb=" N ASN S 221 " --> pdb=" O PRO S 230 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 112 through 114 Processing sheet with id= 57, first strand: chain 'S' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR S 151 " --> pdb=" O SER S 167 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'S' and resid 285 through 291 Processing sheet with id= 59, first strand: chain 'S' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN S 294 " --> pdb=" O ALA T 107 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'S' and resid 315 through 317 Processing sheet with id= 61, first strand: chain 'U' and resid 29 through 31 removed outlier: 7.054A pdb=" N TYR U 29 " --> pdb=" O TYR U 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP U 177 " --> pdb=" O SER U 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER U 184 " --> pdb=" O ASP U 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER U 234 " --> pdb=" O ARG U 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU U 219 " --> pdb=" O GLU U 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU U 232 " --> pdb=" O LEU U 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN U 221 " --> pdb=" O PRO U 230 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 112 through 114 Processing sheet with id= 63, first strand: chain 'U' and resid 162 through 167 removed outlier: 4.028A pdb=" N TYR U 151 " --> pdb=" O SER U 167 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'U' and resid 285 through 291 Processing sheet with id= 65, first strand: chain 'U' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN U 294 " --> pdb=" O ALA V 107 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'U' and resid 315 through 317 Processing sheet with id= 67, first strand: chain 'W' and resid 29 through 31 removed outlier: 7.053A pdb=" N TYR W 29 " --> pdb=" O TYR W 176 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP W 177 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER W 184 " --> pdb=" O ASP W 177 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER W 234 " --> pdb=" O ARG W 217 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N LEU W 219 " --> pdb=" O GLU W 232 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU W 232 " --> pdb=" O LEU W 219 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N ASN W 221 " --> pdb=" O PRO W 230 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 112 through 114 Processing sheet with id= 69, first strand: chain 'W' and resid 162 through 167 removed outlier: 4.029A pdb=" N TYR W 151 " --> pdb=" O SER W 167 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'W' and resid 285 through 291 Processing sheet with id= 71, first strand: chain 'W' and resid 293 through 294 removed outlier: 6.332A pdb=" N ASN W 294 " --> pdb=" O ALA X 107 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'W' and resid 315 through 317 2328 hydrogen bonds defined for protein. 6624 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: 18.09 Time building geometry restraints manager: 17.63 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: 15748 1.34 - 1.45: 6688 1.45 - 1.57: 26008 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 48708 Sorted by residual: bond pdb=" N ASN K 16 " pdb=" CA ASN K 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN Q 16 " pdb=" CA ASN Q 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN W 16 " pdb=" CA ASN W 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN E 16 " pdb=" CA ASN E 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N ASN S 16 " pdb=" CA ASN S 16 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.50e+00 ... (remaining 48703 not shown) Histogram of bond angle deviations from ideal: 99.55 - 105.89: 576 105.89 - 112.23: 21964 112.23 - 118.57: 14932 118.57 - 124.91: 27724 124.91 - 131.25: 456 Bond angle restraints: 65652 Sorted by residual: angle pdb=" C TYR K 334 " pdb=" N LYS K 335 " pdb=" CA LYS K 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR E 334 " pdb=" N LYS E 335 " pdb=" CA LYS E 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR Q 334 " pdb=" N LYS Q 335 " pdb=" CA LYS Q 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR W 334 " pdb=" N LYS W 335 " pdb=" CA LYS W 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 angle pdb=" C TYR I 334 " pdb=" N LYS I 335 " pdb=" CA LYS I 335 " ideal model delta sigma weight residual 120.71 124.89 -4.18 1.42e+00 4.96e-01 8.66e+00 ... (remaining 65647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 27152 17.67 - 35.35: 2020 35.35 - 53.02: 272 53.02 - 70.69: 148 70.69 - 88.37: 60 Dihedral angle restraints: 29652 sinusoidal: 12372 harmonic: 17280 Sorted by residual: dihedral pdb=" CA LEU E 39 " pdb=" C LEU E 39 " pdb=" N GLN E 40 " pdb=" CA GLN E 40 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LEU W 39 " pdb=" C LEU W 39 " pdb=" N GLN W 40 " pdb=" CA GLN W 40 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LEU K 39 " pdb=" C LEU K 39 " pdb=" N GLN K 40 " pdb=" CA GLN K 40 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 29649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4552 0.042 - 0.085: 1924 0.085 - 0.127: 552 0.127 - 0.170: 52 0.170 - 0.212: 12 Chirality restraints: 7092 Sorted by residual: chirality pdb=" CA HIS I 92 " pdb=" N HIS I 92 " pdb=" C HIS I 92 " pdb=" CB HIS I 92 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA HIS C 92 " pdb=" N HIS C 92 " pdb=" C HIS C 92 " pdb=" CB HIS C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA HIS U 92 " pdb=" N HIS U 92 " pdb=" C HIS U 92 " pdb=" CB HIS U 92 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 7089 not shown) Planarity restraints: 8640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 58 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO C 58 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO C 58 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 59 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 58 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO I 58 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO I 58 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG I 59 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO U 58 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO U 58 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO U 58 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG U 59 " 0.020 2.00e-02 2.50e+03 ... (remaining 8637 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 3178 2.72 - 3.27: 48538 3.27 - 3.81: 75094 3.81 - 4.36: 99432 4.36 - 4.90: 165486 Nonbonded interactions: 391728 Sorted by model distance: nonbonded pdb=" NZ LYS K 70 " pdb=" OD1 ASP M 23 " model vdw 2.181 2.520 nonbonded pdb=" NZ LYS E 70 " pdb=" OD1 ASP G 23 " model vdw 2.181 2.520 nonbonded pdb=" OD1 ASP A 23 " pdb=" NZ LYS W 70 " model vdw 2.181 2.520 nonbonded pdb=" NZ LYS Q 70 " pdb=" OD1 ASP S 23 " model vdw 2.181 2.520 nonbonded pdb=" NZ LYS M 70 " pdb=" OD1 ASP O 23 " model vdw 2.181 2.520 ... (remaining 391723 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' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.420 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 111.960 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.400 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.007 0.055 48708 Z= 0.479 Angle : 0.813 4.322 65652 Z= 0.485 Chirality : 0.048 0.212 7092 Planarity : 0.010 0.103 8640 Dihedral : 13.728 88.365 18564 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -0.87 (0.09), residues: 5784 helix: -0.75 (0.09), residues: 2424 sheet: 0.58 (0.14), residues: 1044 loop : -0.75 (0.11), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS U 238 PHE 0.028 0.004 PHE I 367 TYR 0.040 0.005 TYR U 332 ARG 0.016 0.002 ARG I 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1128 time to evaluate : 5.400 Fit side-chains REVERT: A 27 VAL cc_start: 0.8888 (t) cc_final: 0.8624 (m) REVERT: A 85 MET cc_start: 0.3220 (mtm) cc_final: 0.3016 (mtp) REVERT: A 403 LYS cc_start: 0.8006 (tppt) cc_final: 0.7772 (mmtt) REVERT: A 422 ASN cc_start: 0.7779 (m-40) cc_final: 0.7538 (m-40) REVERT: B 94 ASN cc_start: 0.7137 (t0) cc_final: 0.6628 (m110) REVERT: B 101 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7291 (mtp180) REVERT: C 47 LYS cc_start: 0.7600 (mttt) cc_final: 0.7294 (mmtt) REVERT: C 85 MET cc_start: 0.3328 (mtm) cc_final: 0.2633 (mtp) REVERT: C 213 HIS cc_start: 0.8536 (m170) cc_final: 0.8221 (m-70) REVERT: C 216 TYR cc_start: 0.8850 (m-80) cc_final: 0.8329 (m-80) REVERT: C 217 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7386 (mtt-85) REVERT: C 280 SER cc_start: 0.9005 (t) cc_final: 0.8767 (m) REVERT: C 371 GLN cc_start: 0.5537 (mt0) cc_final: 0.4249 (mt0) REVERT: C 386 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8366 (mtt180) REVERT: C 396 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8933 (ttmt) REVERT: C 403 LYS cc_start: 0.7847 (tppt) cc_final: 0.7619 (mmtt) REVERT: C 425 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7008 (mtm180) REVERT: D 94 ASN cc_start: 0.7476 (t0) cc_final: 0.6876 (m110) REVERT: D 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7222 (mmm160) REVERT: E 154 MET cc_start: 0.8986 (ttm) cc_final: 0.8510 (mtp) REVERT: E 208 ASP cc_start: 0.7698 (m-30) cc_final: 0.7426 (m-30) REVERT: E 217 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7362 (mtm-85) REVERT: E 280 SER cc_start: 0.8920 (t) cc_final: 0.8655 (p) REVERT: E 386 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8572 (mtt90) REVERT: E 471 LYS cc_start: 0.7399 (mttt) cc_final: 0.6884 (tttt) REVERT: E 476 GLU cc_start: 0.6492 (tp30) cc_final: 0.6139 (mm-30) REVERT: F 101 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6123 (mtp180) REVERT: G 27 VAL cc_start: 0.8887 (t) cc_final: 0.8628 (m) REVERT: G 85 MET cc_start: 0.3220 (mtm) cc_final: 0.3014 (mtp) REVERT: G 403 LYS cc_start: 0.8009 (tppt) cc_final: 0.7772 (mmtt) REVERT: G 422 ASN cc_start: 0.7778 (m-40) cc_final: 0.7536 (m-40) REVERT: H 94 ASN cc_start: 0.7136 (t0) cc_final: 0.6627 (m110) REVERT: H 101 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7291 (mtp180) REVERT: I 47 LYS cc_start: 0.7596 (mttt) cc_final: 0.7291 (mmtt) REVERT: I 85 MET cc_start: 0.3333 (mtm) cc_final: 0.2641 (mtp) REVERT: I 213 HIS cc_start: 0.8537 (m170) cc_final: 0.8224 (m-70) REVERT: I 216 TYR cc_start: 0.8849 (m-80) cc_final: 0.8329 (m-80) REVERT: I 217 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7388 (mtt-85) REVERT: I 280 SER cc_start: 0.9010 (t) cc_final: 0.8768 (m) REVERT: I 371 GLN cc_start: 0.5536 (mt0) cc_final: 0.4254 (mt0) REVERT: I 386 ARG cc_start: 0.8743 (mtt180) cc_final: 0.8367 (mtt180) REVERT: I 396 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8933 (ttmt) REVERT: I 403 LYS cc_start: 0.7843 (tppt) cc_final: 0.7616 (mmtt) REVERT: I 425 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7011 (mtm180) REVERT: J 94 ASN cc_start: 0.7475 (t0) cc_final: 0.6875 (m110) REVERT: J 101 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7224 (mmm160) REVERT: K 154 MET cc_start: 0.8985 (ttm) cc_final: 0.8510 (mtp) REVERT: K 208 ASP cc_start: 0.7693 (m-30) cc_final: 0.7424 (m-30) REVERT: K 217 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7363 (mtm-85) REVERT: K 280 SER cc_start: 0.8921 (t) cc_final: 0.8657 (p) REVERT: K 386 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8570 (mtt90) REVERT: K 471 LYS cc_start: 0.7394 (mttt) cc_final: 0.6877 (tttt) REVERT: K 476 GLU cc_start: 0.6498 (tp30) cc_final: 0.6140 (mm-30) REVERT: L 101 ARG cc_start: 0.7497 (mtp180) cc_final: 0.6123 (mtp180) REVERT: M 27 VAL cc_start: 0.8884 (t) cc_final: 0.8622 (m) REVERT: M 85 MET cc_start: 0.3210 (mtm) cc_final: 0.3005 (mtp) REVERT: M 403 LYS cc_start: 0.8005 (tppt) cc_final: 0.7770 (mmtt) REVERT: M 422 ASN cc_start: 0.7779 (m-40) cc_final: 0.7537 (m-40) REVERT: N 94 ASN cc_start: 0.7138 (t0) cc_final: 0.6626 (m110) REVERT: N 101 ARG cc_start: 0.7672 (mtp180) cc_final: 0.7292 (mtp180) REVERT: O 47 LYS cc_start: 0.7598 (mttt) cc_final: 0.7294 (mmtt) REVERT: O 85 MET cc_start: 0.3334 (mtm) cc_final: 0.2643 (mtp) REVERT: O 213 HIS cc_start: 0.8538 (m170) cc_final: 0.8225 (m-70) REVERT: O 216 TYR cc_start: 0.8845 (m-80) cc_final: 0.8324 (m-80) REVERT: O 217 ARG cc_start: 0.7885 (mtt-85) cc_final: 0.7389 (mtt-85) REVERT: O 280 SER cc_start: 0.9016 (t) cc_final: 0.8775 (m) REVERT: O 371 GLN cc_start: 0.5540 (mt0) cc_final: 0.4251 (mt0) REVERT: O 386 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8369 (mtt180) REVERT: O 396 LYS cc_start: 0.9176 (ttmm) cc_final: 0.8929 (ttmt) REVERT: O 403 LYS cc_start: 0.7840 (tppt) cc_final: 0.7612 (mmtt) REVERT: O 425 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7010 (mtm180) REVERT: P 94 ASN cc_start: 0.7477 (t0) cc_final: 0.6880 (m110) REVERT: P 101 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7222 (mmm160) REVERT: Q 154 MET cc_start: 0.8984 (ttm) cc_final: 0.8512 (mtp) REVERT: Q 208 ASP cc_start: 0.7694 (m-30) cc_final: 0.7423 (m-30) REVERT: Q 217 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7365 (mtm-85) REVERT: Q 280 SER cc_start: 0.8924 (t) cc_final: 0.8660 (p) REVERT: Q 386 ARG cc_start: 0.8913 (mtt180) cc_final: 0.8570 (mtt90) REVERT: Q 471 LYS cc_start: 0.7393 (mttt) cc_final: 0.6879 (tttt) REVERT: Q 476 GLU cc_start: 0.6501 (tp30) cc_final: 0.6143 (mm-30) REVERT: R 101 ARG cc_start: 0.7504 (mtp180) cc_final: 0.6129 (mtp180) REVERT: S 27 VAL cc_start: 0.8888 (t) cc_final: 0.8624 (m) REVERT: S 85 MET cc_start: 0.3217 (mtm) cc_final: 0.3012 (mtp) REVERT: S 403 LYS cc_start: 0.8004 (tppt) cc_final: 0.7769 (mmtt) REVERT: S 422 ASN cc_start: 0.7777 (m-40) cc_final: 0.7537 (m-40) REVERT: T 94 ASN cc_start: 0.7139 (t0) cc_final: 0.6625 (m110) REVERT: T 101 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7291 (mtp180) REVERT: U 47 LYS cc_start: 0.7597 (mttt) cc_final: 0.7293 (mmtt) REVERT: U 85 MET cc_start: 0.3329 (mtm) cc_final: 0.2636 (mtp) REVERT: U 213 HIS cc_start: 0.8537 (m170) cc_final: 0.8223 (m-70) REVERT: U 216 TYR cc_start: 0.8846 (m-80) cc_final: 0.8325 (m-80) REVERT: U 217 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7384 (mtt-85) REVERT: U 280 SER cc_start: 0.9016 (t) cc_final: 0.8773 (m) REVERT: U 371 GLN cc_start: 0.5543 (mt0) cc_final: 0.4258 (mt0) REVERT: U 386 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8370 (mtt180) REVERT: U 396 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8930 (ttmt) REVERT: U 403 LYS cc_start: 0.7843 (tppt) cc_final: 0.7616 (mmtt) REVERT: U 425 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7006 (mtm180) REVERT: V 94 ASN cc_start: 0.7476 (t0) cc_final: 0.6875 (m110) REVERT: V 101 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7223 (mmm160) REVERT: W 154 MET cc_start: 0.8983 (ttm) cc_final: 0.8509 (mtp) REVERT: W 208 ASP cc_start: 0.7697 (m-30) cc_final: 0.7424 (m-30) REVERT: W 217 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7364 (mtm-85) REVERT: W 280 SER cc_start: 0.8925 (t) cc_final: 0.8660 (p) REVERT: W 386 ARG cc_start: 0.8912 (mtt180) cc_final: 0.8571 (mtt90) REVERT: W 471 LYS cc_start: 0.7392 (mttt) cc_final: 0.6878 (tttt) REVERT: W 476 GLU cc_start: 0.6496 (tp30) cc_final: 0.6143 (mm-30) REVERT: X 101 ARG cc_start: 0.7501 (mtp180) cc_final: 0.6127 (mtp180) outliers start: 0 outliers final: 0 residues processed: 1128 average time/residue: 0.7722 time to fit residues: 1327.2520 Evaluate side-chains 664 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 5.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 20.0000 chunk 436 optimal weight: 0.8980 chunk 242 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 451 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 523 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN C 224 ASN C 270 ASN C 358 ASN C 452 GLN E 224 ASN E 270 ASN E 354 HIS E 358 ASN G 270 ASN I 224 ASN I 270 ASN I 358 ASN I 452 GLN K 224 ASN K 270 ASN K 354 HIS K 358 ASN M 270 ASN O 224 ASN O 270 ASN O 358 ASN O 452 GLN Q 224 ASN Q 270 ASN Q 354 HIS Q 358 ASN S 270 ASN U 224 ASN U 270 ASN U 358 ASN U 452 GLN W 224 ASN W 270 ASN W 354 HIS W 358 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48708 Z= 0.259 Angle : 0.557 4.810 65652 Z= 0.309 Chirality : 0.041 0.157 7092 Planarity : 0.004 0.041 8640 Dihedral : 5.177 20.579 6552 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.36 % Allowed : 7.22 % Favored : 91.42 % 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: 0.48 (0.10), residues: 5784 helix: 0.88 (0.10), residues: 2508 sheet: 0.87 (0.14), residues: 1116 loop : -0.55 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS W 354 PHE 0.013 0.002 PHE E 173 TYR 0.015 0.002 TYR S 345 ARG 0.004 0.000 ARG U 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 759 time to evaluate : 5.988 Fit side-chains REVERT: A 27 VAL cc_start: 0.8516 (t) cc_final: 0.8175 (m) REVERT: A 76 GLU cc_start: 0.6941 (tt0) cc_final: 0.6731 (pt0) REVERT: A 213 HIS cc_start: 0.8201 (m170) cc_final: 0.7879 (m-70) REVERT: A 295 LEU cc_start: 0.7623 (tp) cc_final: 0.7359 (tp) REVERT: A 403 LYS cc_start: 0.8114 (tppt) cc_final: 0.7889 (mmtt) REVERT: B 94 ASN cc_start: 0.7345 (t0) cc_final: 0.6804 (m110) REVERT: C 85 MET cc_start: 0.3105 (mtm) cc_final: 0.2686 (mtp) REVERT: C 213 HIS cc_start: 0.8520 (m170) cc_final: 0.8259 (m-70) REVERT: C 362 MET cc_start: 0.7244 (mmp) cc_final: 0.6963 (mmm) REVERT: C 386 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8431 (mtt180) REVERT: C 403 LYS cc_start: 0.8251 (tppt) cc_final: 0.7867 (mmtt) REVERT: C 425 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.6829 (mtm180) REVERT: D 94 ASN cc_start: 0.7508 (t0) cc_final: 0.6896 (m110) REVERT: D 101 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7100 (tpt170) REVERT: D 103 LYS cc_start: 0.8938 (tptp) cc_final: 0.8683 (tttp) REVERT: E 89 ARG cc_start: 0.6872 (mtm180) cc_final: 0.6581 (mtt180) REVERT: E 213 HIS cc_start: 0.8502 (m170) cc_final: 0.8282 (m170) REVERT: E 386 ARG cc_start: 0.8988 (mtt180) cc_final: 0.8465 (mtt90) REVERT: E 471 LYS cc_start: 0.7609 (mttt) cc_final: 0.6731 (tttt) REVERT: F 101 ARG cc_start: 0.7219 (mtp180) cc_final: 0.5893 (mtp180) REVERT: G 27 VAL cc_start: 0.8519 (t) cc_final: 0.8178 (m) REVERT: G 76 GLU cc_start: 0.6936 (tt0) cc_final: 0.6728 (pt0) REVERT: G 213 HIS cc_start: 0.8204 (m170) cc_final: 0.7881 (m-70) REVERT: G 295 LEU cc_start: 0.7624 (tp) cc_final: 0.7359 (tp) REVERT: G 403 LYS cc_start: 0.8117 (tppt) cc_final: 0.7891 (mmtt) REVERT: H 94 ASN cc_start: 0.7345 (t0) cc_final: 0.6805 (m110) REVERT: I 85 MET cc_start: 0.3095 (mtm) cc_final: 0.2679 (mtp) REVERT: I 213 HIS cc_start: 0.8519 (m170) cc_final: 0.8258 (m-70) REVERT: I 362 MET cc_start: 0.7245 (mmp) cc_final: 0.6966 (mmm) REVERT: I 386 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8431 (mtt180) REVERT: I 403 LYS cc_start: 0.8248 (tppt) cc_final: 0.7862 (mmtt) REVERT: I 425 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.6834 (mtm180) REVERT: J 94 ASN cc_start: 0.7506 (t0) cc_final: 0.6894 (m110) REVERT: J 101 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7099 (tpt170) REVERT: J 103 LYS cc_start: 0.8939 (tptp) cc_final: 0.8683 (tttp) REVERT: K 89 ARG cc_start: 0.6876 (mtm180) cc_final: 0.6587 (mtt180) REVERT: K 213 HIS cc_start: 0.8504 (m170) cc_final: 0.8283 (m170) REVERT: K 386 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8464 (mtt90) REVERT: K 471 LYS cc_start: 0.7603 (mttt) cc_final: 0.6723 (tttt) REVERT: L 101 ARG cc_start: 0.7219 (mtp180) cc_final: 0.5893 (mtp180) REVERT: M 27 VAL cc_start: 0.8513 (t) cc_final: 0.8170 (m) REVERT: M 76 GLU cc_start: 0.6939 (tt0) cc_final: 0.6730 (pt0) REVERT: M 213 HIS cc_start: 0.8201 (m170) cc_final: 0.7880 (m-70) REVERT: M 295 LEU cc_start: 0.7625 (tp) cc_final: 0.7363 (tp) REVERT: M 403 LYS cc_start: 0.8111 (tppt) cc_final: 0.7888 (mmtt) REVERT: N 94 ASN cc_start: 0.7348 (t0) cc_final: 0.6807 (m110) REVERT: O 85 MET cc_start: 0.3100 (mtm) cc_final: 0.2680 (mtp) REVERT: O 213 HIS cc_start: 0.8519 (m170) cc_final: 0.8258 (m-70) REVERT: O 362 MET cc_start: 0.7249 (mmp) cc_final: 0.6968 (mmm) REVERT: O 386 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8433 (mtt180) REVERT: O 403 LYS cc_start: 0.8246 (tppt) cc_final: 0.7858 (mmtt) REVERT: O 425 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6830 (mtm180) REVERT: P 94 ASN cc_start: 0.7511 (t0) cc_final: 0.6897 (m110) REVERT: P 101 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7102 (tpt170) REVERT: P 103 LYS cc_start: 0.8940 (tptp) cc_final: 0.8684 (tttp) REVERT: Q 89 ARG cc_start: 0.6876 (mtm180) cc_final: 0.6587 (mtt180) REVERT: Q 213 HIS cc_start: 0.8505 (m170) cc_final: 0.8283 (m170) REVERT: Q 386 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8460 (mtt90) REVERT: Q 471 LYS cc_start: 0.7606 (mttt) cc_final: 0.6729 (tttt) REVERT: R 101 ARG cc_start: 0.7222 (mtp180) cc_final: 0.5896 (mtp180) REVERT: S 27 VAL cc_start: 0.8517 (t) cc_final: 0.8177 (m) REVERT: S 76 GLU cc_start: 0.6941 (tt0) cc_final: 0.6730 (pt0) REVERT: S 213 HIS cc_start: 0.8199 (m170) cc_final: 0.7878 (m-70) REVERT: S 295 LEU cc_start: 0.7626 (tp) cc_final: 0.7362 (tp) REVERT: S 403 LYS cc_start: 0.8109 (tppt) cc_final: 0.7884 (mmtt) REVERT: T 94 ASN cc_start: 0.7344 (t0) cc_final: 0.6803 (m110) REVERT: U 85 MET cc_start: 0.3100 (mtm) cc_final: 0.2680 (mtp) REVERT: U 213 HIS cc_start: 0.8521 (m170) cc_final: 0.8260 (m-70) REVERT: U 362 MET cc_start: 0.7247 (mmp) cc_final: 0.6965 (mmm) REVERT: U 386 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8435 (mtt180) REVERT: U 403 LYS cc_start: 0.8244 (tppt) cc_final: 0.7861 (mmtt) REVERT: U 425 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6829 (mtm180) REVERT: V 94 ASN cc_start: 0.7511 (t0) cc_final: 0.6896 (m110) REVERT: V 101 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7101 (tpt170) REVERT: V 103 LYS cc_start: 0.8939 (tptp) cc_final: 0.8684 (tttp) REVERT: W 89 ARG cc_start: 0.6873 (mtm180) cc_final: 0.6580 (mtt180) REVERT: W 213 HIS cc_start: 0.8507 (m170) cc_final: 0.8285 (m170) REVERT: W 386 ARG cc_start: 0.8987 (mtt180) cc_final: 0.8464 (mtt90) REVERT: W 471 LYS cc_start: 0.7605 (mttt) cc_final: 0.6727 (tttt) REVERT: X 101 ARG cc_start: 0.7221 (mtp180) cc_final: 0.5893 (mtp180) outliers start: 72 outliers final: 52 residues processed: 815 average time/residue: 0.6850 time to fit residues: 867.3546 Evaluate side-chains 706 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 654 time to evaluate : 5.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 451 SER Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 451 SER Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 451 SER Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 451 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 435 optimal weight: 9.9990 chunk 356 optimal weight: 0.4980 chunk 144 optimal weight: 5.9990 chunk 524 optimal weight: 8.9990 chunk 566 optimal weight: 9.9990 chunk 466 optimal weight: 2.9990 chunk 519 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 420 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS C 452 GLN E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 HIS I 452 GLN K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 422 ASN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 354 HIS O 452 GLN Q 303 GLN S 73 ASN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 422 ASN ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 354 HIS U 452 GLN W 303 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48708 Z= 0.224 Angle : 0.500 4.952 65652 Z= 0.275 Chirality : 0.039 0.138 7092 Planarity : 0.004 0.033 8640 Dihedral : 4.702 18.368 6552 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.74 % Allowed : 9.15 % Favored : 89.12 % 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: 0.73 (0.11), residues: 5784 helix: 1.25 (0.10), residues: 2520 sheet: 0.82 (0.14), residues: 1116 loop : -0.55 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 354 PHE 0.012 0.002 PHE I 173 TYR 0.015 0.002 TYR C 345 ARG 0.003 0.000 ARG I 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 684 time to evaluate : 5.597 Fit side-chains REVERT: A 213 HIS cc_start: 0.8200 (m170) cc_final: 0.7929 (m-70) REVERT: A 243 MET cc_start: 0.8101 (tmm) cc_final: 0.7773 (tmm) REVERT: A 295 LEU cc_start: 0.7771 (tp) cc_final: 0.7446 (tp) REVERT: A 403 LYS cc_start: 0.8237 (tppt) cc_final: 0.7890 (mmtt) REVERT: B 95 TYR cc_start: 0.6607 (OUTLIER) cc_final: 0.5724 (t80) REVERT: C 47 LYS cc_start: 0.8031 (mttt) cc_final: 0.7715 (mmtt) REVERT: C 76 GLU cc_start: 0.6835 (tt0) cc_final: 0.6632 (pt0) REVERT: C 118 LYS cc_start: 0.7355 (mttt) cc_final: 0.6988 (ptmt) REVERT: C 213 HIS cc_start: 0.8545 (m170) cc_final: 0.8287 (m-70) REVERT: C 301 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6858 (ttp-110) REVERT: C 362 MET cc_start: 0.7512 (mmp) cc_final: 0.7241 (mmm) REVERT: C 403 LYS cc_start: 0.8306 (tppt) cc_final: 0.7880 (mmtt) REVERT: C 425 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6787 (mtm180) REVERT: C 478 GLU cc_start: 0.5913 (mp0) cc_final: 0.4998 (tt0) REVERT: D 94 ASN cc_start: 0.7466 (t0) cc_final: 0.6716 (m110) REVERT: D 95 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.5192 (t80) REVERT: D 101 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6951 (tpt170) REVERT: D 103 LYS cc_start: 0.8960 (tptp) cc_final: 0.8730 (tttp) REVERT: E 471 LYS cc_start: 0.7480 (mttt) cc_final: 0.6662 (tttt) REVERT: G 213 HIS cc_start: 0.8202 (m170) cc_final: 0.7931 (m-70) REVERT: G 243 MET cc_start: 0.8099 (tmm) cc_final: 0.7771 (tmm) REVERT: G 295 LEU cc_start: 0.7771 (tp) cc_final: 0.7447 (tp) REVERT: G 403 LYS cc_start: 0.8239 (tppt) cc_final: 0.7893 (mmtt) REVERT: H 95 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5723 (t80) REVERT: I 47 LYS cc_start: 0.8033 (mttt) cc_final: 0.7716 (mmtt) REVERT: I 76 GLU cc_start: 0.6842 (tt0) cc_final: 0.6635 (pt0) REVERT: I 118 LYS cc_start: 0.7356 (mttt) cc_final: 0.6989 (ptmt) REVERT: I 213 HIS cc_start: 0.8543 (m170) cc_final: 0.8285 (m-70) REVERT: I 301 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6857 (ttp-110) REVERT: I 362 MET cc_start: 0.7512 (mmp) cc_final: 0.7241 (mmm) REVERT: I 403 LYS cc_start: 0.8298 (tppt) cc_final: 0.7873 (mmtt) REVERT: I 425 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6788 (mtm180) REVERT: I 478 GLU cc_start: 0.5901 (mp0) cc_final: 0.4988 (tt0) REVERT: J 94 ASN cc_start: 0.7462 (t0) cc_final: 0.6712 (m110) REVERT: J 95 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.5192 (t80) REVERT: J 101 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6949 (tpt170) REVERT: J 103 LYS cc_start: 0.8961 (tptp) cc_final: 0.8730 (tttp) REVERT: K 471 LYS cc_start: 0.7476 (mttt) cc_final: 0.6661 (tttt) REVERT: M 213 HIS cc_start: 0.8198 (m170) cc_final: 0.7930 (m-70) REVERT: M 243 MET cc_start: 0.8100 (tmm) cc_final: 0.7772 (tmm) REVERT: M 295 LEU cc_start: 0.7772 (tp) cc_final: 0.7449 (tp) REVERT: M 403 LYS cc_start: 0.8236 (tppt) cc_final: 0.7890 (mmtt) REVERT: N 95 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5727 (t80) REVERT: O 47 LYS cc_start: 0.8032 (mttt) cc_final: 0.7718 (mmtt) REVERT: O 76 GLU cc_start: 0.6836 (tt0) cc_final: 0.6633 (pt0) REVERT: O 118 LYS cc_start: 0.7360 (mttt) cc_final: 0.6991 (ptmt) REVERT: O 213 HIS cc_start: 0.8544 (m170) cc_final: 0.8284 (m-70) REVERT: O 301 ARG cc_start: 0.7078 (mtm-85) cc_final: 0.6858 (ttp-110) REVERT: O 362 MET cc_start: 0.7511 (mmp) cc_final: 0.7242 (mmm) REVERT: O 403 LYS cc_start: 0.8301 (tppt) cc_final: 0.7871 (mmtt) REVERT: O 425 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6784 (mtm180) REVERT: O 478 GLU cc_start: 0.5910 (mp0) cc_final: 0.4990 (tt0) REVERT: P 94 ASN cc_start: 0.7466 (t0) cc_final: 0.6715 (m110) REVERT: P 95 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5198 (t80) REVERT: P 101 ARG cc_start: 0.7496 (mtp180) cc_final: 0.6948 (tpt170) REVERT: P 103 LYS cc_start: 0.8961 (tptp) cc_final: 0.8731 (tttp) REVERT: Q 471 LYS cc_start: 0.7476 (mttt) cc_final: 0.6661 (tttt) REVERT: S 213 HIS cc_start: 0.8195 (m170) cc_final: 0.7925 (m-70) REVERT: S 243 MET cc_start: 0.8097 (tmm) cc_final: 0.7770 (tmm) REVERT: S 295 LEU cc_start: 0.7773 (tp) cc_final: 0.7450 (tp) REVERT: S 403 LYS cc_start: 0.8234 (tppt) cc_final: 0.7886 (mmtt) REVERT: T 95 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5723 (t80) REVERT: U 47 LYS cc_start: 0.8031 (mttt) cc_final: 0.7715 (mmtt) REVERT: U 76 GLU cc_start: 0.6832 (tt0) cc_final: 0.6628 (pt0) REVERT: U 118 LYS cc_start: 0.7359 (mttt) cc_final: 0.6988 (ptmt) REVERT: U 213 HIS cc_start: 0.8546 (m170) cc_final: 0.8287 (m-70) REVERT: U 301 ARG cc_start: 0.7081 (mtm-85) cc_final: 0.6860 (ttp-110) REVERT: U 362 MET cc_start: 0.7514 (mmp) cc_final: 0.7240 (mmm) REVERT: U 403 LYS cc_start: 0.8299 (tppt) cc_final: 0.7874 (mmtt) REVERT: U 425 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6784 (mtm180) REVERT: U 478 GLU cc_start: 0.5907 (mp0) cc_final: 0.4994 (tt0) REVERT: V 94 ASN cc_start: 0.7466 (t0) cc_final: 0.6715 (m110) REVERT: V 95 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.5195 (t80) REVERT: V 101 ARG cc_start: 0.7498 (mtp180) cc_final: 0.6950 (tpt170) REVERT: V 103 LYS cc_start: 0.8961 (tptp) cc_final: 0.8731 (tttp) REVERT: W 471 LYS cc_start: 0.7473 (mttt) cc_final: 0.6662 (tttt) outliers start: 92 outliers final: 72 residues processed: 744 average time/residue: 0.7130 time to fit residues: 819.0034 Evaluate side-chains 712 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 632 time to evaluate : 5.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain G residue 451 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain M residue 451 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain S residue 451 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 451 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 6.9990 chunk 393 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 525 optimal weight: 8.9990 chunk 556 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 498 optimal weight: 6.9990 chunk 150 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 354 HIS M 422 ASN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 354 HIS ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 48708 Z= 0.300 Angle : 0.537 4.984 65652 Z= 0.291 Chirality : 0.040 0.142 7092 Planarity : 0.004 0.033 8640 Dihedral : 4.736 17.640 6552 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.61 % Allowed : 10.32 % Favored : 87.07 % 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: 0.71 (0.11), residues: 5784 helix: 1.28 (0.10), residues: 2484 sheet: 0.66 (0.14), residues: 1116 loop : -0.49 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS M 354 PHE 0.013 0.002 PHE C 173 TYR 0.014 0.002 TYR A 345 ARG 0.003 0.000 ARG K 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 660 time to evaluate : 6.570 Fit side-chains REVERT: A 213 HIS cc_start: 0.8203 (m170) cc_final: 0.7938 (m-70) REVERT: A 243 MET cc_start: 0.8048 (tmm) cc_final: 0.7714 (tmm) REVERT: A 295 LEU cc_start: 0.7812 (tp) cc_final: 0.7479 (tp) REVERT: A 403 LYS cc_start: 0.8172 (tppt) cc_final: 0.7762 (mmtt) REVERT: B 95 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.5503 (t80) REVERT: C 118 LYS cc_start: 0.7409 (mttt) cc_final: 0.6989 (ptmt) REVERT: C 213 HIS cc_start: 0.8528 (m170) cc_final: 0.8277 (m-70) REVERT: C 362 MET cc_start: 0.7483 (mmp) cc_final: 0.7268 (mmm) REVERT: C 403 LYS cc_start: 0.8350 (tppt) cc_final: 0.7891 (mmtt) REVERT: C 425 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6797 (mtm180) REVERT: C 471 LYS cc_start: 0.7161 (mttt) cc_final: 0.6833 (mttt) REVERT: D 95 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5340 (t80) REVERT: D 101 ARG cc_start: 0.7566 (mtp180) cc_final: 0.6947 (tpt170) REVERT: D 103 LYS cc_start: 0.8916 (tptp) cc_final: 0.8715 (tttp) REVERT: E 196 ILE cc_start: 0.6606 (pt) cc_final: 0.6113 (mm) REVERT: E 471 LYS cc_start: 0.7295 (mttt) cc_final: 0.6716 (tttt) REVERT: F 95 TYR cc_start: 0.6304 (OUTLIER) cc_final: 0.5598 (t80) REVERT: G 213 HIS cc_start: 0.8208 (m170) cc_final: 0.7939 (m-70) REVERT: G 243 MET cc_start: 0.8044 (tmm) cc_final: 0.7710 (tmm) REVERT: G 295 LEU cc_start: 0.7809 (tp) cc_final: 0.7480 (tp) REVERT: G 403 LYS cc_start: 0.8173 (tppt) cc_final: 0.7764 (mmtt) REVERT: H 95 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.5506 (t80) REVERT: I 118 LYS cc_start: 0.7413 (mttt) cc_final: 0.6993 (ptmt) REVERT: I 213 HIS cc_start: 0.8529 (m170) cc_final: 0.8278 (m-70) REVERT: I 362 MET cc_start: 0.7482 (mmp) cc_final: 0.7267 (mmm) REVERT: I 403 LYS cc_start: 0.8342 (tppt) cc_final: 0.7884 (mmtt) REVERT: I 425 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6798 (mtm180) REVERT: I 471 LYS cc_start: 0.7163 (mttt) cc_final: 0.6835 (mttt) REVERT: J 95 TYR cc_start: 0.6144 (OUTLIER) cc_final: 0.5342 (t80) REVERT: J 101 ARG cc_start: 0.7566 (mtp180) cc_final: 0.6946 (tpt170) REVERT: J 103 LYS cc_start: 0.8917 (tptp) cc_final: 0.8716 (tttp) REVERT: K 196 ILE cc_start: 0.6603 (pt) cc_final: 0.6108 (mm) REVERT: K 471 LYS cc_start: 0.7290 (mttt) cc_final: 0.6711 (tttt) REVERT: L 95 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.5597 (t80) REVERT: M 213 HIS cc_start: 0.8205 (m170) cc_final: 0.7938 (m-70) REVERT: M 243 MET cc_start: 0.8048 (tmm) cc_final: 0.7711 (tmm) REVERT: M 295 LEU cc_start: 0.7825 (tp) cc_final: 0.7502 (tp) REVERT: M 403 LYS cc_start: 0.8163 (tppt) cc_final: 0.7760 (mmtt) REVERT: N 95 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.5506 (t80) REVERT: O 118 LYS cc_start: 0.7415 (mttt) cc_final: 0.6990 (ptmt) REVERT: O 213 HIS cc_start: 0.8528 (m170) cc_final: 0.8277 (m-70) REVERT: O 362 MET cc_start: 0.7482 (mmp) cc_final: 0.7266 (mmm) REVERT: O 403 LYS cc_start: 0.8341 (tppt) cc_final: 0.7882 (mmtt) REVERT: O 425 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6799 (mtm180) REVERT: O 471 LYS cc_start: 0.7155 (mttt) cc_final: 0.6824 (mttt) REVERT: P 95 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5346 (t80) REVERT: P 101 ARG cc_start: 0.7562 (mtp180) cc_final: 0.6944 (tpt170) REVERT: P 103 LYS cc_start: 0.8917 (tptp) cc_final: 0.8717 (tttp) REVERT: Q 196 ILE cc_start: 0.6603 (pt) cc_final: 0.6107 (mm) REVERT: Q 471 LYS cc_start: 0.7291 (mttt) cc_final: 0.6712 (tttt) REVERT: R 95 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5597 (t80) REVERT: S 213 HIS cc_start: 0.8200 (m170) cc_final: 0.7934 (m-70) REVERT: S 243 MET cc_start: 0.8045 (tmm) cc_final: 0.7711 (tmm) REVERT: S 295 LEU cc_start: 0.7825 (tp) cc_final: 0.7499 (tp) REVERT: S 403 LYS cc_start: 0.8168 (tppt) cc_final: 0.7760 (mmtt) REVERT: T 95 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5504 (t80) REVERT: U 118 LYS cc_start: 0.7412 (mttt) cc_final: 0.6989 (ptmt) REVERT: U 213 HIS cc_start: 0.8528 (m170) cc_final: 0.8276 (m-70) REVERT: U 362 MET cc_start: 0.7483 (mmp) cc_final: 0.7267 (mmm) REVERT: U 403 LYS cc_start: 0.8344 (tppt) cc_final: 0.7886 (mmtt) REVERT: U 425 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6794 (mtm180) REVERT: U 471 LYS cc_start: 0.7163 (mttt) cc_final: 0.6834 (mttt) REVERT: V 95 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.5341 (t80) REVERT: V 101 ARG cc_start: 0.7564 (mtp180) cc_final: 0.6945 (tpt170) REVERT: V 103 LYS cc_start: 0.8918 (tptp) cc_final: 0.8716 (tttp) REVERT: W 196 ILE cc_start: 0.6604 (pt) cc_final: 0.6110 (mm) REVERT: W 471 LYS cc_start: 0.7291 (mttt) cc_final: 0.6716 (tttt) REVERT: X 95 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5595 (t80) outliers start: 138 outliers final: 95 residues processed: 744 average time/residue: 0.6965 time to fit residues: 811.2903 Evaluate side-chains 736 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 629 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 414 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 475 optimal weight: 8.9990 chunk 384 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 499 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** G 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 HIS G 452 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN M 73 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 452 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 GLN ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 48708 Z= 0.241 Angle : 0.495 7.572 65652 Z= 0.268 Chirality : 0.039 0.137 7092 Planarity : 0.004 0.033 8640 Dihedral : 4.521 16.900 6552 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.95 % Allowed : 10.73 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.11), residues: 5784 helix: 1.31 (0.10), residues: 2520 sheet: 0.58 (0.14), residues: 1116 loop : -0.59 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 92 PHE 0.013 0.002 PHE K 173 TYR 0.014 0.002 TYR A 345 ARG 0.002 0.000 ARG W 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 652 time to evaluate : 5.622 Fit side-chains REVERT: A 213 HIS cc_start: 0.8255 (m170) cc_final: 0.8039 (m-70) REVERT: A 243 MET cc_start: 0.8015 (tmm) cc_final: 0.7693 (tmm) REVERT: A 295 LEU cc_start: 0.7802 (tp) cc_final: 0.7467 (tp) REVERT: A 403 LYS cc_start: 0.8156 (tppt) cc_final: 0.7781 (mmtt) REVERT: B 95 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5510 (t80) REVERT: C 47 LYS cc_start: 0.8051 (mttt) cc_final: 0.7722 (mmtt) REVERT: C 118 LYS cc_start: 0.7314 (mttt) cc_final: 0.6914 (ptmt) REVERT: C 403 LYS cc_start: 0.8379 (tppt) cc_final: 0.7941 (mmtt) REVERT: C 425 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6766 (mtm180) REVERT: C 471 LYS cc_start: 0.7187 (mttt) cc_final: 0.6808 (mttt) REVERT: D 95 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5338 (t80) REVERT: D 101 ARG cc_start: 0.7564 (mtp180) cc_final: 0.6934 (tpt170) REVERT: E 471 LYS cc_start: 0.7293 (mttt) cc_final: 0.6715 (tttt) REVERT: F 95 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.5476 (t80) REVERT: G 213 HIS cc_start: 0.8260 (m170) cc_final: 0.8045 (m-70) REVERT: G 243 MET cc_start: 0.8012 (tmm) cc_final: 0.7689 (tmm) REVERT: G 295 LEU cc_start: 0.7799 (tp) cc_final: 0.7465 (tp) REVERT: G 403 LYS cc_start: 0.8159 (tppt) cc_final: 0.7784 (mmtt) REVERT: H 95 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.5510 (t80) REVERT: I 47 LYS cc_start: 0.8052 (mttt) cc_final: 0.7721 (mmtt) REVERT: I 118 LYS cc_start: 0.7315 (mttt) cc_final: 0.6917 (ptmt) REVERT: I 403 LYS cc_start: 0.8372 (tppt) cc_final: 0.7935 (mmtt) REVERT: I 425 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6768 (mtm180) REVERT: I 471 LYS cc_start: 0.7184 (mttt) cc_final: 0.6805 (mttt) REVERT: J 95 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5338 (t80) REVERT: J 101 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6931 (tpt170) REVERT: K 471 LYS cc_start: 0.7287 (mttt) cc_final: 0.6710 (tttt) REVERT: L 95 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.5475 (t80) REVERT: M 213 HIS cc_start: 0.8256 (m170) cc_final: 0.8041 (m-70) REVERT: M 243 MET cc_start: 0.8016 (tmm) cc_final: 0.7691 (tmm) REVERT: M 295 LEU cc_start: 0.7818 (tp) cc_final: 0.7484 (tp) REVERT: M 403 LYS cc_start: 0.8157 (tppt) cc_final: 0.7782 (mmtt) REVERT: N 95 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.5508 (t80) REVERT: O 47 LYS cc_start: 0.8051 (mttt) cc_final: 0.7722 (mmtt) REVERT: O 118 LYS cc_start: 0.7321 (mttt) cc_final: 0.6916 (ptmt) REVERT: O 403 LYS cc_start: 0.8369 (tppt) cc_final: 0.7931 (mmtt) REVERT: O 425 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6766 (mtm180) REVERT: O 471 LYS cc_start: 0.7181 (mttt) cc_final: 0.6799 (mttt) REVERT: P 95 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5343 (t80) REVERT: P 101 ARG cc_start: 0.7563 (mtp180) cc_final: 0.6932 (tpt170) REVERT: Q 471 LYS cc_start: 0.7285 (mttt) cc_final: 0.6710 (tttt) REVERT: R 95 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.5474 (t80) REVERT: S 213 HIS cc_start: 0.8253 (m170) cc_final: 0.8037 (m-70) REVERT: S 243 MET cc_start: 0.8012 (tmm) cc_final: 0.7690 (tmm) REVERT: S 295 LEU cc_start: 0.7819 (tp) cc_final: 0.7483 (tp) REVERT: S 403 LYS cc_start: 0.8153 (tppt) cc_final: 0.7781 (mmtt) REVERT: T 95 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.5510 (t80) REVERT: U 47 LYS cc_start: 0.8051 (mttt) cc_final: 0.7720 (mmtt) REVERT: U 118 LYS cc_start: 0.7320 (mttt) cc_final: 0.6918 (ptmt) REVERT: U 403 LYS cc_start: 0.8371 (tppt) cc_final: 0.7933 (mmtt) REVERT: U 425 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6765 (mtm180) REVERT: U 471 LYS cc_start: 0.7191 (mttt) cc_final: 0.6811 (mttt) REVERT: V 95 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5341 (t80) REVERT: V 101 ARG cc_start: 0.7564 (mtp180) cc_final: 0.6932 (tpt170) REVERT: W 471 LYS cc_start: 0.7288 (mttt) cc_final: 0.6710 (tttt) REVERT: X 95 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5470 (t80) outliers start: 156 outliers final: 129 residues processed: 744 average time/residue: 0.6683 time to fit residues: 776.3824 Evaluate side-chains 753 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 612 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 294 ASN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 191 LEU Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 438 GLU Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 191 LEU Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 9.9990 chunk 501 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 557 optimal weight: 0.0020 chunk 462 optimal weight: 10.0000 chunk 258 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 184 optimal weight: 0.0010 chunk 292 optimal weight: 5.9990 overall best weight: 1.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 303 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN E 303 GLN G 73 ASN G 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 GLN K 303 GLN M 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 340 GLN Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN W 303 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 48708 Z= 0.137 Angle : 0.431 7.744 65652 Z= 0.235 Chirality : 0.036 0.130 7092 Planarity : 0.003 0.033 8640 Dihedral : 4.111 15.021 6552 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.29 % Allowed : 12.23 % Favored : 85.49 % 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: 0.96 (0.11), residues: 5784 helix: 1.65 (0.10), residues: 2520 sheet: 0.68 (0.14), residues: 1116 loop : -0.55 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 92 PHE 0.010 0.001 PHE K 173 TYR 0.015 0.001 TYR S 378 ARG 0.005 0.000 ARG O 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 677 time to evaluate : 5.222 Fit side-chains REVERT: A 39 LEU cc_start: 0.8250 (mt) cc_final: 0.7889 (tp) REVERT: A 213 HIS cc_start: 0.8330 (m170) cc_final: 0.8114 (m-70) REVERT: A 243 MET cc_start: 0.8038 (tmm) cc_final: 0.7728 (tmm) REVERT: A 295 LEU cc_start: 0.7755 (tp) cc_final: 0.7442 (tp) REVERT: A 403 LYS cc_start: 0.8121 (tppt) cc_final: 0.7706 (mmtt) REVERT: B 95 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5497 (t80) REVERT: C 47 LYS cc_start: 0.7996 (mttt) cc_final: 0.7692 (mmtt) REVERT: C 118 LYS cc_start: 0.7294 (mttt) cc_final: 0.6906 (ptmt) REVERT: C 403 LYS cc_start: 0.8399 (tppt) cc_final: 0.7977 (mmtt) REVERT: C 425 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6613 (mtm180) REVERT: C 471 LYS cc_start: 0.7188 (mttt) cc_final: 0.6786 (mttt) REVERT: D 95 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5477 (t80) REVERT: D 101 ARG cc_start: 0.7487 (mtp180) cc_final: 0.6932 (tpt170) REVERT: E 57 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: E 471 LYS cc_start: 0.7227 (mttt) cc_final: 0.6670 (tttt) REVERT: F 95 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5413 (t80) REVERT: G 39 LEU cc_start: 0.8251 (mt) cc_final: 0.7892 (tp) REVERT: G 213 HIS cc_start: 0.8330 (m170) cc_final: 0.8114 (m-70) REVERT: G 243 MET cc_start: 0.8034 (tmm) cc_final: 0.7725 (tmm) REVERT: G 295 LEU cc_start: 0.7755 (tp) cc_final: 0.7441 (tp) REVERT: G 403 LYS cc_start: 0.8124 (tppt) cc_final: 0.7706 (mmtt) REVERT: H 95 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5494 (t80) REVERT: I 47 LYS cc_start: 0.7997 (mttt) cc_final: 0.7693 (mmtt) REVERT: I 118 LYS cc_start: 0.7299 (mttt) cc_final: 0.6908 (ptmt) REVERT: I 403 LYS cc_start: 0.8393 (tppt) cc_final: 0.7972 (mmtt) REVERT: I 425 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6615 (mtm180) REVERT: I 471 LYS cc_start: 0.7179 (mttt) cc_final: 0.6779 (mttt) REVERT: J 95 TYR cc_start: 0.6173 (OUTLIER) cc_final: 0.5476 (t80) REVERT: J 101 ARG cc_start: 0.7486 (mtp180) cc_final: 0.6935 (tpt170) REVERT: K 57 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: K 471 LYS cc_start: 0.7219 (mttt) cc_final: 0.6667 (tttt) REVERT: L 95 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5408 (t80) REVERT: M 39 LEU cc_start: 0.8250 (mt) cc_final: 0.7890 (tp) REVERT: M 213 HIS cc_start: 0.8331 (m170) cc_final: 0.8116 (m-70) REVERT: M 243 MET cc_start: 0.8036 (tmm) cc_final: 0.7727 (tmm) REVERT: M 295 LEU cc_start: 0.7779 (tp) cc_final: 0.7467 (tp) REVERT: M 403 LYS cc_start: 0.8122 (tppt) cc_final: 0.7705 (mmtt) REVERT: N 95 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5497 (t80) REVERT: N 101 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7173 (mmp-170) REVERT: O 47 LYS cc_start: 0.7994 (mttt) cc_final: 0.7692 (mmtt) REVERT: O 118 LYS cc_start: 0.7298 (mttt) cc_final: 0.6905 (ptmt) REVERT: O 403 LYS cc_start: 0.8393 (tppt) cc_final: 0.7971 (mmtt) REVERT: O 425 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6613 (mtm180) REVERT: O 471 LYS cc_start: 0.7182 (mttt) cc_final: 0.6776 (mttt) REVERT: P 95 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5477 (t80) REVERT: P 101 ARG cc_start: 0.7485 (mtp180) cc_final: 0.6935 (tpt170) REVERT: Q 57 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: Q 471 LYS cc_start: 0.7221 (mttt) cc_final: 0.6670 (tttt) REVERT: R 95 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5410 (t80) REVERT: S 39 LEU cc_start: 0.8249 (mt) cc_final: 0.7888 (tp) REVERT: S 213 HIS cc_start: 0.8326 (m170) cc_final: 0.8113 (m-70) REVERT: S 243 MET cc_start: 0.8032 (tmm) cc_final: 0.7721 (tmm) REVERT: S 295 LEU cc_start: 0.7780 (tp) cc_final: 0.7464 (tp) REVERT: S 403 LYS cc_start: 0.8120 (tppt) cc_final: 0.7701 (mmtt) REVERT: T 95 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5499 (t80) REVERT: T 101 ARG cc_start: 0.7732 (mtp180) cc_final: 0.7174 (mmp-170) REVERT: U 47 LYS cc_start: 0.7993 (mttt) cc_final: 0.7691 (mmtt) REVERT: U 118 LYS cc_start: 0.7299 (mttt) cc_final: 0.6927 (ptmt) REVERT: U 403 LYS cc_start: 0.8395 (tppt) cc_final: 0.7973 (mmtt) REVERT: U 425 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6612 (mtm180) REVERT: U 471 LYS cc_start: 0.7190 (mttt) cc_final: 0.6789 (mttt) REVERT: V 95 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5479 (t80) REVERT: V 101 ARG cc_start: 0.7484 (mtp180) cc_final: 0.6937 (tpt170) REVERT: W 57 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: W 471 LYS cc_start: 0.7221 (mttt) cc_final: 0.6670 (tttt) REVERT: X 95 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.5411 (t80) outliers start: 121 outliers final: 94 residues processed: 748 average time/residue: 0.6545 time to fit residues: 767.6623 Evaluate side-chains 737 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 631 time to evaluate : 6.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 438 GLU Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 438 GLU Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 406 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 469 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 555 optimal weight: 0.0980 chunk 347 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 256 optimal weight: 0.5980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48708 Z= 0.223 Angle : 0.480 6.912 65652 Z= 0.258 Chirality : 0.038 0.131 7092 Planarity : 0.003 0.049 8640 Dihedral : 4.267 15.502 6552 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.25 % Allowed : 11.60 % Favored : 85.15 % 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: 0.78 (0.11), residues: 5784 helix: 1.50 (0.10), residues: 2556 sheet: 0.57 (0.14), residues: 1116 loop : -0.69 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 238 PHE 0.012 0.002 PHE K 173 TYR 0.014 0.001 TYR A 345 ARG 0.011 0.000 ARG O 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 623 time to evaluate : 5.780 Fit side-chains REVERT: A 243 MET cc_start: 0.7986 (tmm) cc_final: 0.7633 (tmm) REVERT: A 295 LEU cc_start: 0.7894 (tp) cc_final: 0.7576 (tp) REVERT: A 403 LYS cc_start: 0.8178 (tppt) cc_final: 0.7740 (mmtt) REVERT: B 95 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5390 (t80) REVERT: B 101 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7189 (mmp-170) REVERT: C 80 ARG cc_start: 0.4498 (OUTLIER) cc_final: 0.4246 (ptm-80) REVERT: C 118 LYS cc_start: 0.7260 (mttt) cc_final: 0.6960 (ptmt) REVERT: C 403 LYS cc_start: 0.8446 (tppt) cc_final: 0.8029 (mmtt) REVERT: C 425 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6674 (mtm180) REVERT: C 471 LYS cc_start: 0.7197 (mttt) cc_final: 0.6768 (mttt) REVERT: D 95 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5568 (t80) REVERT: D 101 ARG cc_start: 0.7552 (mtp180) cc_final: 0.6947 (tpt170) REVERT: E 471 LYS cc_start: 0.7292 (mttt) cc_final: 0.6766 (tttt) REVERT: E 475 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6629 (t0) REVERT: F 95 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5432 (t80) REVERT: G 243 MET cc_start: 0.7979 (tmm) cc_final: 0.7627 (tmm) REVERT: G 295 LEU cc_start: 0.7892 (tp) cc_final: 0.7575 (tp) REVERT: G 403 LYS cc_start: 0.8182 (tppt) cc_final: 0.7743 (mmtt) REVERT: H 95 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5390 (t80) REVERT: H 101 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7193 (mmp-170) REVERT: I 80 ARG cc_start: 0.4490 (OUTLIER) cc_final: 0.4242 (ptm-80) REVERT: I 118 LYS cc_start: 0.7264 (mttt) cc_final: 0.6961 (ptmt) REVERT: I 403 LYS cc_start: 0.8442 (tppt) cc_final: 0.8026 (mmtt) REVERT: I 425 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6674 (mtm180) REVERT: I 471 LYS cc_start: 0.7194 (mttt) cc_final: 0.6765 (mttt) REVERT: J 95 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5563 (t80) REVERT: J 101 ARG cc_start: 0.7552 (mtp180) cc_final: 0.6946 (tpt170) REVERT: K 471 LYS cc_start: 0.7285 (mttt) cc_final: 0.6763 (tttt) REVERT: K 475 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6629 (t0) REVERT: L 95 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5433 (t80) REVERT: M 243 MET cc_start: 0.7989 (tmm) cc_final: 0.7636 (tmm) REVERT: M 295 LEU cc_start: 0.7901 (tp) cc_final: 0.7580 (tp) REVERT: M 403 LYS cc_start: 0.8176 (tppt) cc_final: 0.7735 (mmtt) REVERT: N 95 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.5391 (t80) REVERT: N 101 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7186 (mmp-170) REVERT: O 80 ARG cc_start: 0.4487 (OUTLIER) cc_final: 0.4240 (ptm-80) REVERT: O 118 LYS cc_start: 0.7263 (mttt) cc_final: 0.6959 (ptmt) REVERT: O 403 LYS cc_start: 0.8439 (tppt) cc_final: 0.8022 (mmtt) REVERT: O 425 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6675 (mtm180) REVERT: O 471 LYS cc_start: 0.7191 (mttt) cc_final: 0.6757 (mttt) REVERT: P 95 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5566 (t80) REVERT: P 101 ARG cc_start: 0.7554 (mtp180) cc_final: 0.6947 (tpt170) REVERT: Q 471 LYS cc_start: 0.7289 (mttt) cc_final: 0.6766 (tttt) REVERT: Q 475 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.6634 (t0) REVERT: R 95 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5431 (t80) REVERT: S 243 MET cc_start: 0.7982 (tmm) cc_final: 0.7629 (tmm) REVERT: S 295 LEU cc_start: 0.7898 (tp) cc_final: 0.7576 (tp) REVERT: S 403 LYS cc_start: 0.8174 (tppt) cc_final: 0.7734 (mmtt) REVERT: T 95 TYR cc_start: 0.6411 (OUTLIER) cc_final: 0.5387 (t80) REVERT: T 101 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7188 (mmp-170) REVERT: U 80 ARG cc_start: 0.4490 (OUTLIER) cc_final: 0.4241 (ptm-80) REVERT: U 118 LYS cc_start: 0.7262 (mttt) cc_final: 0.6960 (ptmt) REVERT: U 403 LYS cc_start: 0.8444 (tppt) cc_final: 0.8028 (mmtt) REVERT: U 425 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6674 (mtm180) REVERT: U 471 LYS cc_start: 0.7207 (mttt) cc_final: 0.6767 (mttt) REVERT: V 95 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.5567 (t80) REVERT: V 101 ARG cc_start: 0.7552 (mtp180) cc_final: 0.6949 (tpt170) REVERT: W 471 LYS cc_start: 0.7288 (mttt) cc_final: 0.6767 (tttt) REVERT: W 475 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6634 (t0) REVERT: X 95 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5428 (t80) outliers start: 172 outliers final: 139 residues processed: 736 average time/residue: 0.6576 time to fit residues: 763.6105 Evaluate side-chains 747 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 588 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 191 LEU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 438 GLU Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain Q residue 475 ASP Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 438 GLU Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain W residue 475 ASP Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 352 optimal weight: 2.9990 chunk 378 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 436 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 48708 Z= 0.252 Angle : 0.502 8.155 65652 Z= 0.268 Chirality : 0.039 0.132 7092 Planarity : 0.003 0.031 8640 Dihedral : 4.347 16.092 6552 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.44 % Allowed : 11.90 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.11), residues: 5784 helix: 1.42 (0.10), residues: 2556 sheet: 0.50 (0.14), residues: 1116 loop : -0.75 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 92 PHE 0.013 0.002 PHE Q 173 TYR 0.013 0.002 TYR S 378 ARG 0.006 0.000 ARG O 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 625 time to evaluate : 5.869 Fit side-chains REVERT: A 243 MET cc_start: 0.7962 (tmm) cc_final: 0.7611 (tmm) REVERT: A 295 LEU cc_start: 0.7888 (tp) cc_final: 0.7564 (tp) REVERT: A 403 LYS cc_start: 0.8206 (tppt) cc_final: 0.7750 (mmtt) REVERT: B 95 TYR cc_start: 0.6430 (OUTLIER) cc_final: 0.5385 (t80) REVERT: C 80 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4646 (ptm-80) REVERT: C 118 LYS cc_start: 0.7274 (mttt) cc_final: 0.6976 (ptmt) REVERT: C 403 LYS cc_start: 0.8455 (tppt) cc_final: 0.8035 (mmtt) REVERT: C 425 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6656 (mtm180) REVERT: C 471 LYS cc_start: 0.7277 (mttt) cc_final: 0.6817 (mttt) REVERT: D 95 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5562 (t80) REVERT: D 101 ARG cc_start: 0.7558 (mtp180) cc_final: 0.6922 (tpt170) REVERT: E 471 LYS cc_start: 0.7283 (mttt) cc_final: 0.6774 (tttt) REVERT: E 475 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6763 (t0) REVERT: F 95 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5404 (t80) REVERT: G 243 MET cc_start: 0.7956 (tmm) cc_final: 0.7605 (tmm) REVERT: G 295 LEU cc_start: 0.7884 (tp) cc_final: 0.7561 (tp) REVERT: G 403 LYS cc_start: 0.8210 (tppt) cc_final: 0.7752 (mmtt) REVERT: H 95 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5384 (t80) REVERT: I 80 ARG cc_start: 0.4877 (OUTLIER) cc_final: 0.4639 (ptm-80) REVERT: I 118 LYS cc_start: 0.7277 (mttt) cc_final: 0.6976 (ptmt) REVERT: I 403 LYS cc_start: 0.8447 (tppt) cc_final: 0.8027 (mmtt) REVERT: I 425 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6655 (mtm180) REVERT: I 471 LYS cc_start: 0.7274 (mttt) cc_final: 0.6814 (mttt) REVERT: J 95 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5559 (t80) REVERT: J 101 ARG cc_start: 0.7558 (mtp180) cc_final: 0.6924 (tpt170) REVERT: K 471 LYS cc_start: 0.7275 (mttt) cc_final: 0.6771 (tttt) REVERT: K 475 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6764 (t0) REVERT: L 95 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5402 (t80) REVERT: M 243 MET cc_start: 0.7962 (tmm) cc_final: 0.7610 (tmm) REVERT: M 295 LEU cc_start: 0.7894 (tp) cc_final: 0.7576 (tp) REVERT: M 403 LYS cc_start: 0.8203 (tppt) cc_final: 0.7746 (mmtt) REVERT: N 95 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5391 (t80) REVERT: N 101 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7135 (mmp-170) REVERT: O 80 ARG cc_start: 0.4874 (OUTLIER) cc_final: 0.4637 (ptm-80) REVERT: O 118 LYS cc_start: 0.7278 (mttt) cc_final: 0.6974 (ptmt) REVERT: O 403 LYS cc_start: 0.8444 (tppt) cc_final: 0.8025 (mmtt) REVERT: O 425 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6655 (mtm180) REVERT: O 471 LYS cc_start: 0.7270 (mttt) cc_final: 0.6807 (mttt) REVERT: P 95 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5560 (t80) REVERT: P 101 ARG cc_start: 0.7558 (mtp180) cc_final: 0.6927 (tpt170) REVERT: Q 471 LYS cc_start: 0.7276 (mttt) cc_final: 0.6771 (tttt) REVERT: Q 475 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6768 (t0) REVERT: R 95 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5399 (t80) REVERT: S 243 MET cc_start: 0.7955 (tmm) cc_final: 0.7606 (tmm) REVERT: S 295 LEU cc_start: 0.7897 (tp) cc_final: 0.7579 (tp) REVERT: S 403 LYS cc_start: 0.8203 (tppt) cc_final: 0.7747 (mmtt) REVERT: T 95 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5387 (t80) REVERT: T 101 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7135 (mmp-170) REVERT: U 80 ARG cc_start: 0.4878 (OUTLIER) cc_final: 0.4636 (ptm-80) REVERT: U 118 LYS cc_start: 0.7275 (mttt) cc_final: 0.6972 (ptmt) REVERT: U 403 LYS cc_start: 0.8448 (tppt) cc_final: 0.8029 (mmtt) REVERT: U 425 ARG cc_start: 0.7208 (mtm-85) cc_final: 0.6654 (mtm180) REVERT: U 471 LYS cc_start: 0.7283 (mttt) cc_final: 0.6829 (mttt) REVERT: V 95 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5560 (t80) REVERT: V 101 ARG cc_start: 0.7560 (mtp180) cc_final: 0.6927 (tpt170) REVERT: W 471 LYS cc_start: 0.7276 (mttt) cc_final: 0.6773 (tttt) REVERT: W 475 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6763 (t0) REVERT: X 95 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5401 (t80) outliers start: 182 outliers final: 148 residues processed: 747 average time/residue: 0.6442 time to fit residues: 761.2287 Evaluate side-chains 774 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 606 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain K residue 475 ASP Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 18 ASN Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain Q residue 475 ASP Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 18 ASN Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 91 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 438 GLU Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain W residue 475 ASP Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 10.0000 chunk 531 optimal weight: 4.9990 chunk 485 optimal weight: 4.9990 chunk 517 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 467 optimal weight: 10.0000 chunk 489 optimal weight: 5.9990 chunk 515 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 48708 Z= 0.373 Angle : 0.582 9.115 65652 Z= 0.308 Chirality : 0.042 0.158 7092 Planarity : 0.004 0.038 8640 Dihedral : 4.665 17.516 6552 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.33 % Allowed : 12.17 % Favored : 84.50 % 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: 0.46 (0.10), residues: 5784 helix: 1.21 (0.10), residues: 2520 sheet: 0.33 (0.14), residues: 1116 loop : -0.73 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 238 PHE 0.015 0.002 PHE W 173 TYR 0.016 0.002 TYR W 334 ARG 0.004 0.001 ARG O 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 594 time to evaluate : 5.513 Fit side-chains REVERT: A 295 LEU cc_start: 0.7856 (tp) cc_final: 0.7540 (tp) REVERT: A 403 LYS cc_start: 0.8253 (tppt) cc_final: 0.7759 (mmtt) REVERT: B 95 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.5441 (t80) REVERT: C 118 LYS cc_start: 0.7336 (mttt) cc_final: 0.6985 (ptmt) REVERT: C 403 LYS cc_start: 0.8404 (tppt) cc_final: 0.7936 (mmtt) REVERT: C 425 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6740 (mtm180) REVERT: C 471 LYS cc_start: 0.7226 (mttt) cc_final: 0.6758 (mttt) REVERT: D 95 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5278 (t80) REVERT: D 101 ARG cc_start: 0.7569 (mtp180) cc_final: 0.6951 (tpt170) REVERT: E 471 LYS cc_start: 0.7295 (mttt) cc_final: 0.6797 (tttt) REVERT: F 95 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5460 (t80) REVERT: G 295 LEU cc_start: 0.7848 (tp) cc_final: 0.7535 (tp) REVERT: G 403 LYS cc_start: 0.8259 (tppt) cc_final: 0.7763 (mmtt) REVERT: H 95 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5442 (t80) REVERT: I 118 LYS cc_start: 0.7340 (mttt) cc_final: 0.6986 (ptmt) REVERT: I 403 LYS cc_start: 0.8398 (tppt) cc_final: 0.7928 (mmtt) REVERT: I 425 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6743 (mtm180) REVERT: I 471 LYS cc_start: 0.7225 (mttt) cc_final: 0.6758 (mttt) REVERT: J 95 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5275 (t80) REVERT: J 101 ARG cc_start: 0.7568 (mtp180) cc_final: 0.6951 (tpt170) REVERT: K 471 LYS cc_start: 0.7287 (mttt) cc_final: 0.6793 (tttt) REVERT: L 95 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5462 (t80) REVERT: M 295 LEU cc_start: 0.7859 (tp) cc_final: 0.7543 (tp) REVERT: M 403 LYS cc_start: 0.8254 (tppt) cc_final: 0.7756 (mmtt) REVERT: N 95 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5443 (t80) REVERT: O 118 LYS cc_start: 0.7341 (mttt) cc_final: 0.6986 (ptmt) REVERT: O 403 LYS cc_start: 0.8395 (tppt) cc_final: 0.7928 (mmtt) REVERT: O 425 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6740 (mtm180) REVERT: O 471 LYS cc_start: 0.7221 (mttt) cc_final: 0.6748 (mttt) REVERT: P 95 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5280 (t80) REVERT: P 101 ARG cc_start: 0.7569 (mtp180) cc_final: 0.6951 (tpt170) REVERT: Q 154 MET cc_start: 0.9090 (ttm) cc_final: 0.8739 (mtp) REVERT: Q 471 LYS cc_start: 0.7288 (mttt) cc_final: 0.6793 (tttt) REVERT: R 95 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5460 (t80) REVERT: S 295 LEU cc_start: 0.7855 (tp) cc_final: 0.7539 (tp) REVERT: S 403 LYS cc_start: 0.8254 (tppt) cc_final: 0.7758 (mmtt) REVERT: T 95 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.5441 (t80) REVERT: U 118 LYS cc_start: 0.7334 (mttt) cc_final: 0.6982 (ptmt) REVERT: U 403 LYS cc_start: 0.8399 (tppt) cc_final: 0.7933 (mmtt) REVERT: U 425 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6739 (mtm180) REVERT: U 471 LYS cc_start: 0.7232 (mttt) cc_final: 0.6761 (mttt) REVERT: V 95 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5279 (t80) REVERT: V 101 ARG cc_start: 0.7568 (mtp180) cc_final: 0.6974 (tpt170) REVERT: W 154 MET cc_start: 0.9088 (ttm) cc_final: 0.8738 (mtp) REVERT: W 471 LYS cc_start: 0.7290 (mttt) cc_final: 0.6795 (tttt) REVERT: X 95 TYR cc_start: 0.6176 (OUTLIER) cc_final: 0.5459 (t80) outliers start: 176 outliers final: 141 residues processed: 712 average time/residue: 0.6349 time to fit residues: 719.0323 Evaluate side-chains 743 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 590 time to evaluate : 5.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 434 LYS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain K residue 451 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 294 ASN Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 434 LYS Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain Q residue 451 SER Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 434 LYS Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 5.9990 chunk 547 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 380 optimal weight: 3.9990 chunk 573 optimal weight: 1.9990 chunk 528 optimal weight: 5.9990 chunk 456 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 48708 Z= 0.193 Angle : 0.481 7.935 65652 Z= 0.258 Chirality : 0.038 0.132 7092 Planarity : 0.003 0.046 8640 Dihedral : 4.287 16.961 6552 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.87 % Allowed : 12.81 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 5784 helix: 1.39 (0.10), residues: 2556 sheet: 0.39 (0.14), residues: 1116 loop : -0.74 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 92 PHE 0.012 0.001 PHE A 173 TYR 0.016 0.001 TYR G 378 ARG 0.011 0.000 ARG O 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11568 Ramachandran restraints generated. 5784 Oldfield, 0 Emsley, 5784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 618 time to evaluate : 5.590 Fit side-chains REVERT: A 295 LEU cc_start: 0.7889 (tp) cc_final: 0.7580 (tp) REVERT: A 403 LYS cc_start: 0.8211 (tppt) cc_final: 0.7751 (mmtt) REVERT: B 95 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5354 (t80) REVERT: B 101 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7142 (mmp-170) REVERT: C 118 LYS cc_start: 0.7353 (mttt) cc_final: 0.6952 (ptmt) REVERT: C 403 LYS cc_start: 0.8380 (tppt) cc_final: 0.7948 (mmtt) REVERT: C 425 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6678 (mtm180) REVERT: C 471 LYS cc_start: 0.7249 (mttt) cc_final: 0.6845 (mttt) REVERT: D 95 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5629 (t80) REVERT: D 101 ARG cc_start: 0.7596 (mtp180) cc_final: 0.6952 (tpt170) REVERT: E 154 MET cc_start: 0.9034 (ttm) cc_final: 0.8442 (mtp) REVERT: E 471 LYS cc_start: 0.7290 (mttt) cc_final: 0.6784 (tttt) REVERT: F 93 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5312 (m-30) REVERT: F 95 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5384 (t80) REVERT: G 295 LEU cc_start: 0.7880 (tp) cc_final: 0.7575 (tp) REVERT: G 403 LYS cc_start: 0.8218 (tppt) cc_final: 0.7736 (mmtt) REVERT: H 95 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.5355 (t80) REVERT: H 101 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7144 (mmp-170) REVERT: I 118 LYS cc_start: 0.7358 (mttt) cc_final: 0.6955 (ptmt) REVERT: I 403 LYS cc_start: 0.8374 (tppt) cc_final: 0.7942 (mmtt) REVERT: I 425 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6683 (mtm180) REVERT: I 471 LYS cc_start: 0.7245 (mttt) cc_final: 0.6841 (mttt) REVERT: J 95 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5625 (t80) REVERT: J 101 ARG cc_start: 0.7594 (mtp180) cc_final: 0.6951 (tpt170) REVERT: K 154 MET cc_start: 0.9030 (ttm) cc_final: 0.8438 (mtp) REVERT: K 471 LYS cc_start: 0.7286 (mttt) cc_final: 0.6780 (tttt) REVERT: L 93 ASP cc_start: 0.6131 (OUTLIER) cc_final: 0.5308 (m-30) REVERT: L 95 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5387 (t80) REVERT: M 295 LEU cc_start: 0.7890 (tp) cc_final: 0.7577 (tp) REVERT: M 403 LYS cc_start: 0.8210 (tppt) cc_final: 0.7749 (mmtt) REVERT: N 95 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5355 (t80) REVERT: N 101 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7137 (mmp-170) REVERT: O 118 LYS cc_start: 0.7358 (mttt) cc_final: 0.6952 (ptmt) REVERT: O 403 LYS cc_start: 0.8368 (tppt) cc_final: 0.7938 (mmtt) REVERT: O 425 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6679 (mtm180) REVERT: O 471 LYS cc_start: 0.7242 (mttt) cc_final: 0.6835 (mttt) REVERT: P 95 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5628 (t80) REVERT: P 101 ARG cc_start: 0.7597 (mtp180) cc_final: 0.6954 (tpt170) REVERT: Q 154 MET cc_start: 0.9041 (ttm) cc_final: 0.8433 (mtp) REVERT: Q 471 LYS cc_start: 0.7285 (mttt) cc_final: 0.6780 (tttt) REVERT: R 93 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5306 (m-30) REVERT: R 95 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5385 (t80) REVERT: S 295 LEU cc_start: 0.7841 (tp) cc_final: 0.7527 (tp) REVERT: S 403 LYS cc_start: 0.8209 (tppt) cc_final: 0.7750 (mmtt) REVERT: T 95 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5355 (t80) REVERT: T 101 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7142 (mmp-170) REVERT: U 118 LYS cc_start: 0.7353 (mttt) cc_final: 0.6950 (ptmt) REVERT: U 403 LYS cc_start: 0.8373 (tppt) cc_final: 0.7943 (mmtt) REVERT: U 425 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6678 (mtm180) REVERT: U 471 LYS cc_start: 0.7251 (mttt) cc_final: 0.6848 (mttt) REVERT: V 95 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5631 (t80) REVERT: V 101 ARG cc_start: 0.7597 (mtp180) cc_final: 0.6956 (tpt170) REVERT: W 154 MET cc_start: 0.9045 (ttm) cc_final: 0.8435 (mtp) REVERT: W 471 LYS cc_start: 0.7286 (mttt) cc_final: 0.6782 (tttt) REVERT: X 93 ASP cc_start: 0.6133 (OUTLIER) cc_final: 0.5311 (m-30) REVERT: X 95 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5383 (t80) outliers start: 152 outliers final: 129 residues processed: 721 average time/residue: 0.6443 time to fit residues: 738.3439 Evaluate side-chains 751 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 606 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 374 GLU Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 414 SER Chi-restraints excluded: chain I residue 434 LYS Chi-restraints excluded: chain I residue 440 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 95 TYR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 199 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 220 THR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 438 GLU Chi-restraints excluded: chain K residue 440 LEU Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 95 TYR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 191 LEU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 286 MET Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 374 GLU Chi-restraints excluded: chain M residue 414 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 170 MET Chi-restraints excluded: chain O residue 199 THR Chi-restraints excluded: chain O residue 204 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 325 GLU Chi-restraints excluded: chain O residue 414 SER Chi-restraints excluded: chain O residue 440 LEU Chi-restraints excluded: chain P residue 93 ASP Chi-restraints excluded: chain P residue 95 TYR Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 152 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 204 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 228 LEU Chi-restraints excluded: chain Q residue 324 THR Chi-restraints excluded: chain Q residue 339 VAL Chi-restraints excluded: chain Q residue 438 GLU Chi-restraints excluded: chain Q residue 440 LEU Chi-restraints excluded: chain R residue 93 ASP Chi-restraints excluded: chain R residue 95 TYR Chi-restraints excluded: chain S residue 18 ASN Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 199 THR Chi-restraints excluded: chain S residue 204 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 286 MET Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 414 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 95 TYR Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 170 MET Chi-restraints excluded: chain U residue 199 THR Chi-restraints excluded: chain U residue 204 VAL Chi-restraints excluded: chain U residue 228 LEU Chi-restraints excluded: chain U residue 324 THR Chi-restraints excluded: chain U residue 325 GLU Chi-restraints excluded: chain U residue 414 SER Chi-restraints excluded: chain U residue 440 LEU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 95 TYR Chi-restraints excluded: chain W residue 90 VAL Chi-restraints excluded: chain W residue 133 VAL Chi-restraints excluded: chain W residue 152 GLU Chi-restraints excluded: chain W residue 199 THR Chi-restraints excluded: chain W residue 204 VAL Chi-restraints excluded: chain W residue 220 THR Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 440 LEU Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 8.9990 chunk 486 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 421 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 469 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** I 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 303 GLN ** O 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 303 GLN ** S 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123072 restraints weight = 56498.602| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.47 r_work: 0.3041 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 48708 Z= 0.268 Angle : 0.524 8.294 65652 Z= 0.278 Chirality : 0.039 0.149 7092 Planarity : 0.004 0.044 8640 Dihedral : 4.409 16.529 6552 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.97 % Allowed : 12.70 % Favored : 84.33 % 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: 0.53 (0.11), residues: 5784 helix: 1.31 (0.10), residues: 2556 sheet: 0.34 (0.14), residues: 1116 loop : -0.76 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 238 PHE 0.014 0.002 PHE K 173 TYR 0.013 0.002 TYR Q 334 ARG 0.011 0.000 ARG O 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13408.77 seconds wall clock time: 240 minutes 42.00 seconds (14442.00 seconds total)