Starting phenix.real_space_refine on Mon Mar 25 06:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdc_43146/03_2024/8vdc_43146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdc_43146/03_2024/8vdc_43146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdc_43146/03_2024/8vdc_43146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdc_43146/03_2024/8vdc_43146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdc_43146/03_2024/8vdc_43146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdc_43146/03_2024/8vdc_43146.pdb" } resolution = 3.5 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= 0.000 sd= 0.004 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 29496 2.51 5 N 7992 2.21 5 O 9444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47064 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} 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: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 103 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 22.54, per 1000 atoms: 0.48 Number of scatterers: 47064 At special positions: 0 Unit cell: (179.55, 179.55, 143.64, 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 9444 8.00 N 7992 7.00 C 29496 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: 17.05 Conformation dependent library (CDL) restraints added in 7.8 seconds 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10896 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 72 sheets defined 47.5% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG A 59 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 132 through 148 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: 3.633A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 445 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG C 59 " --> pdb=" O TYR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 132 through 148 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: 3.633A pdb=" N LEU C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS C 304 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 445 Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 34 through 40 Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG E 59 " --> pdb=" O TYR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 80 Processing helix chain 'E' and resid 93 through 108 Processing helix chain 'E' and resid 117 through 131 Processing helix chain 'E' and resid 132 through 148 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: 3.632A pdb=" N LEU E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS E 304 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 445 Processing helix chain 'E' and resid 451 through 458 Processing helix chain 'E' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 80 Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 117 through 131 Processing helix chain 'G' and resid 132 through 148 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: 3.633A pdb=" N LEU G 282 " --> pdb=" O TYR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS G 304 " --> pdb=" O ARG G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR G 378 " --> pdb=" O GLU G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG G 386 " --> pdb=" O GLY G 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR G 389 " --> pdb=" O GLN G 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 445 Processing helix chain 'G' and resid 451 through 458 Processing helix chain 'G' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 34 through 40 Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG I 59 " --> pdb=" O TYR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 80 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 117 through 131 Processing helix chain 'I' and resid 132 through 148 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: 3.633A pdb=" N LEU I 282 " --> pdb=" O TYR I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS I 304 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR I 378 " --> pdb=" O GLU I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG I 386 " --> pdb=" O GLY I 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR I 389 " --> pdb=" O GLN I 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG I 400 " --> pdb=" O LYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 445 Processing helix chain 'I' and resid 451 through 458 Processing helix chain 'I' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 34 through 40 Processing helix chain 'K' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG K 59 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 80 Processing helix chain 'K' and resid 93 through 108 Processing helix chain 'K' and resid 117 through 131 Processing helix chain 'K' and resid 132 through 148 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: 3.632A pdb=" N LEU K 282 " --> pdb=" O TYR K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS K 304 " --> pdb=" O ARG K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR K 378 " --> pdb=" O GLU K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG K 386 " --> pdb=" O GLY K 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 445 Processing helix chain 'K' and resid 451 through 458 Processing helix chain 'K' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS K 470 " --> pdb=" O GLU K 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 34 through 40 Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG M 59 " --> pdb=" O TYR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 80 Processing helix chain 'M' and resid 93 through 108 Processing helix chain 'M' and resid 117 through 131 Processing helix chain 'M' and resid 132 through 148 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: 3.633A pdb=" N LEU M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS M 304 " --> pdb=" O ARG M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR M 378 " --> pdb=" O GLU M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG M 386 " --> pdb=" O GLY M 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR M 389 " --> pdb=" O GLN M 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG M 400 " --> pdb=" O LYS M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 445 Processing helix chain 'M' and resid 451 through 458 Processing helix chain 'M' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS M 470 " --> pdb=" O GLU M 466 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 34 through 40 Processing helix chain 'O' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER O 46 " --> pdb=" O VAL O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG O 59 " --> pdb=" O TYR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL O 75 " --> pdb=" O THR O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 80 Processing helix chain 'O' and resid 93 through 108 Processing helix chain 'O' and resid 117 through 131 Processing helix chain 'O' and resid 132 through 148 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: 3.633A pdb=" N LEU O 282 " --> pdb=" O TYR O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS O 304 " --> pdb=" O ARG O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 356 Processing helix chain 'O' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR O 378 " --> pdb=" O GLU O 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG O 386 " --> pdb=" O GLY O 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR O 389 " --> pdb=" O GLN O 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG O 400 " --> pdb=" O LYS O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 445 Processing helix chain 'O' and resid 451 through 458 Processing helix chain 'O' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS O 470 " --> pdb=" O GLU O 466 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 34 through 40 Processing helix chain 'Q' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER Q 46 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG Q 59 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 80 Processing helix chain 'Q' and resid 93 through 108 Processing helix chain 'Q' and resid 117 through 131 Processing helix chain 'Q' and resid 132 through 148 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: 3.632A pdb=" N LEU Q 282 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS Q 304 " --> pdb=" O ARG Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 356 Processing helix chain 'Q' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR Q 378 " --> pdb=" O GLU Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG Q 386 " --> pdb=" O GLY Q 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR Q 389 " --> pdb=" O GLN Q 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG Q 400 " --> pdb=" O LYS Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 445 Processing helix chain 'Q' and resid 451 through 458 Processing helix chain 'Q' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS Q 470 " --> pdb=" O GLU Q 466 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 34 through 40 Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG S 59 " --> pdb=" O TYR S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL S 75 " --> pdb=" O THR S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 80 Processing helix chain 'S' and resid 93 through 108 Processing helix chain 'S' and resid 117 through 131 Processing helix chain 'S' and resid 132 through 148 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: 3.633A pdb=" N LEU S 282 " --> pdb=" O TYR S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS S 304 " --> pdb=" O ARG S 301 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 356 Processing helix chain 'S' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR S 378 " --> pdb=" O GLU S 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG S 386 " --> pdb=" O GLY S 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR S 389 " --> pdb=" O GLN S 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG S 400 " --> pdb=" O LYS S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 445 Processing helix chain 'S' and resid 451 through 458 Processing helix chain 'S' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS S 470 " --> pdb=" O GLU S 466 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 34 through 40 Processing helix chain 'U' and resid 42 through 55 removed outlier: 3.664A pdb=" N SER U 46 " --> pdb=" O VAL U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 68 removed outlier: 3.741A pdb=" N ARG U 59 " --> pdb=" O TYR U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL U 75 " --> pdb=" O THR U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 80 Processing helix chain 'U' and resid 93 through 108 Processing helix chain 'U' and resid 117 through 131 Processing helix chain 'U' and resid 132 through 148 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: 3.633A pdb=" N LEU U 282 " --> pdb=" O TYR U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS U 304 " --> pdb=" O ARG U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 338 through 356 Processing helix chain 'U' and resid 371 through 380 removed outlier: 3.707A pdb=" N TYR U 378 " --> pdb=" O GLU U 374 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 412 removed outlier: 3.647A pdb=" N ARG U 386 " --> pdb=" O GLY U 382 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR U 389 " --> pdb=" O GLN U 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG U 400 " --> pdb=" O LYS U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 445 Processing helix chain 'U' and resid 451 through 458 Processing helix chain 'U' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS U 470 " --> pdb=" O GLU U 466 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 21 Processing helix chain 'W' and resid 34 through 40 Processing helix chain 'W' and resid 42 through 55 removed outlier: 3.663A pdb=" N SER W 46 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 68 removed outlier: 3.742A pdb=" N ARG W 59 " --> pdb=" O TYR W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 76 removed outlier: 3.646A pdb=" N VAL W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 80 Processing helix chain 'W' and resid 93 through 108 Processing helix chain 'W' and resid 117 through 131 Processing helix chain 'W' and resid 132 through 148 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: 3.632A pdb=" N LEU W 282 " --> pdb=" O TYR W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 305 removed outlier: 4.129A pdb=" N LYS W 304 " --> pdb=" O ARG W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 356 Processing helix chain 'W' and resid 371 through 380 removed outlier: 3.708A pdb=" N TYR W 378 " --> pdb=" O GLU W 374 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 412 removed outlier: 3.646A pdb=" N ARG W 386 " --> pdb=" O GLY W 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR W 389 " --> pdb=" O GLN W 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG W 400 " --> pdb=" O LYS W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 445 Processing helix chain 'W' and resid 451 through 458 Processing helix chain 'W' and resid 466 through 479 removed outlier: 3.794A pdb=" N LYS W 470 " --> pdb=" O GLU W 466 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 30 through 31 removed outlier: 5.759A pdb=" N ASP A 177 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A 184 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER A 234 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU A 219 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU A 232 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 11.220A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP A 329 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP C 177 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 184 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER C 234 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU C 219 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU C 232 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.943A 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 290 removed outlier: 3.863A pdb=" N ASP C 329 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP E 177 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER E 184 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER E 234 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU E 219 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU E 232 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP E 329 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP G 177 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER G 184 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER G 234 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU G 219 " --> pdb=" O GLU G 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU G 232 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 11.220A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP G 329 " --> pdb=" O LYS G 290 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP I 177 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER I 184 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER I 234 " --> pdb=" O ARG I 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU I 219 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU I 232 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.943A 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 290 removed outlier: 3.863A pdb=" N ASP I 329 " --> pdb=" O LYS I 290 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'I' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP K 177 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER K 184 " --> pdb=" O ASP K 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER K 234 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU K 219 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU K 232 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP K 329 " --> pdb=" O LYS K 290 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'K' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP M 177 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER M 184 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER M 234 " --> pdb=" O ARG M 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU M 219 " --> pdb=" O GLU M 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU M 232 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 11.220A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP M 329 " --> pdb=" O LYS M 290 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'M' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP O 177 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER O 184 " --> pdb=" O ASP O 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER O 234 " --> pdb=" O ARG O 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU O 219 " --> pdb=" O GLU O 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU O 232 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.943A 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 290 removed outlier: 3.863A pdb=" N ASP O 329 " --> pdb=" O LYS O 290 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP Q 177 " --> pdb=" O SER Q 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER Q 184 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER Q 234 " --> pdb=" O ARG Q 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU Q 232 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP Q 329 " --> pdb=" O LYS Q 290 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Q' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP S 177 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER S 184 " --> pdb=" O ASP S 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER S 234 " --> pdb=" O ARG S 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU S 219 " --> pdb=" O GLU S 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU S 232 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 11.220A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP S 329 " --> pdb=" O LYS S 290 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'S' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP U 177 " --> pdb=" O SER U 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER U 184 " --> pdb=" O ASP U 177 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER U 234 " --> pdb=" O ARG U 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU U 219 " --> pdb=" O GLU U 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU U 232 " --> pdb=" O LEU U 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.943A 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 290 removed outlier: 3.863A pdb=" N ASP U 329 " --> pdb=" O LYS U 290 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 310 through 312 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 30 through 31 removed outlier: 5.759A pdb=" N ASP W 177 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER W 184 " --> pdb=" O ASP W 177 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER W 234 " --> pdb=" O ARG W 217 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N LEU W 219 " --> pdb=" O GLU W 232 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU W 232 " --> pdb=" O LEU W 219 " (cutoff:3.500A) removed outlier: 11.221A 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: 3.942A 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 290 removed outlier: 3.863A pdb=" N ASP W 329 " --> pdb=" O LYS W 290 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'W' and resid 310 through 312 Processing sheet with id= 72, first strand: chain 'W' and resid 315 through 317 2304 hydrogen bonds defined for protein. 6552 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: 18.98 Time building geometry restraints manager: 18.62 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: 15712 1.34 - 1.45: 5730 1.45 - 1.57: 26162 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 47868 Sorted by residual: bond pdb=" N ASN K 16 " pdb=" CA ASN K 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN Q 16 " pdb=" CA ASN Q 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN W 16 " pdb=" CA ASN W 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN E 16 " pdb=" CA ASN E 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" N ASN O 16 " pdb=" CA ASN O 16 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.32e+00 ... (remaining 47863 not shown) Histogram of bond angle deviations from ideal: 99.61 - 105.94: 576 105.94 - 112.27: 22124 112.27 - 118.60: 14436 118.60 - 124.93: 27004 124.93 - 131.26: 360 Bond angle restraints: 64500 Sorted by residual: angle pdb=" N HIS U 92 " pdb=" CA HIS U 92 " pdb=" C HIS U 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS C 92 " pdb=" CA HIS C 92 " pdb=" C HIS C 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS O 92 " pdb=" CA HIS O 92 " pdb=" C HIS O 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS I 92 " pdb=" CA HIS I 92 " pdb=" C HIS I 92 " ideal model delta sigma weight residual 113.38 116.47 -3.09 1.23e+00 6.61e-01 6.32e+00 angle pdb=" N HIS S 92 " pdb=" CA HIS S 92 " pdb=" C HIS S 92 " ideal model delta sigma weight residual 113.38 116.46 -3.08 1.23e+00 6.61e-01 6.29e+00 ... (remaining 64495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 26796 17.68 - 35.36: 1944 35.36 - 53.04: 312 53.04 - 70.72: 84 70.72 - 88.40: 48 Dihedral angle restraints: 29184 sinusoidal: 12204 harmonic: 16980 Sorted by residual: dihedral pdb=" CA ILE W 444 " pdb=" C ILE W 444 " pdb=" N ASP W 445 " pdb=" CA ASP W 445 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE E 444 " pdb=" C ILE E 444 " pdb=" N ASP E 445 " pdb=" CA ASP E 445 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE Q 444 " pdb=" C ILE Q 444 " pdb=" N ASP Q 445 " pdb=" CA ASP Q 445 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 29181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3492 0.031 - 0.061: 2234 0.061 - 0.092: 824 0.092 - 0.123: 350 0.123 - 0.153: 72 Chirality restraints: 6972 Sorted by residual: chirality pdb=" CA ILE W 175 " pdb=" N ILE W 175 " pdb=" C ILE W 175 " pdb=" CB ILE W 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE Q 175 " pdb=" N ILE Q 175 " pdb=" C ILE Q 175 " pdb=" CB ILE Q 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE E 175 " pdb=" N ILE E 175 " pdb=" C ILE E 175 " pdb=" CB ILE E 175 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 6969 not shown) Planarity restraints: 8484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS W 388 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C LYS W 388 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS W 388 " -0.020 2.00e-02 2.50e+03 pdb=" N THR W 389 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 388 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C LYS Q 388 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS Q 388 " -0.020 2.00e-02 2.50e+03 pdb=" N THR Q 389 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 388 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.91e+00 pdb=" C LYS A 388 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 389 " -0.018 2.00e-02 2.50e+03 ... (remaining 8481 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 18450 2.88 - 3.39: 44862 3.39 - 3.89: 75120 3.89 - 4.40: 89024 4.40 - 4.90: 148086 Nonbonded interactions: 375542 Sorted by model distance: nonbonded pdb=" OG SER O 145 " pdb=" OD2 ASP O 257 " model vdw 2.377 2.440 nonbonded pdb=" OG SER U 145 " pdb=" OD2 ASP U 257 " model vdw 2.377 2.440 nonbonded pdb=" OG SER E 145 " pdb=" OD2 ASP E 257 " model vdw 2.378 2.440 nonbonded pdb=" OG SER K 145 " pdb=" OD2 ASP K 257 " model vdw 2.378 2.440 nonbonded pdb=" OG SER W 145 " pdb=" OD2 ASP W 257 " model vdw 2.378 2.440 ... (remaining 375537 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 12.520 Check model and map are aligned: 0.700 Set scattering table: 0.510 Process input model: 114.630 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.430 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.006 0.043 47868 Z= 0.392 Angle : 0.752 5.491 64500 Z= 0.449 Chirality : 0.046 0.153 6972 Planarity : 0.010 0.087 8484 Dihedral : 13.426 88.398 18288 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.09), residues: 5688 helix: -1.40 (0.08), residues: 2388 sheet: -0.02 (0.16), residues: 1020 loop : -1.47 (0.10), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 238 PHE 0.023 0.004 PHE S 173 TYR 0.039 0.004 TYR E 66 ARG 0.015 0.003 ARG W 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 6.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ARG cc_start: 0.5030 (tpt170) cc_final: 0.3085 (ptp-110) REVERT: C 154 MET cc_start: 0.8744 (ttm) cc_final: 0.8285 (mtp) REVERT: C 279 MET cc_start: 0.8950 (mmm) cc_final: 0.8729 (mmm) REVERT: C 320 GLU cc_start: 0.7402 (pt0) cc_final: 0.7179 (tm-30) REVERT: E 239 SER cc_start: 0.8583 (m) cc_final: 0.8377 (p) REVERT: E 279 MET cc_start: 0.8878 (mmm) cc_final: 0.8578 (mmt) REVERT: E 355 MET cc_start: 0.9009 (ttp) cc_final: 0.8584 (ttm) REVERT: I 80 ARG cc_start: 0.5031 (tpt170) cc_final: 0.3089 (ptp-110) REVERT: I 154 MET cc_start: 0.8743 (ttm) cc_final: 0.8284 (mtp) REVERT: I 279 MET cc_start: 0.8952 (mmm) cc_final: 0.8730 (mmm) REVERT: I 320 GLU cc_start: 0.7403 (pt0) cc_final: 0.7177 (tm-30) REVERT: K 239 SER cc_start: 0.8583 (m) cc_final: 0.8375 (p) REVERT: K 279 MET cc_start: 0.8878 (mmm) cc_final: 0.8578 (mmt) REVERT: K 355 MET cc_start: 0.9007 (ttp) cc_final: 0.8587 (ttm) REVERT: O 80 ARG cc_start: 0.5027 (tpt170) cc_final: 0.3087 (ptp-110) REVERT: O 154 MET cc_start: 0.8743 (ttm) cc_final: 0.8283 (mtp) REVERT: O 279 MET cc_start: 0.8950 (mmm) cc_final: 0.8725 (mmm) REVERT: O 320 GLU cc_start: 0.7403 (pt0) cc_final: 0.7179 (tm-30) REVERT: Q 239 SER cc_start: 0.8586 (m) cc_final: 0.8381 (p) REVERT: Q 279 MET cc_start: 0.8878 (mmm) cc_final: 0.8578 (mmt) REVERT: Q 355 MET cc_start: 0.9015 (ttp) cc_final: 0.8584 (ttm) REVERT: U 80 ARG cc_start: 0.5027 (tpt170) cc_final: 0.3085 (ptp-110) REVERT: U 154 MET cc_start: 0.8746 (ttm) cc_final: 0.8284 (mtp) REVERT: U 279 MET cc_start: 0.8948 (mmm) cc_final: 0.8724 (mmm) REVERT: U 320 GLU cc_start: 0.7402 (pt0) cc_final: 0.7178 (tm-30) REVERT: W 239 SER cc_start: 0.8585 (m) cc_final: 0.8378 (p) REVERT: W 279 MET cc_start: 0.8880 (mmm) cc_final: 0.8574 (mmt) REVERT: W 355 MET cc_start: 0.9018 (ttp) cc_final: 0.8581 (ttm) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.7688 time to fit residues: 512.0683 Evaluate side-chains 216 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 476 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 228 optimal weight: 0.0970 chunk 442 optimal weight: 5.9990 chunk 171 optimal weight: 0.0770 chunk 268 optimal weight: 0.7980 chunk 329 optimal weight: 1.9990 chunk 512 optimal weight: 3.9990 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 40 GLN A 73 ASN A 307 ASN C 26 ASN C 73 ASN C 307 ASN E 26 ASN E 73 ASN E 307 ASN E 354 HIS G 26 ASN G 40 GLN G 73 ASN G 307 ASN I 26 ASN I 73 ASN I 307 ASN K 26 ASN K 73 ASN K 307 ASN K 354 HIS M 26 ASN M 40 GLN M 73 ASN M 307 ASN O 26 ASN O 73 ASN O 307 ASN Q 26 ASN Q 73 ASN Q 307 ASN Q 354 HIS S 26 ASN S 40 GLN S 73 ASN S 307 ASN U 26 ASN U 73 ASN U 307 ASN W 26 ASN W 73 ASN W 307 ASN W 354 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 47868 Z= 0.171 Angle : 0.506 6.956 64500 Z= 0.285 Chirality : 0.040 0.140 6972 Planarity : 0.004 0.042 8484 Dihedral : 4.878 27.110 6444 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.31 % Allowed : 4.69 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 5688 helix: 0.98 (0.10), residues: 2520 sheet: 0.11 (0.15), residues: 1116 loop : -0.78 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Q 238 PHE 0.016 0.001 PHE U 173 TYR 0.011 0.001 TYR A 147 ARG 0.004 0.000 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 268 time to evaluate : 5.618 Fit side-chains REVERT: C 93 ASP cc_start: 0.7938 (t0) cc_final: 0.7646 (t0) REVERT: C 320 GLU cc_start: 0.7596 (pt0) cc_final: 0.7193 (tm-30) REVERT: D 103 LYS cc_start: 0.8700 (tppt) cc_final: 0.7885 (ttpp) REVERT: I 93 ASP cc_start: 0.7936 (t0) cc_final: 0.7645 (t0) REVERT: I 320 GLU cc_start: 0.7595 (pt0) cc_final: 0.7195 (tm-30) REVERT: J 103 LYS cc_start: 0.8701 (tppt) cc_final: 0.7885 (ttpp) REVERT: O 93 ASP cc_start: 0.7939 (t0) cc_final: 0.7647 (t0) REVERT: O 320 GLU cc_start: 0.7598 (pt0) cc_final: 0.7198 (tm-30) REVERT: P 103 LYS cc_start: 0.8701 (tppt) cc_final: 0.7887 (ttpp) REVERT: U 93 ASP cc_start: 0.7944 (t0) cc_final: 0.7646 (t0) REVERT: U 320 GLU cc_start: 0.7594 (pt0) cc_final: 0.7196 (tm-30) REVERT: V 103 LYS cc_start: 0.8699 (tppt) cc_final: 0.7886 (ttpp) outliers start: 16 outliers final: 12 residues processed: 280 average time/residue: 0.6506 time to fit residues: 297.0820 Evaluate side-chains 217 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 5.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 284 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 426 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 141 optimal weight: 0.0470 chunk 513 optimal weight: 6.9990 chunk 554 optimal weight: 2.9990 chunk 456 optimal weight: 0.8980 chunk 508 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 411 optimal weight: 5.9990 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 HIS C 354 HIS G 354 HIS I 354 HIS M 354 HIS O 354 HIS S 354 HIS U 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 47868 Z= 0.225 Angle : 0.494 8.186 64500 Z= 0.274 Chirality : 0.040 0.142 6972 Planarity : 0.003 0.041 8484 Dihedral : 4.642 25.484 6444 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.92 % Allowed : 5.15 % Favored : 93.93 % 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: 0.65 (0.11), residues: 5688 helix: 1.58 (0.11), residues: 2520 sheet: 0.02 (0.15), residues: 1116 loop : -0.71 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 92 PHE 0.017 0.002 PHE U 173 TYR 0.016 0.001 TYR W 84 ARG 0.005 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 6.245 Fit side-chains REVERT: B 103 LYS cc_start: 0.8660 (tppt) cc_final: 0.8150 (ttpp) REVERT: C 93 ASP cc_start: 0.7961 (t0) cc_final: 0.7623 (t0) REVERT: C 320 GLU cc_start: 0.7587 (pt0) cc_final: 0.7175 (tm-30) REVERT: D 103 LYS cc_start: 0.8636 (tppt) cc_final: 0.7980 (ttpp) REVERT: E 279 MET cc_start: 0.8962 (tpp) cc_final: 0.8455 (mmt) REVERT: H 103 LYS cc_start: 0.8660 (tppt) cc_final: 0.8153 (ttpp) REVERT: I 93 ASP cc_start: 0.7957 (t0) cc_final: 0.7622 (t0) REVERT: I 320 GLU cc_start: 0.7589 (pt0) cc_final: 0.7176 (tm-30) REVERT: J 103 LYS cc_start: 0.8638 (tppt) cc_final: 0.7981 (ttpp) REVERT: K 279 MET cc_start: 0.8970 (tpp) cc_final: 0.8461 (mmt) REVERT: N 103 LYS cc_start: 0.8662 (tppt) cc_final: 0.8151 (ttpp) REVERT: O 93 ASP cc_start: 0.7959 (t0) cc_final: 0.7620 (t0) REVERT: O 320 GLU cc_start: 0.7593 (pt0) cc_final: 0.7177 (tm-30) REVERT: P 103 LYS cc_start: 0.8636 (tppt) cc_final: 0.7981 (ttpp) REVERT: Q 279 MET cc_start: 0.8961 (tpp) cc_final: 0.8453 (mmt) REVERT: T 103 LYS cc_start: 0.8660 (tppt) cc_final: 0.8151 (ttpp) REVERT: U 93 ASP cc_start: 0.7962 (t0) cc_final: 0.7623 (t0) REVERT: U 320 GLU cc_start: 0.7586 (pt0) cc_final: 0.7176 (tm-30) REVERT: V 103 LYS cc_start: 0.8638 (tppt) cc_final: 0.7981 (ttpp) REVERT: W 279 MET cc_start: 0.8962 (tpp) cc_final: 0.8451 (mmt) outliers start: 48 outliers final: 36 residues processed: 272 average time/residue: 0.6485 time to fit residues: 285.3361 Evaluate side-chains 252 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 506 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 344 optimal weight: 0.5980 chunk 514 optimal weight: 4.9990 chunk 545 optimal weight: 0.2980 chunk 269 optimal weight: 5.9990 chunk 488 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 ASN G 307 ASN I 307 ASN O 307 ASN S 307 ASN U 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 47868 Z= 0.205 Angle : 0.467 7.770 64500 Z= 0.258 Chirality : 0.039 0.140 6972 Planarity : 0.003 0.040 8484 Dihedral : 4.440 22.970 6444 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.06 % Allowed : 5.32 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 5688 helix: 1.93 (0.11), residues: 2520 sheet: -0.12 (0.15), residues: 1116 loop : -0.69 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS U 238 PHE 0.020 0.002 PHE G 173 TYR 0.016 0.001 TYR W 84 ARG 0.005 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 224 time to evaluate : 6.035 Fit side-chains REVERT: A 196 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6584 (mm) REVERT: C 93 ASP cc_start: 0.7871 (t0) cc_final: 0.7601 (t0) REVERT: D 103 LYS cc_start: 0.8673 (tppt) cc_final: 0.8068 (ttpp) REVERT: E 279 MET cc_start: 0.8965 (tpp) cc_final: 0.8460 (mmt) REVERT: F 103 LYS cc_start: 0.8769 (tppt) cc_final: 0.8214 (ttpp) REVERT: G 196 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6579 (mm) REVERT: I 93 ASP cc_start: 0.7873 (t0) cc_final: 0.7603 (t0) REVERT: J 103 LYS cc_start: 0.8677 (tppt) cc_final: 0.8072 (ttpp) REVERT: K 279 MET cc_start: 0.8968 (tpp) cc_final: 0.8463 (mmt) REVERT: L 103 LYS cc_start: 0.8771 (tppt) cc_final: 0.8214 (ttpp) REVERT: M 196 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6579 (mm) REVERT: O 93 ASP cc_start: 0.7874 (t0) cc_final: 0.7601 (t0) REVERT: P 103 LYS cc_start: 0.8676 (tppt) cc_final: 0.8071 (ttpp) REVERT: Q 279 MET cc_start: 0.8963 (tpp) cc_final: 0.8460 (mmt) REVERT: R 103 LYS cc_start: 0.8770 (tppt) cc_final: 0.8212 (ttpp) REVERT: S 196 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6587 (mm) REVERT: U 93 ASP cc_start: 0.7878 (t0) cc_final: 0.7602 (t0) REVERT: V 103 LYS cc_start: 0.8675 (tppt) cc_final: 0.8071 (ttpp) REVERT: W 279 MET cc_start: 0.8963 (tpp) cc_final: 0.8458 (mmt) REVERT: X 103 LYS cc_start: 0.8771 (tppt) cc_final: 0.8214 (ttpp) outliers start: 55 outliers final: 42 residues processed: 268 average time/residue: 0.6409 time to fit residues: 278.3529 Evaluate side-chains 258 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 212 time to evaluate : 6.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 196 ILE Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 454 optimal weight: 0.7980 chunk 309 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 405 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 465 optimal weight: 0.7980 chunk 376 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 489 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 ASN K 307 ASN M 307 ASN Q 307 ASN W 307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 47868 Z= 0.234 Angle : 0.476 7.495 64500 Z= 0.262 Chirality : 0.040 0.138 6972 Planarity : 0.003 0.042 8484 Dihedral : 4.417 21.681 6444 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.25 % Allowed : 6.03 % Favored : 92.72 % 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: 0.88 (0.11), residues: 5688 helix: 2.00 (0.11), residues: 2520 sheet: -0.23 (0.15), residues: 1116 loop : -0.68 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS U 238 PHE 0.019 0.002 PHE A 173 TYR 0.016 0.001 TYR Q 84 ARG 0.005 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 6.817 Fit side-chains REVERT: B 103 LYS cc_start: 0.8736 (tppt) cc_final: 0.8255 (ttpp) REVERT: C 93 ASP cc_start: 0.7972 (t0) cc_final: 0.7610 (t0) REVERT: H 103 LYS cc_start: 0.8734 (tppt) cc_final: 0.8254 (ttpp) REVERT: I 93 ASP cc_start: 0.7940 (t0) cc_final: 0.7611 (t0) REVERT: N 103 LYS cc_start: 0.8733 (tppt) cc_final: 0.8253 (ttpp) REVERT: O 93 ASP cc_start: 0.7970 (t0) cc_final: 0.7608 (t0) REVERT: T 103 LYS cc_start: 0.8733 (tppt) cc_final: 0.8253 (ttpp) REVERT: U 93 ASP cc_start: 0.7978 (t0) cc_final: 0.7612 (t0) outliers start: 65 outliers final: 56 residues processed: 276 average time/residue: 0.6704 time to fit residues: 300.4032 Evaluate side-chains 256 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 5.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 183 optimal weight: 5.9990 chunk 490 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 545 optimal weight: 0.1980 chunk 452 optimal weight: 0.9980 chunk 252 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Q 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 47868 Z= 0.263 Angle : 0.493 7.783 64500 Z= 0.269 Chirality : 0.040 0.139 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.472 21.648 6444 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.46 % Allowed : 6.13 % Favored : 92.42 % 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: 0.85 (0.11), residues: 5688 helix: 2.01 (0.11), residues: 2508 sheet: -0.31 (0.15), residues: 1116 loop : -0.71 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 238 PHE 0.018 0.002 PHE S 173 TYR 0.017 0.001 TYR E 84 ARG 0.005 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 5.694 Fit side-chains REVERT: B 103 LYS cc_start: 0.8605 (tppt) cc_final: 0.8222 (ttpp) REVERT: C 93 ASP cc_start: 0.7955 (t0) cc_final: 0.7622 (t0) REVERT: D 103 LYS cc_start: 0.8871 (tppt) cc_final: 0.8061 (ttpp) REVERT: F 103 LYS cc_start: 0.8706 (tppt) cc_final: 0.8323 (ttpp) REVERT: H 103 LYS cc_start: 0.8605 (tppt) cc_final: 0.8222 (ttpp) REVERT: I 93 ASP cc_start: 0.7952 (t0) cc_final: 0.7619 (t0) REVERT: J 103 LYS cc_start: 0.8869 (tppt) cc_final: 0.8061 (ttpp) REVERT: L 103 LYS cc_start: 0.8707 (tppt) cc_final: 0.8323 (ttpp) REVERT: N 103 LYS cc_start: 0.8605 (tppt) cc_final: 0.8244 (ttpp) REVERT: O 93 ASP cc_start: 0.7959 (t0) cc_final: 0.7620 (t0) REVERT: P 103 LYS cc_start: 0.8868 (tppt) cc_final: 0.8064 (ttpp) REVERT: R 103 LYS cc_start: 0.8707 (tppt) cc_final: 0.8321 (ttpp) REVERT: T 103 LYS cc_start: 0.8603 (tppt) cc_final: 0.8221 (ttpp) REVERT: U 93 ASP cc_start: 0.7964 (t0) cc_final: 0.7623 (t0) REVERT: V 103 LYS cc_start: 0.8869 (tppt) cc_final: 0.8061 (ttpp) REVERT: X 103 LYS cc_start: 0.8708 (tppt) cc_final: 0.8322 (ttpp) outliers start: 76 outliers final: 66 residues processed: 276 average time/residue: 0.6186 time to fit residues: 278.2675 Evaluate side-chains 266 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 200 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 362 MET Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 196 ILE Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 526 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 398 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 459 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 543 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 331 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 47868 Z= 0.294 Angle : 0.504 8.162 64500 Z= 0.275 Chirality : 0.041 0.136 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.508 22.155 6444 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 6.32 % Favored : 92.22 % 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: 5688 helix: 1.88 (0.11), residues: 2520 sheet: -0.40 (0.15), residues: 1116 loop : -0.83 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 238 PHE 0.018 0.002 PHE S 173 TYR 0.017 0.002 TYR W 84 ARG 0.005 0.000 ARG N 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 213 time to evaluate : 6.230 Fit side-chains REVERT: B 103 LYS cc_start: 0.8586 (tppt) cc_final: 0.8270 (ttpp) REVERT: D 103 LYS cc_start: 0.8846 (tppt) cc_final: 0.7990 (ttpp) REVERT: F 103 LYS cc_start: 0.8632 (tppt) cc_final: 0.8261 (ttpp) REVERT: H 103 LYS cc_start: 0.8586 (tppt) cc_final: 0.8268 (ttpp) REVERT: J 103 LYS cc_start: 0.8848 (tppt) cc_final: 0.7990 (ttpp) REVERT: L 103 LYS cc_start: 0.8630 (tppt) cc_final: 0.8261 (ttpp) REVERT: N 103 LYS cc_start: 0.8585 (tppt) cc_final: 0.8266 (ttpp) REVERT: P 103 LYS cc_start: 0.8850 (tppt) cc_final: 0.7992 (ttpp) REVERT: R 103 LYS cc_start: 0.8667 (tppt) cc_final: 0.8296 (ttpp) REVERT: T 103 LYS cc_start: 0.8585 (tppt) cc_final: 0.8268 (ttpp) REVERT: V 103 LYS cc_start: 0.8845 (tppt) cc_final: 0.7992 (ttpp) REVERT: X 103 LYS cc_start: 0.8668 (tppt) cc_final: 0.8297 (ttpp) outliers start: 76 outliers final: 67 residues processed: 285 average time/residue: 0.6819 time to fit residues: 309.3935 Evaluate side-chains 259 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 192 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 362 MET Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 336 optimal weight: 6.9990 chunk 217 optimal weight: 0.6980 chunk 324 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 427 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 47868 Z= 0.285 Angle : 0.497 8.045 64500 Z= 0.272 Chirality : 0.040 0.135 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.499 21.829 6444 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.46 % Allowed : 6.59 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.11), residues: 5688 helix: 1.90 (0.11), residues: 2520 sheet: -0.43 (0.15), residues: 1116 loop : -0.90 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 238 PHE 0.018 0.002 PHE M 173 TYR 0.016 0.001 TYR K 84 ARG 0.006 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 199 time to evaluate : 5.710 Fit side-chains REVERT: B 103 LYS cc_start: 0.8577 (tppt) cc_final: 0.8276 (ttpp) REVERT: D 103 LYS cc_start: 0.8779 (tppt) cc_final: 0.7971 (ttpp) REVERT: F 103 LYS cc_start: 0.8725 (tppt) cc_final: 0.8432 (ttpp) REVERT: H 103 LYS cc_start: 0.8577 (tppt) cc_final: 0.8274 (ttpp) REVERT: J 103 LYS cc_start: 0.8775 (tppt) cc_final: 0.7922 (ttpp) REVERT: L 103 LYS cc_start: 0.8722 (tppt) cc_final: 0.8429 (ttpp) REVERT: N 103 LYS cc_start: 0.8576 (tppt) cc_final: 0.8274 (ttpp) REVERT: P 103 LYS cc_start: 0.8776 (tppt) cc_final: 0.7923 (ttpp) REVERT: R 103 LYS cc_start: 0.8724 (tppt) cc_final: 0.8428 (ttpp) REVERT: T 103 LYS cc_start: 0.8575 (tppt) cc_final: 0.8275 (ttpp) REVERT: V 103 LYS cc_start: 0.8779 (tppt) cc_final: 0.7973 (ttpp) REVERT: X 103 LYS cc_start: 0.8724 (tppt) cc_final: 0.8431 (ttpp) outliers start: 76 outliers final: 68 residues processed: 271 average time/residue: 0.6794 time to fit residues: 298.2729 Evaluate side-chains 256 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 188 time to evaluate : 6.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 339 VAL Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 339 VAL Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 494 optimal weight: 4.9990 chunk 520 optimal weight: 8.9990 chunk 475 optimal weight: 7.9990 chunk 506 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 457 optimal weight: 0.0070 chunk 479 optimal weight: 4.9990 chunk 504 optimal weight: 2.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 47868 Z= 0.330 Angle : 0.522 8.415 64500 Z= 0.284 Chirality : 0.041 0.135 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.568 22.489 6444 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.38 % Allowed : 6.80 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.11), residues: 5688 helix: 1.80 (0.11), residues: 2520 sheet: -0.45 (0.15), residues: 1116 loop : -0.98 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 238 PHE 0.018 0.002 PHE M 173 TYR 0.017 0.002 TYR Q 84 ARG 0.007 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 5.769 Fit side-chains REVERT: B 103 LYS cc_start: 0.8531 (tppt) cc_final: 0.8286 (ttpp) REVERT: D 103 LYS cc_start: 0.8779 (tppt) cc_final: 0.7918 (ttpp) REVERT: F 103 LYS cc_start: 0.8726 (tppt) cc_final: 0.8430 (ttpp) REVERT: H 103 LYS cc_start: 0.8531 (tppt) cc_final: 0.8285 (ttpp) REVERT: J 103 LYS cc_start: 0.8771 (tppt) cc_final: 0.7915 (ttpp) REVERT: L 103 LYS cc_start: 0.8723 (tppt) cc_final: 0.8428 (ttpp) REVERT: N 103 LYS cc_start: 0.8531 (tppt) cc_final: 0.8283 (ttpp) REVERT: P 103 LYS cc_start: 0.8774 (tppt) cc_final: 0.7913 (ttpp) REVERT: R 103 LYS cc_start: 0.8723 (tppt) cc_final: 0.8426 (ttpp) REVERT: T 103 LYS cc_start: 0.8529 (tppt) cc_final: 0.8285 (ttpp) REVERT: V 103 LYS cc_start: 0.8777 (tppt) cc_final: 0.7918 (ttpp) REVERT: X 103 LYS cc_start: 0.8724 (tppt) cc_final: 0.8428 (ttpp) outliers start: 72 outliers final: 72 residues processed: 261 average time/residue: 0.6313 time to fit residues: 267.7419 Evaluate side-chains 261 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain I residue 406 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 406 GLU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 339 VAL Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 188 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain O residue 406 GLU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 406 GLU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 339 VAL Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 188 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 263 THR Chi-restraints excluded: chain U residue 339 VAL Chi-restraints excluded: chain U residue 406 GLU Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Chi-restraints excluded: chain W residue 263 THR Chi-restraints excluded: chain W residue 406 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 332 optimal weight: 0.6980 chunk 535 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 561 optimal weight: 0.3980 chunk 517 optimal weight: 0.8980 chunk 447 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 345 optimal weight: 0.0770 chunk 274 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 303 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 47868 Z= 0.104 Angle : 0.403 5.881 64500 Z= 0.224 Chirality : 0.037 0.132 6972 Planarity : 0.003 0.038 8484 Dihedral : 3.996 17.250 6444 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.00 % Allowed : 7.30 % Favored : 91.71 % 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: 1.04 (0.11), residues: 5688 helix: 2.32 (0.11), residues: 2520 sheet: -0.36 (0.15), residues: 1116 loop : -0.74 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 354 PHE 0.015 0.001 PHE O 173 TYR 0.017 0.001 TYR W 84 ARG 0.008 0.000 ARG N 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11376 Ramachandran restraints generated. 5688 Oldfield, 0 Emsley, 5688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 221 time to evaluate : 5.771 Fit side-chains REVERT: A 376 MET cc_start: 0.7762 (mmm) cc_final: 0.7520 (mtt) REVERT: B 103 LYS cc_start: 0.8470 (tppt) cc_final: 0.8209 (ttpp) REVERT: C 93 ASP cc_start: 0.7826 (t0) cc_final: 0.7477 (t0) REVERT: D 103 LYS cc_start: 0.9013 (tppt) cc_final: 0.8285 (ttpp) REVERT: E 286 MET cc_start: 0.8730 (mtm) cc_final: 0.8526 (mtm) REVERT: F 103 LYS cc_start: 0.8716 (tppt) cc_final: 0.8469 (ttpp) REVERT: G 376 MET cc_start: 0.7755 (mmm) cc_final: 0.7512 (mtt) REVERT: H 103 LYS cc_start: 0.8470 (tppt) cc_final: 0.8207 (ttpp) REVERT: I 93 ASP cc_start: 0.7829 (t0) cc_final: 0.7484 (t0) REVERT: J 103 LYS cc_start: 0.9009 (tppt) cc_final: 0.8282 (ttpp) REVERT: K 286 MET cc_start: 0.8733 (mtm) cc_final: 0.8529 (mtm) REVERT: L 103 LYS cc_start: 0.8716 (tppt) cc_final: 0.8468 (ttpp) REVERT: M 376 MET cc_start: 0.7761 (mmm) cc_final: 0.7516 (mtt) REVERT: N 103 LYS cc_start: 0.8470 (tppt) cc_final: 0.8206 (ttpp) REVERT: O 93 ASP cc_start: 0.7830 (t0) cc_final: 0.7475 (t0) REVERT: P 103 LYS cc_start: 0.9010 (tppt) cc_final: 0.8284 (ttpp) REVERT: R 103 LYS cc_start: 0.8716 (tppt) cc_final: 0.8465 (ttpp) REVERT: S 376 MET cc_start: 0.7765 (mmm) cc_final: 0.7526 (mtt) REVERT: T 103 LYS cc_start: 0.8467 (tppt) cc_final: 0.8208 (ttpp) REVERT: U 93 ASP cc_start: 0.7830 (t0) cc_final: 0.7476 (t0) REVERT: V 103 LYS cc_start: 0.9015 (tppt) cc_final: 0.8287 (ttpp) REVERT: W 286 MET cc_start: 0.8731 (mtm) cc_final: 0.8528 (mtm) REVERT: X 103 LYS cc_start: 0.8717 (tppt) cc_final: 0.8468 (ttpp) outliers start: 52 outliers final: 44 residues processed: 273 average time/residue: 0.6410 time to fit residues: 283.7186 Evaluate side-chains 249 residues out of total 5208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 205 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 196 ILE Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 370 THR Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 193 THR Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 193 THR Chi-restraints excluded: chain S residue 370 THR Chi-restraints excluded: chain S residue 406 GLU Chi-restraints excluded: chain U residue 37 ASP Chi-restraints excluded: chain U residue 133 VAL Chi-restraints excluded: chain U residue 193 THR Chi-restraints excluded: chain U residue 196 ILE Chi-restraints excluded: chain U residue 339 VAL Chi-restraints excluded: chain V residue 100 THR Chi-restraints excluded: chain W residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 355 optimal weight: 7.9990 chunk 476 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 412 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 448 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 460 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.080329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.063332 restraints weight = 114425.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.065220 restraints weight = 66874.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.066393 restraints weight = 48818.783| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 47868 Z= 0.241 Angle : 0.471 7.835 64500 Z= 0.255 Chirality : 0.039 0.135 6972 Planarity : 0.003 0.037 8484 Dihedral : 4.231 19.582 6444 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.00 % Allowed : 7.28 % Favored : 91.72 % 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: 5688 helix: 2.25 (0.11), residues: 2508 sheet: -0.38 (0.15), residues: 1116 loop : -0.79 (0.11), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 238 PHE 0.025 0.002 PHE O 173 TYR 0.019 0.001 TYR A 84 ARG 0.007 0.000 ARG D 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7139.07 seconds wall clock time: 132 minutes 47.95 seconds (7967.95 seconds total)