Starting phenix.real_space_refine on Mon Mar 25 19:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8b_43033/03_2024/8v8b_43033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8b_43033/03_2024/8v8b_43033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8b_43033/03_2024/8v8b_43033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8b_43033/03_2024/8v8b_43033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8b_43033/03_2024/8v8b_43033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8b_43033/03_2024/8v8b_43033.pdb" } resolution = 2.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 31733 2.51 5 N 8528 2.21 5 O 10283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50700 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "B" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "C" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "D" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "E" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "F" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "G" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "H" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "I" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "J" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "K" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "L" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain: "M" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3900 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Time building chain proxies: 23.76, per 1000 atoms: 0.47 Number of scatterers: 50700 At special positions: 0 Unit cell: (186.84, 186.84, 137.16, 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 156 16.00 O 10283 8.00 N 8528 7.00 C 31733 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: 18.87 Conformation dependent library (CDL) restraints added in 8.9 seconds 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11752 Finding SS restraints... Secondary structure from input PDB file: 247 helices and 65 sheets defined 51.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.795A pdb=" N ARG A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 22 Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 132 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR A 423 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.795A pdb=" N ARG B 14 " --> pdb=" O THR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG B 57 " --> pdb=" O MET B 53 " (cutoff:3.500A) Proline residue: B 58 - end of helix Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 358 Processing helix chain 'B' and resid 373 through 411 removed outlier: 3.665A pdb=" N TYR B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR B 423 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 removed outlier: 3.906A pdb=" N GLU B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 469 " --> pdb=" O PRO B 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG C 14 " --> pdb=" O THR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 22 Processing helix chain 'C' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 68 removed outlier: 3.693A pdb=" N SER C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG C 57 " --> pdb=" O MET C 53 " (cutoff:3.500A) Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'C' and resid 261 through 284 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 338 through 341 Processing helix chain 'C' and resid 342 through 358 Processing helix chain 'C' and resid 373 through 411 removed outlier: 3.665A pdb=" N TYR C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.101A pdb=" N THR C 423 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 469 " --> pdb=" O PRO C 465 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG D 14 " --> pdb=" O THR D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 22 Processing helix chain 'D' and resid 34 through 41 removed outlier: 3.614A pdb=" N GLN D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 68 removed outlier: 3.693A pdb=" N SER D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG D 57 " --> pdb=" O MET D 53 " (cutoff:3.500A) Proline residue: D 58 - end of helix Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 132 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 261 through 284 Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 342 through 358 Processing helix chain 'D' and resid 373 through 411 removed outlier: 3.665A pdb=" N TYR D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR D 423 " --> pdb=" O ASP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU D 468 " --> pdb=" O ASP D 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 469 " --> pdb=" O PRO D 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.795A pdb=" N ARG E 14 " --> pdb=" O THR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 22 Processing helix chain 'E' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG E 57 " --> pdb=" O MET E 53 " (cutoff:3.500A) Proline residue: E 58 - end of helix Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 132 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 261 through 284 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 342 through 358 Processing helix chain 'E' and resid 373 through 411 removed outlier: 3.665A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR E 423 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG F 14 " --> pdb=" O THR F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 22 Processing helix chain 'F' and resid 34 through 41 removed outlier: 3.614A pdb=" N GLN F 40 " --> pdb=" O SER F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG F 57 " --> pdb=" O MET F 53 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 132 Processing helix chain 'F' and resid 132 through 148 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 261 through 284 Processing helix chain 'F' and resid 296 through 307 Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 342 through 358 Processing helix chain 'F' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.101A pdb=" N THR F 423 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU F 468 " --> pdb=" O ASP F 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS F 470 " --> pdb=" O GLU F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG G 14 " --> pdb=" O THR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 22 Processing helix chain 'G' and resid 34 through 41 removed outlier: 3.614A pdb=" N GLN G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 68 removed outlier: 3.693A pdb=" N SER G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG G 57 " --> pdb=" O MET G 53 " (cutoff:3.500A) Proline residue: G 58 - end of helix Processing helix chain 'G' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR G 97 " --> pdb=" O ASP G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 132 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 258 through 260 No H-bonds generated for 'chain 'G' and resid 258 through 260' Processing helix chain 'G' and resid 261 through 284 Processing helix chain 'G' and resid 296 through 307 Processing helix chain 'G' and resid 338 through 341 Processing helix chain 'G' and resid 342 through 358 Processing helix chain 'G' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR G 378 " --> pdb=" O GLU G 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG G 386 " --> pdb=" O GLY G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR G 423 " --> pdb=" O ASP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE G 459 " --> pdb=" O LEU G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU G 468 " --> pdb=" O ASP G 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL G 469 " --> pdb=" O PRO G 465 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG H 14 " --> pdb=" O THR H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 22 Processing helix chain 'H' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 68 removed outlier: 3.691A pdb=" N SER H 46 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG H 57 " --> pdb=" O MET H 53 " (cutoff:3.500A) Proline residue: H 58 - end of helix Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.705A pdb=" N VAL H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 132 Processing helix chain 'H' and resid 132 through 148 Processing helix chain 'H' and resid 223 through 225 No H-bonds generated for 'chain 'H' and resid 223 through 225' Processing helix chain 'H' and resid 258 through 260 No H-bonds generated for 'chain 'H' and resid 258 through 260' Processing helix chain 'H' and resid 261 through 284 Processing helix chain 'H' and resid 296 through 307 Processing helix chain 'H' and resid 338 through 341 Processing helix chain 'H' and resid 342 through 358 Processing helix chain 'H' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG H 386 " --> pdb=" O GLY H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR H 423 " --> pdb=" O ASP H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'H' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE H 459 " --> pdb=" O LEU H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU H 468 " --> pdb=" O ASP H 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 469 " --> pdb=" O PRO H 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS H 470 " --> pdb=" O GLU H 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG I 14 " --> pdb=" O THR I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 22 Processing helix chain 'I' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN I 40 " --> pdb=" O SER I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG I 57 " --> pdb=" O MET I 53 " (cutoff:3.500A) Proline residue: I 58 - end of helix Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.705A pdb=" N VAL I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 132 through 148 Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'I' and resid 258 through 260 No H-bonds generated for 'chain 'I' and resid 258 through 260' Processing helix chain 'I' and resid 261 through 284 Processing helix chain 'I' and resid 296 through 307 Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 342 through 358 Processing helix chain 'I' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR I 378 " --> pdb=" O GLU I 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG I 386 " --> pdb=" O GLY I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR I 423 " --> pdb=" O ASP I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 446 Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE I 459 " --> pdb=" O LEU I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU I 468 " --> pdb=" O ASP I 464 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 469 " --> pdb=" O PRO I 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS I 470 " --> pdb=" O GLU I 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG J 14 " --> pdb=" O THR J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 22 Processing helix chain 'J' and resid 34 through 41 removed outlier: 3.614A pdb=" N GLN J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER J 46 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS J 47 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG J 57 " --> pdb=" O MET J 53 " (cutoff:3.500A) Proline residue: J 58 - end of helix Processing helix chain 'J' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR J 97 " --> pdb=" O ASP J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 132 through 148 Processing helix chain 'J' and resid 223 through 225 No H-bonds generated for 'chain 'J' and resid 223 through 225' Processing helix chain 'J' and resid 258 through 260 No H-bonds generated for 'chain 'J' and resid 258 through 260' Processing helix chain 'J' and resid 261 through 284 Processing helix chain 'J' and resid 296 through 307 Processing helix chain 'J' and resid 338 through 341 Processing helix chain 'J' and resid 342 through 358 Processing helix chain 'J' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR J 378 " --> pdb=" O GLU J 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG J 386 " --> pdb=" O GLY J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR J 423 " --> pdb=" O ASP J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 446 Processing helix chain 'J' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE J 459 " --> pdb=" O LEU J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 475 removed outlier: 3.906A pdb=" N GLU J 468 " --> pdb=" O ASP J 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL J 469 " --> pdb=" O PRO J 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS J 470 " --> pdb=" O GLU J 466 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG K 14 " --> pdb=" O THR K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 22 Processing helix chain 'K' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN K 40 " --> pdb=" O SER K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG K 57 " --> pdb=" O MET K 53 " (cutoff:3.500A) Proline residue: K 58 - end of helix Processing helix chain 'K' and resid 71 through 76 removed outlier: 3.705A pdb=" N VAL K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 3.558A pdb=" N TYR K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 132 Processing helix chain 'K' and resid 132 through 148 Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'K' and resid 258 through 260 No H-bonds generated for 'chain 'K' and resid 258 through 260' Processing helix chain 'K' and resid 261 through 284 Processing helix chain 'K' and resid 296 through 307 Processing helix chain 'K' and resid 338 through 341 Processing helix chain 'K' and resid 342 through 358 Processing helix chain 'K' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR K 378 " --> pdb=" O GLU K 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG K 386 " --> pdb=" O GLY K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR K 423 " --> pdb=" O ASP K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 446 Processing helix chain 'K' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE K 459 " --> pdb=" O LEU K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU K 468 " --> pdb=" O ASP K 464 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 469 " --> pdb=" O PRO K 465 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS K 470 " --> pdb=" O GLU K 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 14 removed outlier: 3.794A pdb=" N ARG L 14 " --> pdb=" O THR L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 22 Processing helix chain 'L' and resid 34 through 41 removed outlier: 3.614A pdb=" N GLN L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 68 removed outlier: 3.691A pdb=" N SER L 46 " --> pdb=" O VAL L 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Proline residue: L 58 - end of helix Processing helix chain 'L' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR L 97 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 132 Processing helix chain 'L' and resid 132 through 148 Processing helix chain 'L' and resid 223 through 225 No H-bonds generated for 'chain 'L' and resid 223 through 225' Processing helix chain 'L' and resid 258 through 260 No H-bonds generated for 'chain 'L' and resid 258 through 260' Processing helix chain 'L' and resid 261 through 284 Processing helix chain 'L' and resid 296 through 307 Processing helix chain 'L' and resid 338 through 341 Processing helix chain 'L' and resid 342 through 358 Processing helix chain 'L' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR L 378 " --> pdb=" O GLU L 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG L 386 " --> pdb=" O GLY L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR L 423 " --> pdb=" O ASP L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 446 Processing helix chain 'L' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE L 459 " --> pdb=" O LEU L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU L 468 " --> pdb=" O ASP L 464 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL L 469 " --> pdb=" O PRO L 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS L 470 " --> pdb=" O GLU L 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 14 removed outlier: 3.795A pdb=" N ARG M 14 " --> pdb=" O THR M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 22 Processing helix chain 'M' and resid 34 through 41 removed outlier: 3.615A pdb=" N GLN M 40 " --> pdb=" O SER M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 68 removed outlier: 3.692A pdb=" N SER M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Proline residue: M 58 - end of helix Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.704A pdb=" N VAL M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 108 removed outlier: 3.559A pdb=" N TYR M 97 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 132 Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 223 through 225 No H-bonds generated for 'chain 'M' and resid 223 through 225' Processing helix chain 'M' and resid 258 through 260 No H-bonds generated for 'chain 'M' and resid 258 through 260' Processing helix chain 'M' and resid 261 through 284 Processing helix chain 'M' and resid 296 through 307 Processing helix chain 'M' and resid 338 through 341 Processing helix chain 'M' and resid 342 through 358 Processing helix chain 'M' and resid 373 through 411 removed outlier: 3.666A pdb=" N TYR M 378 " --> pdb=" O GLU M 374 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG M 386 " --> pdb=" O GLY M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 424 removed outlier: 4.102A pdb=" N THR M 423 " --> pdb=" O ASP M 420 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 446 Processing helix chain 'M' and resid 451 through 459 removed outlier: 3.634A pdb=" N PHE M 459 " --> pdb=" O LEU M 455 " (cutoff:3.500A) Processing helix chain 'M' and resid 464 through 475 removed outlier: 3.905A pdb=" N GLU M 468 " --> pdb=" O ASP M 464 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL M 469 " --> pdb=" O PRO M 465 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LYS M 470 " --> pdb=" O GLU M 466 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP A 177 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER A 184 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 215 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG A 217 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id= 3, first strand: chain 'A' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR A 151 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET A 286 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 315 through 317 Processing sheet with id= 6, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP B 177 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER B 184 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL B 215 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN B 233 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG B 217 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= 8, first strand: chain 'B' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR B 151 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 286 through 291 removed outlier: 3.837A pdb=" N MET B 286 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 315 through 317 Processing sheet with id= 11, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP C 177 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER C 184 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL C 215 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN C 233 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 217 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 112 through 114 Processing sheet with id= 13, first strand: chain 'C' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR C 151 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET C 286 " --> pdb=" O ILE C 333 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 315 through 317 Processing sheet with id= 16, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP D 177 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER D 184 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 215 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN D 233 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG D 217 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 112 through 114 Processing sheet with id= 18, first strand: chain 'D' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR D 151 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 286 through 291 removed outlier: 3.837A pdb=" N MET D 286 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 315 through 317 Processing sheet with id= 21, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP E 177 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER E 184 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL E 215 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN E 233 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG E 217 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'E' and resid 112 through 114 Processing sheet with id= 23, first strand: chain 'E' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR E 151 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'E' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET E 286 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'E' and resid 315 through 317 Processing sheet with id= 26, first strand: chain 'F' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP F 177 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER F 184 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL F 215 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN F 233 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG F 217 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'F' and resid 112 through 114 Processing sheet with id= 28, first strand: chain 'F' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR F 151 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'F' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET F 286 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'F' and resid 315 through 317 Processing sheet with id= 31, first strand: chain 'G' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP G 177 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER G 184 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL G 215 " --> pdb=" O ASN G 233 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ASN G 233 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG G 217 " --> pdb=" O ARG G 231 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'G' and resid 112 through 114 Processing sheet with id= 33, first strand: chain 'G' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR G 151 " --> pdb=" O SER G 167 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 286 through 291 removed outlier: 3.837A pdb=" N MET G 286 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 315 through 317 Processing sheet with id= 36, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP H 177 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER H 184 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL H 215 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ASN H 233 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG H 217 " --> pdb=" O ARG H 231 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 112 through 114 Processing sheet with id= 38, first strand: chain 'H' and resid 162 through 167 removed outlier: 4.196A pdb=" N TYR H 151 " --> pdb=" O SER H 167 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'H' and resid 286 through 291 removed outlier: 3.837A pdb=" N MET H 286 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'H' and resid 315 through 317 Processing sheet with id= 41, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.145A pdb=" N ASP I 177 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER I 184 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL I 215 " --> pdb=" O ASN I 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN I 233 " --> pdb=" O VAL I 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG I 217 " --> pdb=" O ARG I 231 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'I' and resid 112 through 114 Processing sheet with id= 43, first strand: chain 'I' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR I 151 " --> pdb=" O SER I 167 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET I 286 " --> pdb=" O ILE I 333 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'I' and resid 315 through 317 Processing sheet with id= 46, first strand: chain 'J' and resid 30 through 31 removed outlier: 6.145A pdb=" N ASP J 177 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER J 184 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL J 215 " --> pdb=" O ASN J 233 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ASN J 233 " --> pdb=" O VAL J 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG J 217 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= 48, first strand: chain 'J' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR J 151 " --> pdb=" O SER J 167 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET J 286 " --> pdb=" O ILE J 333 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 315 through 317 Processing sheet with id= 51, first strand: chain 'K' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP K 177 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER K 184 " --> pdb=" O ASP K 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL K 215 " --> pdb=" O ASN K 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN K 233 " --> pdb=" O VAL K 215 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG K 217 " --> pdb=" O ARG K 231 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'K' and resid 112 through 114 Processing sheet with id= 53, first strand: chain 'K' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR K 151 " --> pdb=" O SER K 167 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET K 286 " --> pdb=" O ILE K 333 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 315 through 317 Processing sheet with id= 56, first strand: chain 'L' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP L 177 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER L 184 " --> pdb=" O ASP L 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL L 215 " --> pdb=" O ASN L 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN L 233 " --> pdb=" O VAL L 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG L 217 " --> pdb=" O ARG L 231 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'L' and resid 112 through 114 Processing sheet with id= 58, first strand: chain 'L' and resid 162 through 167 removed outlier: 4.195A pdb=" N TYR L 151 " --> pdb=" O SER L 167 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'L' and resid 286 through 291 removed outlier: 3.838A pdb=" N MET L 286 " --> pdb=" O ILE L 333 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'L' and resid 315 through 317 Processing sheet with id= 61, first strand: chain 'M' and resid 30 through 31 removed outlier: 6.146A pdb=" N ASP M 177 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER M 184 " --> pdb=" O ASP M 177 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL M 215 " --> pdb=" O ASN M 233 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN M 233 " --> pdb=" O VAL M 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG M 217 " --> pdb=" O ARG M 231 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'M' and resid 112 through 114 Processing sheet with id= 63, first strand: chain 'M' and resid 162 through 167 removed outlier: 4.196A pdb=" N TYR M 151 " --> pdb=" O SER M 167 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'M' and resid 286 through 291 removed outlier: 3.837A pdb=" N MET M 286 " --> pdb=" O ILE M 333 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'M' and resid 315 through 317 2535 hydrogen bonds defined for protein. 7371 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: 20.18 Time building geometry restraints manager: 20.48 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: 16767 1.34 - 1.46: 7021 1.46 - 1.58: 27471 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 51571 Sorted by residual: bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET I 1 " pdb=" CA MET I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N MET L 1 " pdb=" CA MET L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 ... (remaining 51566 not shown) Histogram of bond angle deviations from ideal: 99.31 - 105.70: 571 105.70 - 112.09: 21811 112.09 - 118.48: 16587 118.48 - 124.88: 30038 124.88 - 131.27: 569 Bond angle restraints: 69576 Sorted by residual: angle pdb=" CA GLN F 340 " pdb=" CB GLN F 340 " pdb=" CG GLN F 340 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 angle pdb=" CA GLN D 340 " pdb=" CB GLN D 340 " pdb=" CG GLN D 340 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.26e+00 angle pdb=" CA GLN C 340 " pdb=" CB GLN C 340 " pdb=" CG GLN C 340 " ideal model delta sigma weight residual 114.10 120.18 -6.08 2.00e+00 2.50e-01 9.25e+00 angle pdb=" CA GLN M 340 " pdb=" CB GLN M 340 " pdb=" CG GLN M 340 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.19e+00 angle pdb=" CA GLN I 340 " pdb=" CB GLN I 340 " pdb=" CG GLN I 340 " ideal model delta sigma weight residual 114.10 120.16 -6.06 2.00e+00 2.50e-01 9.19e+00 ... (remaining 69571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 27427 14.17 - 28.34: 2974 28.34 - 42.51: 682 42.51 - 56.68: 179 56.68 - 70.85: 146 Dihedral angle restraints: 31408 sinusoidal: 13078 harmonic: 18330 Sorted by residual: dihedral pdb=" CA LEU H 20 " pdb=" C LEU H 20 " pdb=" N PHE H 21 " pdb=" CA PHE H 21 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LEU L 20 " pdb=" C LEU L 20 " pdb=" N PHE L 21 " pdb=" CA PHE L 21 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LEU I 20 " pdb=" C LEU I 20 " pdb=" N PHE I 21 " pdb=" CA PHE I 21 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 31405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4883 0.047 - 0.095: 1764 0.095 - 0.142: 696 0.142 - 0.190: 150 0.190 - 0.237: 47 Chirality restraints: 7540 Sorted by residual: chirality pdb=" CA LYS D 260 " pdb=" N LYS D 260 " pdb=" C LYS D 260 " pdb=" CB LYS D 260 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS F 260 " pdb=" N LYS F 260 " pdb=" C LYS F 260 " pdb=" CB LYS F 260 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LYS G 260 " pdb=" N LYS G 260 " pdb=" C LYS G 260 " pdb=" CB LYS G 260 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 7537 not shown) Planarity restraints: 9191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 84 " -0.020 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR D 84 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 84 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 84 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 84 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR D 84 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 84 " 0.039 2.00e-02 2.50e+03 pdb=" OH TYR D 84 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 84 " 0.019 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR K 84 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR K 84 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR K 84 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR K 84 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR K 84 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR K 84 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR K 84 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 84 " -0.019 2.00e-02 2.50e+03 2.58e-02 1.33e+01 pdb=" CG TYR J 84 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR J 84 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR J 84 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR J 84 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR J 84 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR J 84 " 0.039 2.00e-02 2.50e+03 pdb=" OH TYR J 84 " -0.038 2.00e-02 2.50e+03 ... (remaining 9188 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 14688 2.84 - 3.35: 47990 3.35 - 3.87: 83991 3.87 - 4.38: 100202 4.38 - 4.90: 164018 Nonbonded interactions: 410889 Sorted by model distance: nonbonded pdb=" NE2 GLN I 340 " pdb=" OE1 GLU I 343 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN F 340 " pdb=" OE1 GLU F 343 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN L 340 " pdb=" OE1 GLU L 343 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN B 340 " pdb=" OE1 GLU B 343 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN E 340 " pdb=" OE1 GLU E 343 " model vdw 2.320 2.520 ... (remaining 410884 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.230 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 123.720 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.360 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.005 0.033 51571 Z= 0.326 Angle : 0.873 6.617 69576 Z= 0.536 Chirality : 0.059 0.237 7540 Planarity : 0.010 0.102 9191 Dihedral : 13.660 70.849 19656 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.09), residues: 6162 helix: -1.18 (0.08), residues: 2704 sheet: 1.23 (0.14), residues: 1040 loop : -0.28 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS E 238 PHE 0.037 0.003 PHE C 101 TYR 0.044 0.005 TYR E 66 ARG 0.030 0.003 ARG F 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1021 time to evaluate : 5.468 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8650 (mtt) cc_final: 0.8429 (mtt) REVERT: A 129 ASP cc_start: 0.6959 (t0) cc_final: 0.6610 (t0) REVERT: A 213 HIS cc_start: 0.6497 (m-70) cc_final: 0.6273 (m170) REVERT: A 286 MET cc_start: 0.8758 (ttm) cc_final: 0.8317 (mtp) REVERT: A 376 MET cc_start: 0.8663 (mmm) cc_final: 0.8352 (tpt) REVERT: A 425 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7087 (mtm-85) REVERT: A 452 GLN cc_start: 0.6677 (mm-40) cc_final: 0.6351 (mp-120) REVERT: A 456 MET cc_start: 0.7546 (mtt) cc_final: 0.7276 (mtt) REVERT: B 53 MET cc_start: 0.8650 (mtt) cc_final: 0.8361 (mtm) REVERT: B 163 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7637 (mmt180) REVERT: B 211 THR cc_start: 0.8097 (m) cc_final: 0.7860 (p) REVERT: B 221 ASN cc_start: 0.7799 (p0) cc_final: 0.7309 (p0) REVERT: B 286 MET cc_start: 0.8812 (ttm) cc_final: 0.8439 (mtp) REVERT: B 301 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7972 (mtm-85) REVERT: B 365 ASP cc_start: 0.8058 (m-30) cc_final: 0.7638 (m-30) REVERT: B 440 LEU cc_start: 0.8086 (tp) cc_final: 0.7608 (tt) REVERT: B 452 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6607 (mp10) REVERT: B 456 MET cc_start: 0.7433 (mtt) cc_final: 0.7194 (mtt) REVERT: C 53 MET cc_start: 0.8619 (mtt) cc_final: 0.8372 (mtm) REVERT: C 185 ILE cc_start: 0.8349 (mt) cc_final: 0.7992 (mt) REVERT: C 211 THR cc_start: 0.8319 (m) cc_final: 0.7994 (p) REVERT: C 221 ASN cc_start: 0.7823 (p0) cc_final: 0.7607 (p0) REVERT: C 279 MET cc_start: 0.9145 (mtp) cc_final: 0.8934 (mtp) REVERT: C 301 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8090 (mtm-85) REVERT: C 365 ASP cc_start: 0.7796 (m-30) cc_final: 0.7411 (m-30) REVERT: C 452 GLN cc_start: 0.6984 (mm-40) cc_final: 0.6590 (mp-120) REVERT: C 456 MET cc_start: 0.7556 (mtt) cc_final: 0.7284 (mtt) REVERT: D 189 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.8055 (mtp85) REVERT: D 209 LEU cc_start: 0.8415 (tt) cc_final: 0.8207 (tp) REVERT: D 211 THR cc_start: 0.8024 (m) cc_final: 0.7731 (p) REVERT: D 221 ASN cc_start: 0.7810 (p0) cc_final: 0.7278 (p0) REVERT: D 286 MET cc_start: 0.8772 (ttm) cc_final: 0.8366 (mtp) REVERT: D 292 ASN cc_start: 0.8250 (t0) cc_final: 0.7978 (m-40) REVERT: D 363 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7091 (mppt) REVERT: E 1 MET cc_start: 0.5031 (mmm) cc_final: 0.4726 (mmt) REVERT: E 85 MET cc_start: 0.9077 (mtt) cc_final: 0.8804 (mtt) REVERT: E 163 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7626 (mmt180) REVERT: E 182 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7758 (mtp180) REVERT: E 211 THR cc_start: 0.8361 (m) cc_final: 0.8048 (p) REVERT: E 229 THR cc_start: 0.7326 (p) cc_final: 0.7004 (t) REVERT: E 286 MET cc_start: 0.8851 (ttm) cc_final: 0.8360 (mtp) REVERT: E 301 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7926 (mtm110) REVERT: E 363 LYS cc_start: 0.8115 (mmtp) cc_final: 0.6921 (mppt) REVERT: E 425 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.7033 (mtm-85) REVERT: E 452 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6557 (mp-120) REVERT: F 53 MET cc_start: 0.8595 (mtt) cc_final: 0.8380 (mtt) REVERT: F 134 GLU cc_start: 0.7810 (tt0) cc_final: 0.7548 (tt0) REVERT: F 211 THR cc_start: 0.8198 (m) cc_final: 0.7954 (p) REVERT: F 362 MET cc_start: 0.8411 (ptm) cc_final: 0.8108 (ptp) REVERT: F 365 ASP cc_start: 0.7978 (m-30) cc_final: 0.7445 (m-30) REVERT: F 376 MET cc_start: 0.8688 (mmm) cc_final: 0.8350 (tpt) REVERT: G 129 ASP cc_start: 0.7036 (t0) cc_final: 0.6642 (t0) REVERT: G 211 THR cc_start: 0.8185 (m) cc_final: 0.7885 (p) REVERT: G 213 HIS cc_start: 0.6423 (m-70) cc_final: 0.6208 (m-70) REVERT: G 221 ASN cc_start: 0.7975 (p0) cc_final: 0.7404 (p0) REVERT: G 279 MET cc_start: 0.9172 (mtp) cc_final: 0.8834 (mtp) REVERT: G 286 MET cc_start: 0.8815 (ttm) cc_final: 0.8338 (mtp) REVERT: G 422 ASN cc_start: 0.7935 (t0) cc_final: 0.7693 (t0) REVERT: G 452 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6672 (mp10) REVERT: H 163 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7748 (mmt180) REVERT: H 191 LEU cc_start: 0.8512 (mt) cc_final: 0.8211 (mm) REVERT: H 211 THR cc_start: 0.8182 (m) cc_final: 0.7912 (p) REVERT: H 229 THR cc_start: 0.7131 (p) cc_final: 0.6881 (t) REVERT: H 286 MET cc_start: 0.8757 (ttm) cc_final: 0.8494 (mtp) REVERT: H 365 ASP cc_start: 0.7966 (m-30) cc_final: 0.7580 (m-30) REVERT: H 371 GLN cc_start: 0.7446 (mt0) cc_final: 0.7243 (mt0) REVERT: H 452 GLN cc_start: 0.6785 (mm-40) cc_final: 0.6402 (mp-120) REVERT: I 53 MET cc_start: 0.8544 (mtt) cc_final: 0.8332 (mtt) REVERT: I 129 ASP cc_start: 0.7099 (t0) cc_final: 0.6839 (t0) REVERT: I 185 ILE cc_start: 0.8363 (mt) cc_final: 0.8161 (mt) REVERT: I 211 THR cc_start: 0.8222 (m) cc_final: 0.7881 (p) REVERT: I 221 ASN cc_start: 0.7769 (p0) cc_final: 0.7317 (p0) REVERT: I 376 MET cc_start: 0.8545 (mmm) cc_final: 0.8344 (tpt) REVERT: I 440 LEU cc_start: 0.8175 (tp) cc_final: 0.7729 (tt) REVERT: J 163 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7616 (mmt180) REVERT: J 191 LEU cc_start: 0.8639 (mt) cc_final: 0.8367 (mm) REVERT: J 211 THR cc_start: 0.8248 (m) cc_final: 0.7915 (p) REVERT: J 221 ASN cc_start: 0.8032 (p0) cc_final: 0.7550 (p0) REVERT: J 229 THR cc_start: 0.7334 (p) cc_final: 0.7122 (m) REVERT: J 301 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7897 (mmm-85) REVERT: J 452 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6524 (mm110) REVERT: K 211 THR cc_start: 0.8134 (m) cc_final: 0.7860 (p) REVERT: K 229 THR cc_start: 0.7322 (p) cc_final: 0.7042 (t) REVERT: K 286 MET cc_start: 0.8667 (ttm) cc_final: 0.8278 (mtp) REVERT: K 363 LYS cc_start: 0.8071 (mmtp) cc_final: 0.6995 (mppt) REVERT: K 376 MET cc_start: 0.8623 (mmm) cc_final: 0.8231 (tpp) REVERT: L 53 MET cc_start: 0.8590 (mtt) cc_final: 0.8325 (mtt) REVERT: L 211 THR cc_start: 0.7946 (m) cc_final: 0.7720 (p) REVERT: L 221 ASN cc_start: 0.7910 (p0) cc_final: 0.7351 (p0) REVERT: L 286 MET cc_start: 0.8743 (ttm) cc_final: 0.8376 (mtp) REVERT: L 362 MET cc_start: 0.8449 (ptm) cc_final: 0.8073 (ptp) REVERT: L 452 GLN cc_start: 0.6847 (mm-40) cc_final: 0.6297 (mp-120) REVERT: M 11 THR cc_start: 0.7476 (p) cc_final: 0.7209 (t) REVERT: M 211 THR cc_start: 0.8141 (m) cc_final: 0.7852 (p) REVERT: M 221 ASN cc_start: 0.7917 (p0) cc_final: 0.7355 (p0) REVERT: M 286 MET cc_start: 0.8750 (ttm) cc_final: 0.8260 (mtp) REVERT: M 362 MET cc_start: 0.8269 (ptm) cc_final: 0.7938 (ptp) REVERT: M 422 ASN cc_start: 0.7724 (t0) cc_final: 0.7519 (t0) REVERT: M 452 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6743 (mp-120) outliers start: 13 outliers final: 3 residues processed: 1034 average time/residue: 1.7500 time to fit residues: 2218.5752 Evaluate side-chains 685 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 682 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain K residue 96 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 515 optimal weight: 4.9990 chunk 463 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 478 optimal weight: 6.9990 chunk 185 optimal weight: 0.0980 chunk 291 optimal weight: 0.9980 chunk 356 optimal weight: 0.9980 chunk 554 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 112 GLN A 221 ASN A 336 GLN B 22 ASN B 112 GLN B 336 GLN B 422 ASN C 22 ASN C 112 GLN C 336 GLN C 371 GLN C 422 ASN D 22 ASN D 112 GLN D 336 GLN D 371 GLN D 422 ASN D 429 ASN E 22 ASN E 112 GLN E 221 ASN E 336 GLN E 340 GLN E 371 GLN F 22 ASN F 221 ASN F 336 GLN F 422 ASN F 452 GLN G 22 ASN G 112 GLN G 336 GLN G 371 GLN H 22 ASN H 112 GLN H 221 ASN H 336 GLN H 422 ASN I 22 ASN I 336 GLN I 371 GLN I 422 ASN J 22 ASN J 112 GLN J 336 GLN J 422 ASN K 22 ASN K 112 GLN K 221 ASN K 336 GLN K 422 ASN L 22 ASN L 112 GLN L 336 GLN L 371 GLN L 422 ASN M 22 ASN M 112 GLN M 336 GLN M 429 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 51571 Z= 0.178 Angle : 0.567 5.224 69576 Z= 0.323 Chirality : 0.042 0.150 7540 Planarity : 0.004 0.038 9191 Dihedral : 4.913 21.588 6945 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.65 % Allowed : 8.46 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.10), residues: 6162 helix: 1.33 (0.09), residues: 2717 sheet: 1.62 (0.15), residues: 1014 loop : -0.09 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 92 PHE 0.026 0.002 PHE M 235 TYR 0.021 0.002 TYR J 66 ARG 0.005 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 756 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8592 (mtt) cc_final: 0.8288 (mtt) REVERT: A 125 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: A 213 HIS cc_start: 0.6578 (m-70) cc_final: 0.6341 (m170) REVERT: A 286 MET cc_start: 0.8808 (ttm) cc_final: 0.8283 (mtp) REVERT: A 365 ASP cc_start: 0.7474 (m-30) cc_final: 0.7219 (m-30) REVERT: A 452 GLN cc_start: 0.6607 (mm-40) cc_final: 0.6060 (mp-120) REVERT: A 456 MET cc_start: 0.7322 (mtt) cc_final: 0.7026 (mtt) REVERT: B 53 MET cc_start: 0.8525 (mtt) cc_final: 0.8167 (mtm) REVERT: B 125 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 163 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7667 (mmt180) REVERT: B 206 THR cc_start: 0.7972 (t) cc_final: 0.7728 (t) REVERT: B 221 ASN cc_start: 0.7824 (p0) cc_final: 0.7338 (p0) REVERT: B 286 MET cc_start: 0.8904 (ttm) cc_final: 0.8461 (mtp) REVERT: B 301 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7969 (mtm-85) REVERT: B 365 ASP cc_start: 0.7906 (m-30) cc_final: 0.7447 (m-30) REVERT: B 440 LEU cc_start: 0.8042 (tp) cc_final: 0.7577 (tt) REVERT: B 452 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6552 (mp10) REVERT: B 456 MET cc_start: 0.7386 (mtt) cc_final: 0.7166 (mtt) REVERT: C 1 MET cc_start: 0.5197 (mmt) cc_final: 0.4472 (mmt) REVERT: C 185 ILE cc_start: 0.8129 (mt) cc_final: 0.7880 (mt) REVERT: C 221 ASN cc_start: 0.7880 (p0) cc_final: 0.7646 (p0) REVERT: C 279 MET cc_start: 0.9033 (mtp) cc_final: 0.8738 (mtp) REVERT: C 362 MET cc_start: 0.8253 (ptp) cc_final: 0.7999 (ptp) REVERT: C 365 ASP cc_start: 0.7814 (m-30) cc_final: 0.7465 (m-30) REVERT: C 429 ASN cc_start: 0.8414 (m110) cc_final: 0.7980 (t0) REVERT: C 456 MET cc_start: 0.7393 (mtt) cc_final: 0.7162 (mtt) REVERT: D 125 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: D 221 ASN cc_start: 0.7770 (p0) cc_final: 0.7295 (p0) REVERT: D 286 MET cc_start: 0.8806 (ttm) cc_final: 0.8301 (mtp) REVERT: D 363 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7260 (mppt) REVERT: D 422 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7549 (m-40) REVERT: E 1 MET cc_start: 0.5316 (mmm) cc_final: 0.5113 (mmt) REVERT: E 125 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: E 159 ASP cc_start: 0.6058 (m-30) cc_final: 0.5793 (t0) REVERT: E 211 THR cc_start: 0.8368 (m) cc_final: 0.8039 (p) REVERT: E 363 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7084 (mppt) REVERT: E 452 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6664 (mm-40) REVERT: F 53 MET cc_start: 0.8595 (mtt) cc_final: 0.8306 (mtt) REVERT: F 211 THR cc_start: 0.8089 (m) cc_final: 0.7830 (p) REVERT: F 362 MET cc_start: 0.8538 (ptm) cc_final: 0.8075 (ptp) REVERT: F 365 ASP cc_start: 0.7844 (m-30) cc_final: 0.7383 (m-30) REVERT: F 376 MET cc_start: 0.8560 (mmm) cc_final: 0.8360 (tpt) REVERT: G 47 LYS cc_start: 0.7238 (tppp) cc_final: 0.6919 (ttmp) REVERT: G 129 ASP cc_start: 0.6973 (t0) cc_final: 0.6549 (t0) REVERT: G 211 THR cc_start: 0.8140 (m) cc_final: 0.7839 (p) REVERT: G 213 HIS cc_start: 0.6309 (m-70) cc_final: 0.6016 (m-70) REVERT: G 221 ASN cc_start: 0.7930 (p0) cc_final: 0.7393 (p0) REVERT: G 279 MET cc_start: 0.9115 (mtp) cc_final: 0.8821 (mtp) REVERT: G 286 MET cc_start: 0.8860 (ttm) cc_final: 0.8328 (mtp) REVERT: G 422 ASN cc_start: 0.7826 (t0) cc_final: 0.7592 (t0) REVERT: G 452 GLN cc_start: 0.6968 (mm-40) cc_final: 0.6605 (mp10) REVERT: H 163 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7725 (mmt180) REVERT: H 211 THR cc_start: 0.8053 (m) cc_final: 0.7734 (p) REVERT: H 217 ARG cc_start: 0.7579 (mtt90) cc_final: 0.7331 (mtt180) REVERT: H 229 THR cc_start: 0.7221 (p) cc_final: 0.6966 (t) REVERT: H 323 GLU cc_start: 0.6359 (mt-10) cc_final: 0.6154 (mt-10) REVERT: H 365 ASP cc_start: 0.7902 (m-30) cc_final: 0.7513 (m-30) REVERT: H 452 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6598 (mp10) REVERT: I 47 LYS cc_start: 0.7389 (mtmt) cc_final: 0.7003 (tptp) REVERT: I 53 MET cc_start: 0.8539 (mtt) cc_final: 0.8315 (mtt) REVERT: I 125 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: I 129 ASP cc_start: 0.6907 (t0) cc_final: 0.6643 (t0) REVERT: I 211 THR cc_start: 0.8164 (m) cc_final: 0.7839 (p) REVERT: I 286 MET cc_start: 0.8840 (ttm) cc_final: 0.8561 (mtp) REVERT: I 440 LEU cc_start: 0.8245 (tp) cc_final: 0.7872 (tt) REVERT: J 163 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7641 (mmt180) REVERT: J 211 THR cc_start: 0.8135 (m) cc_final: 0.7794 (p) REVERT: J 221 ASN cc_start: 0.7925 (p0) cc_final: 0.7460 (p0) REVERT: J 301 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7911 (mmm-85) REVERT: J 309 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8579 (mp) REVERT: J 323 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6196 (mt-10) REVERT: J 403 LYS cc_start: 0.7606 (mttt) cc_final: 0.7191 (mppt) REVERT: J 422 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: J 452 GLN cc_start: 0.6589 (mm-40) cc_final: 0.6383 (mm110) REVERT: K 185 ILE cc_start: 0.8256 (mt) cc_final: 0.8023 (mt) REVERT: K 211 THR cc_start: 0.8075 (m) cc_final: 0.7742 (p) REVERT: K 286 MET cc_start: 0.8714 (ttm) cc_final: 0.8430 (mtp) REVERT: K 422 ASN cc_start: 0.7840 (t160) cc_final: 0.7569 (m-40) REVERT: K 440 LEU cc_start: 0.8278 (tp) cc_final: 0.7904 (tt) REVERT: L 47 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7588 (ttmt) REVERT: L 53 MET cc_start: 0.8604 (mtt) cc_final: 0.8285 (mtt) REVERT: L 125 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: L 156 ARG cc_start: 0.6767 (mmm160) cc_final: 0.6566 (mmm160) REVERT: L 211 THR cc_start: 0.8034 (m) cc_final: 0.7729 (p) REVERT: L 221 ASN cc_start: 0.7919 (p0) cc_final: 0.7333 (p0) REVERT: L 286 MET cc_start: 0.8832 (ttm) cc_final: 0.8518 (mtp) REVERT: L 362 MET cc_start: 0.8416 (ptm) cc_final: 0.8037 (ptp) REVERT: L 422 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7380 (m110) REVERT: M 211 THR cc_start: 0.8078 (m) cc_final: 0.7824 (p) REVERT: M 286 MET cc_start: 0.8848 (ttm) cc_final: 0.8313 (mtp) REVERT: M 422 ASN cc_start: 0.7851 (t0) cc_final: 0.7569 (t0) REVERT: M 452 GLN cc_start: 0.6841 (mm-40) cc_final: 0.6592 (mp10) outliers start: 149 outliers final: 42 residues processed: 853 average time/residue: 1.6543 time to fit residues: 1756.9784 Evaluate side-chains 750 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 697 time to evaluate : 5.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 422 ASN Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 396 LYS Chi-restraints excluded: chain H residue 444 ILE Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 450 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 422 ASN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 422 ASN Chi-restraints excluded: chain L residue 444 ILE Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 315 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 308 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 461 optimal weight: 4.9990 chunk 377 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 555 optimal weight: 0.8980 chunk 600 optimal weight: 0.0030 chunk 495 optimal weight: 1.9990 chunk 551 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 445 optimal weight: 10.0000 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN B 221 ASN B 422 ASN C 221 ASN C 371 GLN C 422 ASN D 221 ASN D 371 GLN D 422 ASN E 221 ASN E 340 GLN F 221 ASN F 422 ASN F 452 GLN G 221 ASN G 340 GLN H 112 GLN H 422 ASN I 112 GLN I 221 ASN I 336 GLN I 371 GLN I 422 ASN J 221 ASN K 221 ASN L 371 GLN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 GLN M 429 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 51571 Z= 0.173 Angle : 0.528 7.519 69576 Z= 0.296 Chirality : 0.040 0.130 7540 Planarity : 0.003 0.035 9191 Dihedral : 4.524 15.769 6942 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.68 % Allowed : 9.56 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.10), residues: 6162 helix: 1.91 (0.10), residues: 2743 sheet: 1.20 (0.14), residues: 1131 loop : -0.28 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 354 PHE 0.025 0.002 PHE M 235 TYR 0.018 0.002 TYR I 66 ARG 0.005 0.000 ARG F 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 724 time to evaluate : 5.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8556 (mtt) cc_final: 0.8204 (mtt) REVERT: A 125 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 129 ASP cc_start: 0.6941 (t0) cc_final: 0.6543 (t0) REVERT: A 213 HIS cc_start: 0.6647 (m-70) cc_final: 0.6383 (m170) REVERT: A 286 MET cc_start: 0.8811 (ttm) cc_final: 0.8290 (mtp) REVERT: A 365 ASP cc_start: 0.7556 (m-30) cc_final: 0.7262 (m-30) REVERT: A 452 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6180 (mp-120) REVERT: A 456 MET cc_start: 0.7335 (mtt) cc_final: 0.7045 (mtt) REVERT: B 53 MET cc_start: 0.8481 (mtt) cc_final: 0.8108 (mtm) REVERT: B 125 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: B 129 ASP cc_start: 0.6801 (t0) cc_final: 0.6545 (t0) REVERT: B 159 ASP cc_start: 0.6502 (m-30) cc_final: 0.5957 (t0) REVERT: B 163 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7611 (mmt180) REVERT: B 221 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7398 (p0) REVERT: B 286 MET cc_start: 0.8906 (ttm) cc_final: 0.8477 (mtp) REVERT: B 365 ASP cc_start: 0.7738 (m-30) cc_final: 0.7309 (m-30) REVERT: B 440 LEU cc_start: 0.8019 (tp) cc_final: 0.7495 (tt) REVERT: B 452 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6554 (mm-40) REVERT: B 456 MET cc_start: 0.7371 (mtt) cc_final: 0.7131 (mtt) REVERT: C 47 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7531 (mtmm) REVERT: C 185 ILE cc_start: 0.8199 (mt) cc_final: 0.7927 (mt) REVERT: C 279 MET cc_start: 0.9063 (mtp) cc_final: 0.8827 (mtp) REVERT: C 362 MET cc_start: 0.8284 (ptp) cc_final: 0.7997 (ptp) REVERT: C 365 ASP cc_start: 0.7832 (m-30) cc_final: 0.7445 (m-30) REVERT: C 429 ASN cc_start: 0.8447 (m110) cc_final: 0.8156 (t0) REVERT: C 450 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7063 (mp) REVERT: C 456 MET cc_start: 0.7413 (mtt) cc_final: 0.7160 (mtt) REVERT: D 125 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 221 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7456 (p0) REVERT: D 286 MET cc_start: 0.8790 (ttm) cc_final: 0.8273 (mtp) REVERT: D 294 ASN cc_start: 0.6758 (m110) cc_final: 0.6528 (m110) REVERT: D 363 LYS cc_start: 0.8220 (mmtp) cc_final: 0.7142 (mppt) REVERT: D 422 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7312 (m110) REVERT: D 452 GLN cc_start: 0.6758 (mm-40) cc_final: 0.6544 (mp10) REVERT: E 125 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: E 159 ASP cc_start: 0.6182 (m-30) cc_final: 0.5769 (t0) REVERT: E 192 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.5880 (tmm-80) REVERT: E 211 THR cc_start: 0.8238 (m) cc_final: 0.8007 (p) REVERT: E 292 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7671 (t0) REVERT: F 53 MET cc_start: 0.8598 (mtt) cc_final: 0.8287 (mtt) REVERT: F 192 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6848 (mmm-85) REVERT: F 365 ASP cc_start: 0.7829 (m-30) cc_final: 0.7239 (m-30) REVERT: F 376 MET cc_start: 0.8531 (mmm) cc_final: 0.8318 (tpt) REVERT: G 47 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6857 (ttmp) REVERT: G 129 ASP cc_start: 0.6883 (t0) cc_final: 0.6488 (t0) REVERT: G 211 THR cc_start: 0.8074 (m) cc_final: 0.7844 (p) REVERT: G 213 HIS cc_start: 0.6255 (m-70) cc_final: 0.5868 (m-70) REVERT: G 221 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7317 (p0) REVERT: G 279 MET cc_start: 0.9186 (mtp) cc_final: 0.8863 (mtp) REVERT: G 422 ASN cc_start: 0.7822 (t0) cc_final: 0.7582 (t0) REVERT: G 452 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6812 (mp10) REVERT: H 163 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7684 (mmt180) REVERT: H 211 THR cc_start: 0.8066 (m) cc_final: 0.7812 (p) REVERT: H 309 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8710 (tp) REVERT: H 365 ASP cc_start: 0.7981 (m-30) cc_final: 0.7544 (m-30) REVERT: H 452 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6630 (mp10) REVERT: I 47 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6982 (tptp) REVERT: I 129 ASP cc_start: 0.6885 (t0) cc_final: 0.6642 (t0) REVERT: I 170 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8847 (mtp) REVERT: I 185 ILE cc_start: 0.8344 (mt) cc_final: 0.8058 (mt) REVERT: I 211 THR cc_start: 0.8155 (m) cc_final: 0.7902 (p) REVERT: I 363 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7916 (mttp) REVERT: I 365 ASP cc_start: 0.7655 (m-30) cc_final: 0.7305 (m-30) REVERT: I 440 LEU cc_start: 0.8206 (tp) cc_final: 0.7795 (tt) REVERT: J 11 THR cc_start: 0.7532 (t) cc_final: 0.7310 (m) REVERT: J 163 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7600 (mmt180) REVERT: J 211 THR cc_start: 0.8135 (m) cc_final: 0.7905 (p) REVERT: J 301 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7843 (mmm-85) REVERT: J 309 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8599 (mp) REVERT: J 323 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6209 (mt-10) REVERT: J 403 LYS cc_start: 0.7569 (mttt) cc_final: 0.7251 (mppt) REVERT: J 440 LEU cc_start: 0.8338 (tp) cc_final: 0.7896 (tt) REVERT: K 211 THR cc_start: 0.7994 (m) cc_final: 0.7746 (p) REVERT: K 286 MET cc_start: 0.8742 (ttm) cc_final: 0.8423 (mtp) REVERT: K 363 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (mttp) REVERT: K 422 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7685 (m-40) REVERT: L 53 MET cc_start: 0.8532 (mtt) cc_final: 0.8186 (mtt) REVERT: L 211 THR cc_start: 0.8076 (m) cc_final: 0.7849 (p) REVERT: L 286 MET cc_start: 0.8808 (ttm) cc_final: 0.8494 (mtp) REVERT: L 422 ASN cc_start: 0.7785 (t0) cc_final: 0.7507 (m110) REVERT: L 452 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6347 (mp10) REVERT: M 47 LYS cc_start: 0.7324 (tppp) cc_final: 0.6922 (tptp) REVERT: M 365 ASP cc_start: 0.7719 (m-30) cc_final: 0.7296 (m-30) REVERT: M 422 ASN cc_start: 0.7863 (t0) cc_final: 0.7539 (t0) REVERT: M 452 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6846 (mp10) outliers start: 151 outliers final: 52 residues processed: 814 average time/residue: 1.6616 time to fit residues: 1680.1070 Evaluate side-chains 757 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 687 time to evaluate : 5.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 422 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 192 ARG Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 221 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 292 ASN Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 444 ILE Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 315 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 549 optimal weight: 10.0000 chunk 417 optimal weight: 0.1980 chunk 288 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 373 optimal weight: 0.7980 chunk 557 optimal weight: 5.9990 chunk 590 optimal weight: 0.9980 chunk 291 optimal weight: 0.5980 chunk 528 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN B 221 ASN C 371 GLN C 422 ASN D 221 ASN D 371 GLN E 221 ASN E 340 GLN F 221 ASN G 221 ASN G 340 GLN H 112 GLN H 422 ASN I 112 GLN I 221 ASN I 371 GLN I 422 ASN J 221 ASN J 452 GLN L 221 ASN M 22 ASN M 336 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 51571 Z= 0.130 Angle : 0.460 4.916 69576 Z= 0.259 Chirality : 0.038 0.144 7540 Planarity : 0.003 0.028 9191 Dihedral : 4.224 15.377 6942 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.79 % Allowed : 11.14 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 6162 helix: 2.19 (0.10), residues: 2769 sheet: 1.20 (0.14), residues: 1131 loop : -0.37 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 92 PHE 0.027 0.001 PHE G 235 TYR 0.018 0.001 TYR I 218 ARG 0.004 0.000 ARG M 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 716 time to evaluate : 5.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8449 (mtt) cc_final: 0.8089 (mtt) REVERT: A 129 ASP cc_start: 0.6905 (t0) cc_final: 0.6513 (t0) REVERT: A 156 ARG cc_start: 0.7014 (mmm160) cc_final: 0.6773 (mmm160) REVERT: A 213 HIS cc_start: 0.6694 (m-70) cc_final: 0.6400 (m170) REVERT: A 286 MET cc_start: 0.8768 (ttm) cc_final: 0.8224 (mtp) REVERT: A 365 ASP cc_start: 0.7599 (m-30) cc_final: 0.7286 (m-30) REVERT: A 422 ASN cc_start: 0.7800 (t0) cc_final: 0.7522 (m-40) REVERT: A 452 GLN cc_start: 0.6685 (mm-40) cc_final: 0.6154 (mp10) REVERT: A 456 MET cc_start: 0.7284 (mtt) cc_final: 0.7008 (mtt) REVERT: B 47 LYS cc_start: 0.7322 (ttmt) cc_final: 0.7108 (tptp) REVERT: B 53 MET cc_start: 0.8458 (mtt) cc_final: 0.8071 (mtm) REVERT: B 125 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 129 ASP cc_start: 0.6758 (t0) cc_final: 0.6523 (t0) REVERT: B 163 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7552 (mmt180) REVERT: B 221 ASN cc_start: 0.7871 (p0) cc_final: 0.7658 (p0) REVERT: B 365 ASP cc_start: 0.7494 (m-30) cc_final: 0.7116 (m-30) REVERT: B 452 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6415 (mm-40) REVERT: B 456 MET cc_start: 0.7286 (mtt) cc_final: 0.7070 (mtt) REVERT: C 1 MET cc_start: 0.5048 (mmt) cc_final: 0.4309 (mmt) REVERT: C 185 ILE cc_start: 0.8230 (mt) cc_final: 0.7933 (mt) REVERT: C 362 MET cc_start: 0.8279 (ptp) cc_final: 0.7938 (ptp) REVERT: C 363 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7783 (mmtm) REVERT: C 365 ASP cc_start: 0.7743 (m-30) cc_final: 0.7390 (m-30) REVERT: C 403 LYS cc_start: 0.7525 (mttt) cc_final: 0.7217 (mppt) REVERT: C 429 ASN cc_start: 0.8440 (m110) cc_final: 0.8176 (t0) REVERT: C 452 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6584 (mm110) REVERT: C 456 MET cc_start: 0.7371 (mtt) cc_final: 0.7066 (mtt) REVERT: D 125 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 221 ASN cc_start: 0.7940 (p0) cc_final: 0.7557 (p0) REVERT: D 255 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8909 (mmtp) REVERT: D 363 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7795 (mttp) REVERT: D 403 LYS cc_start: 0.7464 (mttt) cc_final: 0.7066 (mppt) REVERT: D 452 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6551 (mp10) REVERT: E 54 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: E 125 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: E 159 ASP cc_start: 0.6194 (m-30) cc_final: 0.5743 (t0) REVERT: E 192 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5840 (tmm-80) REVERT: E 440 LEU cc_start: 0.8266 (tp) cc_final: 0.7806 (tt) REVERT: E 452 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6933 (mp10) REVERT: F 53 MET cc_start: 0.8564 (mtt) cc_final: 0.8248 (mtt) REVERT: F 125 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7564 (mp0) REVERT: F 192 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6967 (mmm-85) REVERT: F 365 ASP cc_start: 0.7909 (m-30) cc_final: 0.7320 (m-30) REVERT: F 376 MET cc_start: 0.8484 (mmm) cc_final: 0.8269 (tpt) REVERT: F 403 LYS cc_start: 0.7492 (mttt) cc_final: 0.7125 (mppt) REVERT: G 47 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6825 (ttmp) REVERT: G 125 GLU cc_start: 0.7827 (mp0) cc_final: 0.7389 (mp0) REVERT: G 129 ASP cc_start: 0.6843 (t0) cc_final: 0.6455 (t0) REVERT: G 213 HIS cc_start: 0.6260 (m-70) cc_final: 0.5919 (m-70) REVERT: G 279 MET cc_start: 0.9128 (mtp) cc_final: 0.8885 (mtp) REVERT: G 422 ASN cc_start: 0.7813 (t0) cc_final: 0.7576 (t0) REVERT: G 452 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6781 (mp10) REVERT: H 54 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: H 163 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7560 (mmt180) REVERT: H 211 THR cc_start: 0.8170 (m) cc_final: 0.7913 (p) REVERT: H 365 ASP cc_start: 0.7968 (m-30) cc_final: 0.7538 (m-30) REVERT: H 422 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7633 (m-40) REVERT: H 452 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6605 (mp10) REVERT: I 129 ASP cc_start: 0.6844 (t0) cc_final: 0.6621 (t0) REVERT: I 170 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8897 (mtp) REVERT: I 185 ILE cc_start: 0.8346 (mt) cc_final: 0.8021 (mt) REVERT: I 221 ASN cc_start: 0.7674 (p0) cc_final: 0.7445 (p0) REVERT: I 363 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7886 (mttp) REVERT: I 440 LEU cc_start: 0.8190 (tp) cc_final: 0.7785 (tt) REVERT: J 11 THR cc_start: 0.7541 (t) cc_final: 0.7329 (m) REVERT: J 163 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7518 (mmt180) REVERT: J 217 ARG cc_start: 0.7539 (mtt-85) cc_final: 0.7276 (mtt90) REVERT: J 221 ASN cc_start: 0.7848 (p0) cc_final: 0.7570 (p0) REVERT: J 301 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7818 (mmm-85) REVERT: J 309 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8562 (mp) REVERT: J 323 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6163 (mt-10) REVERT: J 376 MET cc_start: 0.8647 (tpt) cc_final: 0.8425 (mmt) REVERT: J 403 LYS cc_start: 0.7511 (mttt) cc_final: 0.7188 (mppt) REVERT: J 440 LEU cc_start: 0.8258 (tp) cc_final: 0.7796 (tt) REVERT: K 170 MET cc_start: 0.9103 (mtm) cc_final: 0.8711 (mtm) REVERT: K 286 MET cc_start: 0.8711 (ttm) cc_final: 0.8380 (mtp) REVERT: K 363 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7914 (mttp) REVERT: K 422 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7678 (m-40) REVERT: K 452 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6577 (mp10) REVERT: L 53 MET cc_start: 0.8506 (mtt) cc_final: 0.8104 (mtt) REVERT: L 159 ASP cc_start: 0.6320 (m-30) cc_final: 0.5765 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7671 (p0) cc_final: 0.7292 (p0) REVERT: L 365 ASP cc_start: 0.7617 (m-30) cc_final: 0.7353 (m-30) REVERT: L 403 LYS cc_start: 0.7438 (mttt) cc_final: 0.7042 (mppt) REVERT: L 422 ASN cc_start: 0.7900 (t0) cc_final: 0.7520 (m-40) REVERT: L 425 ARG cc_start: 0.7188 (mtm-85) cc_final: 0.6988 (mtm-85) REVERT: L 452 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6462 (mp10) REVERT: M 47 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6924 (tptp) REVERT: M 134 GLU cc_start: 0.7595 (tt0) cc_final: 0.7359 (tt0) REVERT: M 365 ASP cc_start: 0.7593 (m-30) cc_final: 0.7189 (m-30) REVERT: M 422 ASN cc_start: 0.7859 (t0) cc_final: 0.7519 (t0) REVERT: M 452 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6739 (mp10) outliers start: 101 outliers final: 43 residues processed: 776 average time/residue: 1.7695 time to fit residues: 1687.7455 Evaluate side-chains 737 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 679 time to evaluate : 6.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 192 ARG Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 396 LYS Chi-restraints excluded: chain H residue 422 ASN Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 491 optimal weight: 10.0000 chunk 335 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 439 optimal weight: 0.9980 chunk 243 optimal weight: 0.0000 chunk 503 optimal weight: 4.9990 chunk 408 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 530 optimal weight: 10.0000 chunk 149 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 112 GLN C 112 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 422 ASN D 371 GLN D 422 ASN E 221 ASN F 221 ASN G 221 ASN G 340 GLN H 112 GLN H 371 GLN H 422 ASN I 112 GLN I 350 ASN I 361 ASN I 371 GLN I 422 ASN I 452 GLN J 452 GLN M 22 ASN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 51571 Z= 0.232 Angle : 0.546 5.753 69576 Z= 0.305 Chirality : 0.042 0.133 7540 Planarity : 0.004 0.041 9191 Dihedral : 4.403 15.877 6942 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.43 % Allowed : 11.64 % Favored : 85.93 % 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: 1.38 (0.10), residues: 6162 helix: 1.98 (0.10), residues: 2743 sheet: 1.08 (0.14), residues: 1131 loop : -0.47 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 354 PHE 0.018 0.002 PHE D 235 TYR 0.020 0.002 TYR L 218 ARG 0.007 0.001 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 717 time to evaluate : 6.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8610 (mtt) cc_final: 0.8283 (mtt) REVERT: A 83 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: A 125 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: A 129 ASP cc_start: 0.6968 (t0) cc_final: 0.6539 (t0) REVERT: A 183 ASN cc_start: 0.8390 (m110) cc_final: 0.8157 (m110) REVERT: A 206 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7946 (t) REVERT: A 213 HIS cc_start: 0.6671 (m-70) cc_final: 0.6389 (m170) REVERT: A 255 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8575 (mmmt) REVERT: A 286 MET cc_start: 0.8788 (ttm) cc_final: 0.8289 (mtp) REVERT: A 365 ASP cc_start: 0.7600 (m-30) cc_final: 0.7318 (m-30) REVERT: A 452 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6289 (mp-120) REVERT: A 456 MET cc_start: 0.7340 (mtt) cc_final: 0.7105 (mtt) REVERT: B 47 LYS cc_start: 0.7496 (ttmt) cc_final: 0.7272 (tptp) REVERT: B 53 MET cc_start: 0.8537 (mtt) cc_final: 0.8154 (mtm) REVERT: B 125 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 129 ASP cc_start: 0.6800 (t0) cc_final: 0.6541 (t0) REVERT: B 159 ASP cc_start: 0.6617 (m-30) cc_final: 0.5977 (t0) REVERT: B 163 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7580 (mmt180) REVERT: B 221 ASN cc_start: 0.7936 (p0) cc_final: 0.7626 (p0) REVERT: B 365 ASP cc_start: 0.7539 (m-30) cc_final: 0.7170 (m-30) REVERT: B 429 ASN cc_start: 0.8307 (m-40) cc_final: 0.7979 (t0) REVERT: B 440 LEU cc_start: 0.8104 (tp) cc_final: 0.7565 (tt) REVERT: B 452 GLN cc_start: 0.6793 (mm-40) cc_final: 0.6565 (mm-40) REVERT: B 456 MET cc_start: 0.7313 (mtt) cc_final: 0.7075 (mtt) REVERT: C 185 ILE cc_start: 0.8215 (mt) cc_final: 0.7940 (mt) REVERT: C 235 PHE cc_start: 0.7417 (t80) cc_final: 0.7063 (t80) REVERT: C 362 MET cc_start: 0.8305 (ptp) cc_final: 0.7948 (ptp) REVERT: C 365 ASP cc_start: 0.7802 (m-30) cc_final: 0.7438 (m-30) REVERT: C 452 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6679 (mm110) REVERT: C 456 MET cc_start: 0.7336 (mtt) cc_final: 0.7059 (mtt) REVERT: D 125 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: D 221 ASN cc_start: 0.7940 (p0) cc_final: 0.7609 (p0) REVERT: D 286 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8360 (mtp) REVERT: D 340 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7653 (tp-100) REVERT: D 363 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7823 (mttp) REVERT: D 422 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7317 (m110) REVERT: D 452 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6605 (mp10) REVERT: E 54 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: E 125 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: E 159 ASP cc_start: 0.6290 (m-30) cc_final: 0.5914 (t0) REVERT: E 292 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7890 (t0) REVERT: E 309 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8533 (mp) REVERT: F 47 LYS cc_start: 0.7564 (tppp) cc_final: 0.7180 (tptp) REVERT: F 53 MET cc_start: 0.8627 (mtt) cc_final: 0.8327 (mtt) REVERT: F 219 LEU cc_start: 0.8551 (mp) cc_final: 0.8337 (mt) REVERT: F 365 ASP cc_start: 0.7945 (m-30) cc_final: 0.7362 (m-30) REVERT: G 47 LYS cc_start: 0.7143 (tppp) cc_final: 0.6908 (ttmp) REVERT: G 125 GLU cc_start: 0.7949 (mp0) cc_final: 0.7661 (mp0) REVERT: G 129 ASP cc_start: 0.6916 (t0) cc_final: 0.6518 (t0) REVERT: G 213 HIS cc_start: 0.6124 (m-70) cc_final: 0.5791 (m-70) REVERT: G 221 ASN cc_start: 0.7839 (p0) cc_final: 0.7436 (p0) REVERT: G 279 MET cc_start: 0.9238 (mtp) cc_final: 0.8932 (mtp) REVERT: G 422 ASN cc_start: 0.7853 (t0) cc_final: 0.7608 (t0) REVERT: G 452 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6732 (mp10) REVERT: H 83 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: H 163 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7617 (mmt180) REVERT: H 211 THR cc_start: 0.8272 (m) cc_final: 0.8058 (p) REVERT: H 217 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7080 (mtt180) REVERT: H 365 ASP cc_start: 0.8090 (m-30) cc_final: 0.7675 (m-30) REVERT: H 452 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6613 (mp10) REVERT: I 8 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: I 83 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: I 129 ASP cc_start: 0.6988 (t0) cc_final: 0.6753 (t0) REVERT: I 170 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8891 (mtp) REVERT: I 185 ILE cc_start: 0.8310 (mt) cc_final: 0.8049 (mt) REVERT: I 340 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7517 (tp-100) REVERT: I 440 LEU cc_start: 0.8232 (tp) cc_final: 0.7804 (tt) REVERT: J 11 THR cc_start: 0.7600 (t) cc_final: 0.7394 (m) REVERT: J 54 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: J 163 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7518 (mmt180) REVERT: J 217 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7184 (mtt90) REVERT: J 221 ASN cc_start: 0.7753 (p0) cc_final: 0.7484 (p0) REVERT: J 301 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7916 (mmm-85) REVERT: J 309 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8591 (mp) REVERT: J 323 GLU cc_start: 0.6505 (mt-10) cc_final: 0.6273 (mt-10) REVERT: J 403 LYS cc_start: 0.7558 (mttt) cc_final: 0.7270 (mppt) REVERT: J 440 LEU cc_start: 0.8233 (tp) cc_final: 0.7737 (tt) REVERT: K 170 MET cc_start: 0.9126 (mtm) cc_final: 0.8880 (mtm) REVERT: K 221 ASN cc_start: 0.7822 (p0) cc_final: 0.7415 (p0) REVERT: K 286 MET cc_start: 0.8740 (ttm) cc_final: 0.8454 (mtp) REVERT: K 363 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7931 (mttp) REVERT: K 422 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: K 452 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6580 (mp10) REVERT: L 53 MET cc_start: 0.8591 (mtt) cc_final: 0.8237 (mtt) REVERT: L 159 ASP cc_start: 0.6539 (m-30) cc_final: 0.5954 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7629 (p0) cc_final: 0.7260 (p0) REVERT: L 365 ASP cc_start: 0.7670 (m-30) cc_final: 0.7363 (m-30) REVERT: L 422 ASN cc_start: 0.7967 (t0) cc_final: 0.7560 (m-40) REVERT: L 452 GLN cc_start: 0.6874 (mm-40) cc_final: 0.6454 (mp10) REVERT: M 47 LYS cc_start: 0.7422 (tppp) cc_final: 0.7042 (tptp) REVERT: M 219 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (mt) REVERT: M 365 ASP cc_start: 0.7973 (m-30) cc_final: 0.7511 (m-30) REVERT: M 422 ASN cc_start: 0.7913 (t0) cc_final: 0.7571 (t0) REVERT: M 441 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8071 (tttt) REVERT: M 452 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6721 (mp10) outliers start: 137 outliers final: 64 residues processed: 802 average time/residue: 1.7104 time to fit residues: 1698.6681 Evaluate side-chains 778 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 690 time to evaluate : 5.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 422 ASN Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 217 ARG Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 340 GLN Chi-restraints excluded: chain I residue 362 MET Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 292 ASN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 292 ASN Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 292 ASN Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 441 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 198 optimal weight: 0.8980 chunk 531 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 591 optimal weight: 1.9990 chunk 490 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 221 ASN A 340 GLN B 112 GLN B 422 ASN C 112 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN D 112 GLN D 371 GLN E 112 GLN E 221 ASN E 452 GLN F 221 ASN G 340 GLN H 112 GLN H 371 GLN H 422 ASN I 112 GLN I 221 ASN I 422 ASN I 452 GLN J 452 GLN L 429 ASN M 22 ASN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51571 Z= 0.150 Angle : 0.469 5.434 69576 Z= 0.264 Chirality : 0.039 0.139 7540 Planarity : 0.003 0.035 9191 Dihedral : 4.196 15.532 6942 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.26 % Allowed : 12.51 % Favored : 85.24 % 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: 1.48 (0.10), residues: 6162 helix: 2.17 (0.10), residues: 2743 sheet: 1.08 (0.14), residues: 1131 loop : -0.54 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 92 PHE 0.029 0.001 PHE G 235 TYR 0.021 0.002 TYR L 218 ARG 0.006 0.000 ARG M 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 708 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8513 (mtt) cc_final: 0.8159 (mtt) REVERT: A 129 ASP cc_start: 0.6922 (t0) cc_final: 0.6518 (t0) REVERT: A 183 ASN cc_start: 0.8395 (m110) cc_final: 0.8131 (m110) REVERT: A 206 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7916 (t) REVERT: A 213 HIS cc_start: 0.6694 (m-70) cc_final: 0.6380 (m170) REVERT: A 255 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8846 (mmtp) REVERT: A 286 MET cc_start: 0.8784 (ttm) cc_final: 0.8262 (mtp) REVERT: A 365 ASP cc_start: 0.7565 (m-30) cc_final: 0.7283 (m-30) REVERT: A 422 ASN cc_start: 0.7867 (t0) cc_final: 0.7590 (m-40) REVERT: A 452 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6311 (mp10) REVERT: A 456 MET cc_start: 0.7181 (mtt) cc_final: 0.6970 (mtt) REVERT: B 47 LYS cc_start: 0.7465 (ttmt) cc_final: 0.7246 (tptp) REVERT: B 53 MET cc_start: 0.8472 (mtt) cc_final: 0.8070 (mtm) REVERT: B 125 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 129 ASP cc_start: 0.6747 (t0) cc_final: 0.6491 (t0) REVERT: B 159 ASP cc_start: 0.6614 (m-30) cc_final: 0.5978 (t0) REVERT: B 163 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7532 (mmt180) REVERT: B 221 ASN cc_start: 0.7778 (p0) cc_final: 0.7494 (p0) REVERT: B 365 ASP cc_start: 0.7515 (m-30) cc_final: 0.7131 (m-30) REVERT: B 429 ASN cc_start: 0.8311 (m-40) cc_final: 0.7990 (t0) REVERT: C 1 MET cc_start: 0.5083 (mmt) cc_final: 0.4318 (mmt) REVERT: C 185 ILE cc_start: 0.8221 (mt) cc_final: 0.7921 (mt) REVERT: C 235 PHE cc_start: 0.7485 (t80) cc_final: 0.7187 (t80) REVERT: C 362 MET cc_start: 0.8197 (ptp) cc_final: 0.7869 (ptp) REVERT: C 363 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7768 (mmmm) REVERT: C 365 ASP cc_start: 0.7743 (m-30) cc_final: 0.7405 (m-30) REVERT: C 422 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7305 (m-40) REVERT: C 452 GLN cc_start: 0.7015 (mm-40) cc_final: 0.6666 (mp10) REVERT: D 125 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: D 221 ASN cc_start: 0.7821 (p0) cc_final: 0.7508 (p0) REVERT: D 363 LYS cc_start: 0.8148 (mmtp) cc_final: 0.7817 (mttp) REVERT: D 452 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6580 (mp10) REVERT: E 54 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: E 125 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: E 159 ASP cc_start: 0.6257 (m-30) cc_final: 0.5865 (t0) REVERT: E 309 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8458 (mp) REVERT: E 423 THR cc_start: 0.7893 (p) cc_final: 0.7632 (p) REVERT: F 53 MET cc_start: 0.8603 (mtt) cc_final: 0.8299 (mtt) REVERT: F 365 ASP cc_start: 0.7920 (m-30) cc_final: 0.7314 (m-30) REVERT: F 403 LYS cc_start: 0.7521 (mttt) cc_final: 0.7234 (mppt) REVERT: G 47 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6934 (ttmp) REVERT: G 125 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: G 129 ASP cc_start: 0.6874 (t0) cc_final: 0.6484 (t0) REVERT: G 213 HIS cc_start: 0.6125 (m-70) cc_final: 0.5817 (m-70) REVERT: G 221 ASN cc_start: 0.7704 (p0) cc_final: 0.7307 (p0) REVERT: G 279 MET cc_start: 0.9187 (mtp) cc_final: 0.8902 (mtp) REVERT: G 422 ASN cc_start: 0.7855 (t0) cc_final: 0.7617 (t0) REVERT: G 440 LEU cc_start: 0.8240 (tp) cc_final: 0.7761 (tt) REVERT: G 452 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6742 (mp10) REVERT: H 83 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: H 163 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7573 (mmt180) REVERT: H 217 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7017 (mtt180) REVERT: H 365 ASP cc_start: 0.7998 (m-30) cc_final: 0.7600 (m-30) REVERT: H 422 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7627 (m-40) REVERT: H 452 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6661 (mp10) REVERT: I 8 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: I 83 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: I 129 ASP cc_start: 0.6943 (t0) cc_final: 0.6732 (t0) REVERT: I 170 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8881 (mtp) REVERT: I 185 ILE cc_start: 0.8297 (mt) cc_final: 0.8030 (mt) REVERT: I 235 PHE cc_start: 0.7744 (t80) cc_final: 0.7263 (t80) REVERT: J 54 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: J 163 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7470 (mmt180) REVERT: J 217 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.7351 (mtt90) REVERT: J 301 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7899 (mmm-85) REVERT: J 309 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8611 (mp) REVERT: J 323 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6255 (mt-10) REVERT: J 403 LYS cc_start: 0.7507 (mttt) cc_final: 0.7245 (mppt) REVERT: K 125 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: K 132 ASP cc_start: 0.7646 (t0) cc_final: 0.7382 (t0) REVERT: K 170 MET cc_start: 0.9114 (mtm) cc_final: 0.8726 (mtm) REVERT: K 221 ASN cc_start: 0.7684 (p0) cc_final: 0.7307 (p0) REVERT: K 255 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8680 (mptm) REVERT: K 286 MET cc_start: 0.8752 (ttm) cc_final: 0.8470 (mtp) REVERT: K 363 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7927 (mttp) REVERT: K 422 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7730 (m-40) REVERT: K 452 GLN cc_start: 0.6907 (mm-40) cc_final: 0.6602 (mp10) REVERT: L 32 ASP cc_start: 0.6574 (m-30) cc_final: 0.6311 (m-30) REVERT: L 53 MET cc_start: 0.8516 (mtt) cc_final: 0.8147 (mtt) REVERT: L 143 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8336 (t0) REVERT: L 159 ASP cc_start: 0.6545 (m-30) cc_final: 0.5948 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7606 (p0) cc_final: 0.7297 (p0) REVERT: L 365 ASP cc_start: 0.7718 (m-30) cc_final: 0.7395 (m-30) REVERT: L 403 LYS cc_start: 0.7450 (mttt) cc_final: 0.7104 (mppt) REVERT: L 422 ASN cc_start: 0.7942 (t0) cc_final: 0.7513 (m-40) REVERT: L 440 LEU cc_start: 0.8023 (tp) cc_final: 0.7443 (tt) REVERT: L 452 GLN cc_start: 0.6856 (mm-40) cc_final: 0.6472 (mp10) REVERT: M 47 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7030 (tptp) REVERT: M 219 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8275 (mt) REVERT: M 235 PHE cc_start: 0.7437 (t80) cc_final: 0.7112 (t80) REVERT: M 365 ASP cc_start: 0.7797 (m-30) cc_final: 0.7338 (m-30) REVERT: M 422 ASN cc_start: 0.7887 (t0) cc_final: 0.7549 (t0) REVERT: M 441 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8059 (tttt) REVERT: M 452 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6667 (mp10) outliers start: 127 outliers final: 58 residues processed: 786 average time/residue: 1.7281 time to fit residues: 1674.6480 Evaluate side-chains 777 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 693 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 217 ARG Chi-restraints excluded: chain H residue 422 ASN Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain I residue 362 MET Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 292 ASN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 255 LYS Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 292 ASN Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 441 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 569 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 336 optimal weight: 0.9980 chunk 431 optimal weight: 0.0980 chunk 334 optimal weight: 1.9990 chunk 497 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 588 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 359 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 221 ASN A 340 GLN B 112 GLN B 422 ASN C 112 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN D 371 GLN E 112 GLN E 221 ASN E 452 GLN F 221 ASN G 340 GLN H 112 GLN H 371 GLN I 221 ASN I 371 GLN I 422 ASN I 452 GLN J 452 GLN M 22 ASN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 51571 Z= 0.144 Angle : 0.461 5.263 69576 Z= 0.259 Chirality : 0.038 0.133 7540 Planarity : 0.003 0.038 9191 Dihedral : 4.099 15.221 6942 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.36 % Allowed : 12.99 % Favored : 84.65 % 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: 1.55 (0.10), residues: 6162 helix: 2.25 (0.10), residues: 2769 sheet: 1.09 (0.14), residues: 1131 loop : -0.57 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 92 PHE 0.013 0.001 PHE D 173 TYR 0.020 0.001 TYR L 218 ARG 0.008 0.000 ARG I 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 708 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8483 (mtt) cc_final: 0.8128 (mtt) REVERT: A 129 ASP cc_start: 0.6823 (t0) cc_final: 0.6422 (t0) REVERT: A 159 ASP cc_start: 0.6320 (m-30) cc_final: 0.5788 (t0) REVERT: A 183 ASN cc_start: 0.8387 (m110) cc_final: 0.8119 (m110) REVERT: A 206 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7907 (t) REVERT: A 213 HIS cc_start: 0.6666 (m-70) cc_final: 0.6369 (m170) REVERT: A 255 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8847 (mmtp) REVERT: A 286 MET cc_start: 0.8784 (ttm) cc_final: 0.8267 (mtp) REVERT: A 365 ASP cc_start: 0.7667 (m-30) cc_final: 0.7381 (m-30) REVERT: A 422 ASN cc_start: 0.7829 (t0) cc_final: 0.7574 (m-40) REVERT: A 452 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6295 (mp10) REVERT: B 53 MET cc_start: 0.8425 (mtt) cc_final: 0.8021 (mtm) REVERT: B 125 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: B 129 ASP cc_start: 0.6742 (t0) cc_final: 0.6501 (t0) REVERT: B 159 ASP cc_start: 0.6625 (m-30) cc_final: 0.5973 (t0) REVERT: B 163 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7508 (mmt180) REVERT: B 221 ASN cc_start: 0.7740 (p0) cc_final: 0.7404 (p0) REVERT: B 365 ASP cc_start: 0.7505 (m-30) cc_final: 0.7146 (m-30) REVERT: B 422 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7433 (m-40) REVERT: B 429 ASN cc_start: 0.8329 (m-40) cc_final: 0.8000 (t0) REVERT: B 440 LEU cc_start: 0.8062 (tp) cc_final: 0.7507 (tt) REVERT: C 1 MET cc_start: 0.5019 (mmt) cc_final: 0.4192 (mmt) REVERT: C 185 ILE cc_start: 0.8230 (mt) cc_final: 0.7920 (mt) REVERT: C 235 PHE cc_start: 0.7479 (t80) cc_final: 0.7234 (t80) REVERT: C 362 MET cc_start: 0.8195 (ptp) cc_final: 0.7861 (ptp) REVERT: C 363 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7761 (mmmm) REVERT: C 365 ASP cc_start: 0.7731 (m-30) cc_final: 0.7401 (m-30) REVERT: D 125 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: D 221 ASN cc_start: 0.7691 (p0) cc_final: 0.7399 (p0) REVERT: D 363 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7832 (mttp) REVERT: D 452 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6686 (mp10) REVERT: E 54 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: E 125 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: E 159 ASP cc_start: 0.6266 (m-30) cc_final: 0.5861 (t0) REVERT: E 292 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7957 (t0) REVERT: E 309 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8443 (mp) REVERT: E 423 THR cc_start: 0.7893 (p) cc_final: 0.7635 (p) REVERT: F 53 MET cc_start: 0.8577 (mtt) cc_final: 0.8258 (mtt) REVERT: F 365 ASP cc_start: 0.7904 (m-30) cc_final: 0.7353 (m-30) REVERT: F 403 LYS cc_start: 0.7534 (mttt) cc_final: 0.7101 (mppt) REVERT: G 47 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6948 (ttmp) REVERT: G 129 ASP cc_start: 0.6862 (t0) cc_final: 0.6477 (t0) REVERT: G 213 HIS cc_start: 0.6158 (m-70) cc_final: 0.5871 (m-70) REVERT: G 221 ASN cc_start: 0.7604 (p0) cc_final: 0.7256 (p0) REVERT: G 279 MET cc_start: 0.9166 (mtp) cc_final: 0.8891 (mtp) REVERT: G 422 ASN cc_start: 0.7848 (t0) cc_final: 0.7620 (t0) REVERT: G 452 GLN cc_start: 0.6998 (mm-40) cc_final: 0.6643 (mp10) REVERT: H 1 MET cc_start: 0.5008 (mmt) cc_final: 0.4781 (mmm) REVERT: H 163 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7539 (mmt180) REVERT: H 217 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6976 (mtt180) REVERT: H 365 ASP cc_start: 0.7986 (m-30) cc_final: 0.7610 (m-30) REVERT: H 452 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6658 (mp10) REVERT: I 8 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: I 78 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8365 (m) REVERT: I 83 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: I 159 ASP cc_start: 0.6053 (m-30) cc_final: 0.5512 (t0) REVERT: I 170 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8881 (mtp) REVERT: I 182 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7627 (mtm180) REVERT: I 185 ILE cc_start: 0.8279 (mt) cc_final: 0.7991 (mt) REVERT: I 221 ASN cc_start: 0.7617 (p0) cc_final: 0.7344 (p0) REVERT: I 235 PHE cc_start: 0.7739 (t80) cc_final: 0.7344 (t80) REVERT: I 440 LEU cc_start: 0.8369 (tp) cc_final: 0.8032 (tt) REVERT: J 54 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: J 163 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7452 (mmt180) REVERT: J 217 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7355 (mtt90) REVERT: J 301 ARG cc_start: 0.8152 (mtp-110) cc_final: 0.7888 (mmm-85) REVERT: J 323 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6170 (mt-10) REVERT: J 403 LYS cc_start: 0.7531 (mttt) cc_final: 0.7236 (mppt) REVERT: J 440 LEU cc_start: 0.8293 (tp) cc_final: 0.7923 (tt) REVERT: K 125 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: K 132 ASP cc_start: 0.7628 (t0) cc_final: 0.7372 (t0) REVERT: K 221 ASN cc_start: 0.7637 (p0) cc_final: 0.7264 (p0) REVERT: K 255 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8698 (mptm) REVERT: K 286 MET cc_start: 0.8741 (ttm) cc_final: 0.8401 (mtp) REVERT: K 363 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7922 (mttp) REVERT: K 422 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: K 452 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6572 (mp10) REVERT: L 32 ASP cc_start: 0.6575 (m-30) cc_final: 0.6334 (m-30) REVERT: L 53 MET cc_start: 0.8487 (mtt) cc_final: 0.8121 (mtt) REVERT: L 143 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8326 (t0) REVERT: L 159 ASP cc_start: 0.6543 (m-30) cc_final: 0.5937 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7568 (p0) cc_final: 0.7284 (p0) REVERT: L 365 ASP cc_start: 0.7708 (m-30) cc_final: 0.7390 (m-30) REVERT: L 403 LYS cc_start: 0.7395 (mttt) cc_final: 0.7064 (mppt) REVERT: L 422 ASN cc_start: 0.7935 (t0) cc_final: 0.7521 (m-40) REVERT: L 440 LEU cc_start: 0.8025 (tp) cc_final: 0.7439 (tt) REVERT: L 452 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6451 (mp10) REVERT: M 47 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7097 (tptp) REVERT: M 206 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7918 (t) REVERT: M 235 PHE cc_start: 0.7415 (t80) cc_final: 0.7142 (t80) REVERT: M 255 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8639 (mptp) REVERT: M 365 ASP cc_start: 0.7814 (m-30) cc_final: 0.7369 (m-30) REVERT: M 422 ASN cc_start: 0.7876 (t0) cc_final: 0.7527 (t0) REVERT: M 441 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8178 (tttt) REVERT: M 452 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6619 (mp10) outliers start: 133 outliers final: 64 residues processed: 789 average time/residue: 1.7627 time to fit residues: 1711.8068 Evaluate side-chains 780 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 690 time to evaluate : 6.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 217 ARG Chi-restraints excluded: chain H residue 396 LYS Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 362 MET Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 292 ASN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 255 LYS Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 255 LYS Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 441 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 364 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 351 optimal weight: 0.2980 chunk 177 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 462 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 221 ASN B 112 GLN B 422 ASN C 112 GLN C 221 ASN C 371 GLN C 422 ASN C 429 ASN C 452 GLN D 371 GLN E 112 GLN E 221 ASN E 350 ASN E 361 ASN E 452 GLN F 221 ASN F 350 ASN F 361 ASN G 340 GLN H 112 GLN H 350 ASN H 371 GLN I 340 GLN I 452 GLN J 452 GLN M 221 ASN M 336 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 51571 Z= 0.257 Angle : 0.565 6.591 69576 Z= 0.314 Chirality : 0.043 0.165 7540 Planarity : 0.004 0.048 9191 Dihedral : 4.417 17.449 6942 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 13.24 % Favored : 84.54 % 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: 1.32 (0.10), residues: 6162 helix: 2.02 (0.10), residues: 2717 sheet: 0.97 (0.14), residues: 1144 loop : -0.56 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 354 PHE 0.029 0.002 PHE H 235 TYR 0.021 0.002 TYR L 218 ARG 0.008 0.001 ARG F 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 723 time to evaluate : 6.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8627 (mtt) cc_final: 0.8324 (mtt) REVERT: A 129 ASP cc_start: 0.6981 (t0) cc_final: 0.6549 (t0) REVERT: A 183 ASN cc_start: 0.8446 (m110) cc_final: 0.8189 (m110) REVERT: A 206 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7929 (t) REVERT: A 213 HIS cc_start: 0.6670 (m-70) cc_final: 0.6328 (m170) REVERT: A 286 MET cc_start: 0.8786 (ttm) cc_final: 0.8322 (mtp) REVERT: A 365 ASP cc_start: 0.7608 (m-30) cc_final: 0.7315 (m-30) REVERT: A 422 ASN cc_start: 0.8006 (t0) cc_final: 0.7701 (m-40) REVERT: B 53 MET cc_start: 0.8527 (mtt) cc_final: 0.8168 (mtm) REVERT: B 125 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: B 129 ASP cc_start: 0.6825 (t0) cc_final: 0.6545 (t0) REVERT: B 159 ASP cc_start: 0.6483 (m-30) cc_final: 0.5859 (t0) REVERT: B 163 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7595 (mmt180) REVERT: B 221 ASN cc_start: 0.7781 (p0) cc_final: 0.7456 (p0) REVERT: B 286 MET cc_start: 0.8760 (ttp) cc_final: 0.8378 (mtp) REVERT: B 365 ASP cc_start: 0.7535 (m-30) cc_final: 0.7151 (m-30) REVERT: B 429 ASN cc_start: 0.8307 (m-40) cc_final: 0.7974 (t0) REVERT: B 440 LEU cc_start: 0.8146 (tp) cc_final: 0.7576 (tt) REVERT: C 125 GLU cc_start: 0.7529 (mp0) cc_final: 0.7242 (mp0) REVERT: C 159 ASP cc_start: 0.6432 (m-30) cc_final: 0.5686 (t0) REVERT: C 185 ILE cc_start: 0.8202 (mt) cc_final: 0.7922 (mt) REVERT: C 363 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7792 (mmmm) REVERT: C 365 ASP cc_start: 0.7752 (m-30) cc_final: 0.7413 (m-30) REVERT: D 38 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6661 (tt) REVERT: D 125 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: D 221 ASN cc_start: 0.7626 (p0) cc_final: 0.7347 (p0) REVERT: D 363 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7793 (mttp) REVERT: D 452 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6645 (mp10) REVERT: E 54 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: E 125 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: E 159 ASP cc_start: 0.6396 (m-30) cc_final: 0.5989 (t0) REVERT: E 292 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7892 (t0) REVERT: E 309 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8474 (mp) REVERT: E 423 THR cc_start: 0.7867 (p) cc_final: 0.7631 (p) REVERT: E 452 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6606 (tp40) REVERT: F 53 MET cc_start: 0.8624 (mtt) cc_final: 0.8334 (mtt) REVERT: F 365 ASP cc_start: 0.7926 (m-30) cc_final: 0.7375 (m-30) REVERT: G 47 LYS cc_start: 0.7216 (tppp) cc_final: 0.7013 (ttmp) REVERT: G 125 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: G 129 ASP cc_start: 0.6979 (t0) cc_final: 0.6577 (t0) REVERT: G 213 HIS cc_start: 0.6149 (m-70) cc_final: 0.5805 (m-70) REVERT: G 221 ASN cc_start: 0.7600 (p0) cc_final: 0.7233 (p0) REVERT: G 279 MET cc_start: 0.9248 (mtp) cc_final: 0.8949 (mtp) REVERT: G 422 ASN cc_start: 0.7889 (t0) cc_final: 0.7654 (t0) REVERT: G 452 GLN cc_start: 0.7009 (mm-40) cc_final: 0.6623 (mp10) REVERT: H 1 MET cc_start: 0.5095 (mmt) cc_final: 0.4822 (mmm) REVERT: H 163 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7613 (mmt180) REVERT: H 365 ASP cc_start: 0.8017 (m-30) cc_final: 0.7634 (m-30) REVERT: H 452 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6640 (mp10) REVERT: I 8 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: I 78 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8438 (m) REVERT: I 83 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: I 170 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8898 (mtp) REVERT: I 182 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7646 (mtm180) REVERT: I 185 ILE cc_start: 0.8293 (mt) cc_final: 0.8079 (mt) REVERT: I 235 PHE cc_start: 0.7753 (t80) cc_final: 0.7452 (t80) REVERT: I 363 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7845 (mttp) REVERT: I 422 ASN cc_start: 0.7765 (m110) cc_final: 0.7510 (t0) REVERT: I 440 LEU cc_start: 0.8267 (tp) cc_final: 0.7919 (tt) REVERT: J 54 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: J 163 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7576 (mmt180) REVERT: J 217 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.7383 (mtt90) REVERT: J 309 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8594 (mp) REVERT: J 323 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6319 (mt-10) REVERT: J 403 LYS cc_start: 0.7639 (mttt) cc_final: 0.7333 (mppt) REVERT: J 440 LEU cc_start: 0.8284 (tp) cc_final: 0.7896 (tt) REVERT: K 125 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: K 170 MET cc_start: 0.9145 (mtm) cc_final: 0.8890 (mtm) REVERT: K 221 ASN cc_start: 0.7729 (p0) cc_final: 0.7329 (p0) REVERT: K 255 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8717 (mptm) REVERT: K 286 MET cc_start: 0.8763 (ttm) cc_final: 0.8503 (mtp) REVERT: K 363 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7939 (mttp) REVERT: K 422 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7726 (m-40) REVERT: K 452 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6580 (mp10) REVERT: L 32 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6349 (m-30) REVERT: L 53 MET cc_start: 0.8547 (mtt) cc_final: 0.8232 (mtt) REVERT: L 159 ASP cc_start: 0.6653 (m-30) cc_final: 0.6018 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7601 (p0) cc_final: 0.7277 (p0) REVERT: L 365 ASP cc_start: 0.8095 (m-30) cc_final: 0.7788 (m-30) REVERT: L 422 ASN cc_start: 0.7966 (t0) cc_final: 0.7553 (m-40) REVERT: L 440 LEU cc_start: 0.8073 (tp) cc_final: 0.7483 (tt) REVERT: L 452 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6479 (mp10) REVERT: M 47 LYS cc_start: 0.7588 (tppp) cc_final: 0.7288 (tptp) REVERT: M 235 PHE cc_start: 0.7477 (t80) cc_final: 0.7233 (t80) REVERT: M 365 ASP cc_start: 0.7985 (m-30) cc_final: 0.7512 (m-30) REVERT: M 422 ASN cc_start: 0.7879 (t0) cc_final: 0.7533 (t0) REVERT: M 441 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8065 (tttt) REVERT: M 452 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6600 (mp10) outliers start: 125 outliers final: 70 residues processed: 801 average time/residue: 1.7157 time to fit residues: 1699.2234 Evaluate side-chains 795 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 703 time to evaluate : 5.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 396 LYS Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 362 MET Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 292 ASN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 255 LYS Chi-restraints excluded: chain K residue 292 ASN Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 292 ASN Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain M residue 32 ASP Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 441 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 535 optimal weight: 10.0000 chunk 564 optimal weight: 10.0000 chunk 514 optimal weight: 0.3980 chunk 548 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 430 optimal weight: 0.4980 chunk 168 optimal weight: 0.7980 chunk 495 optimal weight: 1.9990 chunk 519 optimal weight: 0.9980 chunk 546 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 221 ASN A 452 GLN B 112 GLN B 422 ASN C 112 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 422 ASN C 429 ASN C 452 GLN D 371 GLN E 112 GLN E 221 ASN F 221 ASN G 340 GLN G 429 ASN H 112 GLN H 371 GLN H 422 ASN I 112 GLN I 221 ASN I 452 GLN J 452 GLN M 22 ASN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 51571 Z= 0.129 Angle : 0.444 5.268 69576 Z= 0.251 Chirality : 0.038 0.156 7540 Planarity : 0.003 0.033 9191 Dihedral : 4.066 16.284 6942 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.65 % Allowed : 14.23 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 6162 helix: 2.35 (0.10), residues: 2730 sheet: 1.07 (0.14), residues: 1131 loop : -0.64 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 92 PHE 0.012 0.001 PHE D 173 TYR 0.022 0.001 TYR L 218 ARG 0.007 0.000 ARG F 425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 714 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8485 (mtt) cc_final: 0.8129 (mtt) REVERT: A 129 ASP cc_start: 0.6802 (t0) cc_final: 0.6398 (t0) REVERT: A 183 ASN cc_start: 0.8433 (m110) cc_final: 0.8155 (m110) REVERT: A 206 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7899 (t) REVERT: A 213 HIS cc_start: 0.6680 (m-70) cc_final: 0.6355 (m170) REVERT: A 286 MET cc_start: 0.8754 (ttm) cc_final: 0.8201 (mtp) REVERT: A 365 ASP cc_start: 0.7589 (m-30) cc_final: 0.7290 (m-30) REVERT: A 422 ASN cc_start: 0.7851 (t0) cc_final: 0.7598 (m-40) REVERT: B 47 LYS cc_start: 0.7283 (ttmt) cc_final: 0.7024 (tptp) REVERT: B 53 MET cc_start: 0.8485 (mtt) cc_final: 0.8062 (mtm) REVERT: B 125 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 129 ASP cc_start: 0.6747 (t0) cc_final: 0.6492 (t0) REVERT: B 159 ASP cc_start: 0.6489 (m-30) cc_final: 0.5852 (t0) REVERT: B 163 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7543 (mmt180) REVERT: B 221 ASN cc_start: 0.7649 (p0) cc_final: 0.7380 (p0) REVERT: B 365 ASP cc_start: 0.7498 (m-30) cc_final: 0.7148 (m-30) REVERT: B 429 ASN cc_start: 0.8319 (m-40) cc_final: 0.7995 (t0) REVERT: B 440 LEU cc_start: 0.8065 (tp) cc_final: 0.7480 (tt) REVERT: C 1 MET cc_start: 0.4985 (mmt) cc_final: 0.4165 (mmt) REVERT: C 159 ASP cc_start: 0.6160 (m-30) cc_final: 0.5730 (t0) REVERT: C 185 ILE cc_start: 0.8197 (mt) cc_final: 0.7884 (mt) REVERT: C 363 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7739 (mmmm) REVERT: C 365 ASP cc_start: 0.7738 (m-30) cc_final: 0.7411 (m-30) REVERT: D 38 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6599 (tt) REVERT: D 125 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: D 363 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7824 (mttp) REVERT: D 403 LYS cc_start: 0.7522 (mttt) cc_final: 0.7094 (mppt) REVERT: D 452 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6607 (mp10) REVERT: E 54 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: E 125 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: E 159 ASP cc_start: 0.6358 (m-30) cc_final: 0.5897 (t0) REVERT: E 309 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8403 (mp) REVERT: E 423 THR cc_start: 0.7914 (p) cc_final: 0.7658 (p) REVERT: E 452 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6548 (tp40) REVERT: F 53 MET cc_start: 0.8585 (mtt) cc_final: 0.8276 (mtt) REVERT: F 365 ASP cc_start: 0.7866 (m-30) cc_final: 0.7339 (m-30) REVERT: F 403 LYS cc_start: 0.7512 (mttt) cc_final: 0.7057 (mppt) REVERT: G 47 LYS cc_start: 0.7165 (tppp) cc_final: 0.6952 (ttmp) REVERT: G 129 ASP cc_start: 0.6847 (t0) cc_final: 0.6476 (t0) REVERT: G 213 HIS cc_start: 0.6200 (m-70) cc_final: 0.5853 (m-70) REVERT: G 221 ASN cc_start: 0.7514 (p0) cc_final: 0.7215 (p0) REVERT: G 279 MET cc_start: 0.9138 (mtp) cc_final: 0.8838 (mtp) REVERT: G 422 ASN cc_start: 0.7799 (t0) cc_final: 0.7562 (t0) REVERT: G 452 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6535 (mp10) REVERT: H 163 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7525 (mmt180) REVERT: H 365 ASP cc_start: 0.7990 (m-30) cc_final: 0.7651 (m-30) REVERT: H 422 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7499 (m-40) REVERT: H 452 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6622 (mp10) REVERT: I 8 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6720 (mt-10) REVERT: I 78 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8381 (m) REVERT: I 83 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: I 159 ASP cc_start: 0.6092 (m-30) cc_final: 0.5508 (t0) REVERT: I 170 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8889 (mtp) REVERT: I 182 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7633 (mtm180) REVERT: I 185 ILE cc_start: 0.8274 (mt) cc_final: 0.8010 (mt) REVERT: I 221 ASN cc_start: 0.7392 (p0) cc_final: 0.7146 (p0) REVERT: I 235 PHE cc_start: 0.7681 (t80) cc_final: 0.7406 (t80) REVERT: I 440 LEU cc_start: 0.8122 (tp) cc_final: 0.7830 (tt) REVERT: J 54 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: J 163 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7487 (mmt180) REVERT: J 309 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8592 (mp) REVERT: J 323 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6256 (mt-10) REVERT: J 403 LYS cc_start: 0.7548 (mttt) cc_final: 0.7272 (mppt) REVERT: J 440 LEU cc_start: 0.8199 (tp) cc_final: 0.7860 (tt) REVERT: K 221 ASN cc_start: 0.7529 (p0) cc_final: 0.7189 (p0) REVERT: K 255 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8699 (mptm) REVERT: K 286 MET cc_start: 0.8732 (ttm) cc_final: 0.8454 (mtp) REVERT: K 422 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7719 (m-40) REVERT: K 440 LEU cc_start: 0.8299 (tp) cc_final: 0.8039 (tt) REVERT: K 452 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6531 (mp10) REVERT: L 32 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6384 (m-30) REVERT: L 53 MET cc_start: 0.8481 (mtt) cc_final: 0.8121 (mtt) REVERT: L 159 ASP cc_start: 0.6647 (m-30) cc_final: 0.5991 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7534 (p0) cc_final: 0.7244 (p0) REVERT: L 365 ASP cc_start: 0.7704 (m-30) cc_final: 0.7395 (m-30) REVERT: L 440 LEU cc_start: 0.8068 (tp) cc_final: 0.7493 (tt) REVERT: L 452 GLN cc_start: 0.6847 (mm-40) cc_final: 0.6378 (mp10) REVERT: M 47 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7091 (tptp) REVERT: M 159 ASP cc_start: 0.6231 (m-30) cc_final: 0.5739 (t0) REVERT: M 206 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7920 (t) REVERT: M 255 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8688 (mptp) REVERT: M 365 ASP cc_start: 0.7819 (m-30) cc_final: 0.7406 (m-30) REVERT: M 403 LYS cc_start: 0.7439 (mttt) cc_final: 0.7093 (mppt) REVERT: M 422 ASN cc_start: 0.7854 (t0) cc_final: 0.7638 (t0) REVERT: M 441 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8115 (tttt) REVERT: M 452 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6609 (mp10) outliers start: 93 outliers final: 44 residues processed: 769 average time/residue: 1.8034 time to fit residues: 1725.1116 Evaluate side-chains 769 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 703 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 422 ASN Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 178 ASN Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 255 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 376 MET Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 255 LYS Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 441 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 360 optimal weight: 2.9990 chunk 580 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 403 optimal weight: 3.9990 chunk 608 optimal weight: 0.9990 chunk 560 optimal weight: 0.9980 chunk 484 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 374 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 221 ASN A 452 GLN B 112 GLN B 422 ASN C 22 ASN C 112 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 422 ASN C 452 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 GLN E 112 GLN E 221 ASN F 221 ASN G 340 GLN G 429 ASN H 112 GLN H 422 ASN I 452 GLN J 452 GLN L 422 ASN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 51571 Z= 0.170 Angle : 0.483 6.059 69576 Z= 0.271 Chirality : 0.040 0.158 7540 Planarity : 0.003 0.042 9191 Dihedral : 4.126 16.595 6942 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.47 % Allowed : 14.62 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 6162 helix: 2.28 (0.10), residues: 2730 sheet: 1.04 (0.14), residues: 1144 loop : -0.64 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 354 PHE 0.027 0.002 PHE H 235 TYR 0.022 0.002 TYR L 218 ARG 0.008 0.000 ARG F 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12324 Ramachandran restraints generated. 6162 Oldfield, 0 Emsley, 6162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 712 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8560 (mtt) cc_final: 0.8238 (mtt) REVERT: A 129 ASP cc_start: 0.6817 (t0) cc_final: 0.6414 (t0) REVERT: A 206 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7923 (t) REVERT: A 213 HIS cc_start: 0.6630 (m-70) cc_final: 0.6318 (m170) REVERT: A 286 MET cc_start: 0.8777 (ttm) cc_final: 0.8240 (mtp) REVERT: A 365 ASP cc_start: 0.7636 (m-30) cc_final: 0.7346 (m-30) REVERT: A 422 ASN cc_start: 0.7863 (t0) cc_final: 0.7606 (m110) REVERT: A 440 LEU cc_start: 0.8399 (tp) cc_final: 0.8116 (tt) REVERT: B 47 LYS cc_start: 0.7460 (ttmt) cc_final: 0.7177 (tptp) REVERT: B 53 MET cc_start: 0.8518 (mtt) cc_final: 0.8120 (mtm) REVERT: B 125 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 129 ASP cc_start: 0.6759 (t0) cc_final: 0.6503 (t0) REVERT: B 159 ASP cc_start: 0.6514 (m-30) cc_final: 0.5865 (t0) REVERT: B 163 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7548 (mmt180) REVERT: B 211 THR cc_start: 0.7860 (m) cc_final: 0.7327 (p) REVERT: B 221 ASN cc_start: 0.7632 (p0) cc_final: 0.7365 (p0) REVERT: B 365 ASP cc_start: 0.7506 (m-30) cc_final: 0.7133 (m-30) REVERT: B 429 ASN cc_start: 0.8309 (m-40) cc_final: 0.7977 (t0) REVERT: B 440 LEU cc_start: 0.8122 (tp) cc_final: 0.7539 (tt) REVERT: C 1 MET cc_start: 0.4978 (mmt) cc_final: 0.4319 (mmt) REVERT: C 125 GLU cc_start: 0.7422 (mp0) cc_final: 0.7185 (mp0) REVERT: C 159 ASP cc_start: 0.6352 (m-30) cc_final: 0.5751 (t0) REVERT: C 185 ILE cc_start: 0.8201 (mt) cc_final: 0.7896 (mt) REVERT: C 235 PHE cc_start: 0.7470 (t80) cc_final: 0.7217 (t80) REVERT: C 365 ASP cc_start: 0.7715 (m-30) cc_final: 0.7381 (m-30) REVERT: D 38 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6624 (tt) REVERT: D 125 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: D 221 ASN cc_start: 0.7528 (p0) cc_final: 0.7172 (p0) REVERT: D 363 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7842 (mttp) REVERT: D 452 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6607 (mp10) REVERT: E 54 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: E 125 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: E 159 ASP cc_start: 0.6328 (m-30) cc_final: 0.5955 (t0) REVERT: E 309 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8424 (mp) REVERT: E 423 THR cc_start: 0.7922 (p) cc_final: 0.7669 (p) REVERT: E 452 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6644 (tp40) REVERT: F 53 MET cc_start: 0.8598 (mtt) cc_final: 0.8287 (mtt) REVERT: F 219 LEU cc_start: 0.8544 (mp) cc_final: 0.8329 (mt) REVERT: F 365 ASP cc_start: 0.7881 (m-30) cc_final: 0.7351 (m-30) REVERT: F 403 LYS cc_start: 0.7540 (mttt) cc_final: 0.7071 (mppt) REVERT: G 47 LYS cc_start: 0.7166 (tppp) cc_final: 0.6958 (ttmp) REVERT: G 129 ASP cc_start: 0.6850 (t0) cc_final: 0.6475 (t0) REVERT: G 213 HIS cc_start: 0.6246 (m-70) cc_final: 0.5882 (m-70) REVERT: G 221 ASN cc_start: 0.7508 (p0) cc_final: 0.7212 (p0) REVERT: G 279 MET cc_start: 0.9195 (mtp) cc_final: 0.8895 (mtp) REVERT: G 422 ASN cc_start: 0.7807 (t0) cc_final: 0.7568 (t0) REVERT: G 452 GLN cc_start: 0.6960 (mm-40) cc_final: 0.6718 (mp10) REVERT: H 163 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7553 (mmt180) REVERT: H 365 ASP cc_start: 0.7998 (m-30) cc_final: 0.7634 (m-30) REVERT: H 452 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6648 (mp10) REVERT: I 8 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6729 (mt-10) REVERT: I 78 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8410 (m) REVERT: I 83 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: I 159 ASP cc_start: 0.6131 (m-30) cc_final: 0.5544 (t0) REVERT: I 170 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8878 (mtp) REVERT: I 182 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7622 (mtm180) REVERT: I 185 ILE cc_start: 0.8277 (mt) cc_final: 0.8016 (mt) REVERT: I 235 PHE cc_start: 0.7674 (t80) cc_final: 0.7473 (t80) REVERT: I 440 LEU cc_start: 0.8085 (tp) cc_final: 0.7802 (tt) REVERT: J 54 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: J 163 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7525 (mmt180) REVERT: J 323 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6237 (mt-10) REVERT: J 403 LYS cc_start: 0.7541 (mttt) cc_final: 0.7277 (mppt) REVERT: J 440 LEU cc_start: 0.8213 (tp) cc_final: 0.7875 (tt) REVERT: K 221 ASN cc_start: 0.7547 (p0) cc_final: 0.7200 (p0) REVERT: K 235 PHE cc_start: 0.7618 (t80) cc_final: 0.6795 (t80) REVERT: K 255 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8714 (mptm) REVERT: K 286 MET cc_start: 0.8751 (ttm) cc_final: 0.8427 (mtp) REVERT: K 363 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7916 (mttp) REVERT: K 422 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7712 (m-40) REVERT: K 452 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6589 (mp10) REVERT: L 32 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6315 (m-30) REVERT: L 53 MET cc_start: 0.8523 (mtt) cc_final: 0.8083 (mtt) REVERT: L 143 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8298 (t0) REVERT: L 159 ASP cc_start: 0.6589 (m-30) cc_final: 0.5953 (OUTLIER) REVERT: L 221 ASN cc_start: 0.7559 (p0) cc_final: 0.7262 (p0) REVERT: L 365 ASP cc_start: 0.7731 (m-30) cc_final: 0.7402 (m-30) REVERT: L 422 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7402 (m-40) REVERT: L 440 LEU cc_start: 0.8071 (tp) cc_final: 0.7471 (tt) REVERT: L 452 GLN cc_start: 0.6866 (mm-40) cc_final: 0.6423 (mp10) REVERT: M 47 LYS cc_start: 0.7552 (tppp) cc_final: 0.7263 (tptp) REVERT: M 192 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7440 (mtp85) REVERT: M 255 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8672 (mptp) REVERT: M 365 ASP cc_start: 0.7956 (m-30) cc_final: 0.7511 (m-30) REVERT: M 422 ASN cc_start: 0.7871 (t0) cc_final: 0.7579 (t0) REVERT: M 452 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6530 (mp10) outliers start: 83 outliers final: 52 residues processed: 767 average time/residue: 1.8310 time to fit residues: 1758.4921 Evaluate side-chains 770 residues out of total 5629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 699 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain H residue 22 ASN Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 294 ASN Chi-restraints excluded: chain H residue 450 ILE Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 182 ARG Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 292 ASN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 255 LYS Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 363 LYS Chi-restraints excluded: chain K residue 422 ASN Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 292 ASN Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 422 ASN Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 255 LYS Chi-restraints excluded: chain M residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 385 optimal weight: 2.9990 chunk 516 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 446 optimal weight: 0.4980 chunk 71 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 485 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 498 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 0.0770 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 221 ASN B 112 GLN C 22 ASN C 112 GLN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 422 ASN C 452 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 221 ASN F 221 ASN G 340 GLN H 112 GLN ** H 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 ASN I 452 GLN J 452 GLN L 422 ASN ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.185226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.119728 restraints weight = 47195.988| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.03 r_work: 0.3056 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 51571 Z= 0.190 Angle : 0.660 59.200 69576 Z= 0.385 Chirality : 0.040 0.143 7540 Planarity : 0.003 0.050 9191 Dihedral : 4.151 24.534 6942 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.46 % Allowed : 14.75 % Favored : 83.80 % Cbeta Deviations : 0.03 % 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: 1.49 (0.10), residues: 6162 helix: 2.27 (0.10), residues: 2730 sheet: 1.04 (0.14), residues: 1144 loop : -0.65 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 354 PHE 0.014 0.002 PHE H 235 TYR 0.020 0.002 TYR L 218 ARG 0.007 0.000 ARG F 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24595.59 seconds wall clock time: 433 minutes 12.94 seconds (25992.94 seconds total)