Starting phenix.real_space_refine on Sat Mar 23 17:11:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0d_20994/03_2024/6v0d_20994.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0d_20994/03_2024/6v0d_20994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0d_20994/03_2024/6v0d_20994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0d_20994/03_2024/6v0d_20994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0d_20994/03_2024/6v0d_20994.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0d_20994/03_2024/6v0d_20994.pdb" } resolution = 3.49 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= 0.010 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 72 5.16 5 C 24042 2.51 5 N 6522 2.21 5 O 7284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 869": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B ARG 691": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 869": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C ARG 547": "NH1" <-> "NH2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 869": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D ARG 691": "NH1" <-> "NH2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D ARG 869": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 456": "NH1" <-> "NH2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E ARG 672": "NH1" <-> "NH2" Residue "E ARG 691": "NH1" <-> "NH2" Residue "E ARG 797": "NH1" <-> "NH2" Residue "E ARG 869": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 220": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 456": "NH1" <-> "NH2" Residue "F ARG 547": "NH1" <-> "NH2" Residue "F ARG 672": "NH1" <-> "NH2" Residue "F ARG 691": "NH1" <-> "NH2" Residue "F ARG 797": "NH1" <-> "NH2" Residue "F ARG 869": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "B" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "C" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "D" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "E" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "F" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Time building chain proxies: 18.75, per 1000 atoms: 0.49 Number of scatterers: 37920 At special positions: 0 Unit cell: (113.97, 111.35, 238.42, 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 72 16.00 O 7284 8.00 N 6522 7.00 C 24042 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: 13.31 Conformation dependent library (CDL) restraints added in 6.9 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8964 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 60 sheets defined 13.9% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.773A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.205A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.513A pdb=" N ASN A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP A 868 " --> pdb=" O PRO A 865 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 116 through 122 removed outlier: 3.500A pdb=" N GLY B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 248' Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.774A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.205A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.513A pdb=" N ASN B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 4.321A pdb=" N ARG B 743 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL B 802 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 removed outlier: 4.163A pdb=" N ILE B 834 " --> pdb=" O PHE B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP B 868 " --> pdb=" O PRO B 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 869 " --> pdb=" O LYS B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.773A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.205A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.105A pdb=" N LEU C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.514A pdb=" N ASN C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.977A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 Processing helix chain 'C' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE C 834 " --> pdb=" O PHE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP C 868 " --> pdb=" O PRO C 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 869 " --> pdb=" O LYS C 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 248' Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.773A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.205A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.512A pdb=" N ASN D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG D 743 " --> pdb=" O ILE D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL D 802 " --> pdb=" O GLN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 835 removed outlier: 4.161A pdb=" N ILE D 834 " --> pdb=" O PHE D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 removed outlier: 3.562A pdb=" N TRP D 868 " --> pdb=" O PRO D 865 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG D 869 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.500A pdb=" N GLY E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 248' Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.774A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.205A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU E 386 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 560 through 567 removed outlier: 3.514A pdb=" N ASN E 565 " --> pdb=" O PRO E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 removed outlier: 3.651A pdb=" N ALA E 598 " --> pdb=" O PRO E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 631 Processing helix chain 'E' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 744 removed outlier: 4.321A pdb=" N ARG E 743 " --> pdb=" O ILE E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE E 834 " --> pdb=" O PHE E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP E 868 " --> pdb=" O PRO E 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 869 " --> pdb=" O LYS E 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.191A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 248' Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.774A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.204A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 560 through 567 removed outlier: 3.513A pdb=" N ASN F 565 " --> pdb=" O PRO F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA F 598 " --> pdb=" O PRO F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN F 615 " --> pdb=" O ALA F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 711 through 716 removed outlier: 4.062A pdb=" N LEU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG F 743 " --> pdb=" O ILE F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL F 802 " --> pdb=" O GLN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE F 834 " --> pdb=" O PHE F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP F 868 " --> pdb=" O PRO F 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 869 " --> pdb=" O LYS F 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 76 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 281 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR A 432 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 424 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 481 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N SER A 449 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR A 498 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 451 " --> pdb=" O TYR A 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 460 Processing sheet with id=AA9, first strand: chain 'A' and resid 517 through 521 removed outlier: 6.417A pdb=" N ASP A 554 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 546 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 556 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU A 674 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 678 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 680 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A 663 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 659 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 655 " --> pdb=" O ASP A 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 696 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 734 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS A 640 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG A 793 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 776 " --> pdb=" O ARG A 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 807 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 860 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.196A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 76 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 107 through 111 Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AB7, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 281 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 481 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N SER B 449 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N TYR B 498 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE B 451 " --> pdb=" O TYR B 498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AC1, first strand: chain 'B' and resid 517 through 521 removed outlier: 6.418A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU B 674 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 678 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 680 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE B 663 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 659 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 655 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 734 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS B 640 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 754 removed outlier: 6.383A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 807 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 860 " --> pdb=" O GLU B 753 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL C 76 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 93 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 107 through 111 Processing sheet with id=AC6, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AC8, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 281 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 393 through 399 removed outlier: 6.856A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 481 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N SER C 449 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR C 498 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE C 451 " --> pdb=" O TYR C 498 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AD2, first strand: chain 'C' and resid 517 through 521 removed outlier: 6.417A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU C 674 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 678 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL C 680 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE C 663 " --> pdb=" O VAL C 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP C 659 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR C 655 " --> pdb=" O ASP C 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG C 793 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL C 776 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 841 " --> pdb=" O VAL C 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 807 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 860 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL D 76 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 93 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 107 through 111 Processing sheet with id=AD7, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 228 through 229 Processing sheet with id=AD9, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 281 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N SER D 449 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR D 498 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE D 451 " --> pdb=" O TYR D 498 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AE3, first strand: chain 'D' and resid 517 through 521 removed outlier: 6.417A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 636 through 641 removed outlier: 3.503A pdb=" N GLU D 674 " --> pdb=" O ILE D 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 678 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL D 680 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 663 " --> pdb=" O VAL D 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP D 659 " --> pdb=" O TYR D 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR D 655 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU D 734 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS D 640 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 807 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 860 " --> pdb=" O GLU D 753 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL E 76 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER E 93 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 107 through 111 Processing sheet with id=AE8, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 228 through 229 Processing sheet with id=AF1, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 281 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 393 through 399 removed outlier: 6.856A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 481 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N SER E 449 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N TYR E 498 " --> pdb=" O SER E 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE E 451 " --> pdb=" O TYR E 498 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AF4, first strand: chain 'E' and resid 517 through 521 removed outlier: 6.418A pdb=" N ASP E 554 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 546 " --> pdb=" O ASP E 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP E 556 " --> pdb=" O ILE E 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU E 674 " --> pdb=" O ILE E 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 678 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL E 680 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE E 663 " --> pdb=" O VAL E 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP E 659 " --> pdb=" O TYR E 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR E 655 " --> pdb=" O ASP E 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU E 734 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS E 640 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL E 807 " --> pdb=" O ALA E 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 860 " --> pdb=" O GLU E 753 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.198A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL F 76 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER F 93 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 107 through 111 Processing sheet with id=AF9, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.162A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 281 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N SER F 449 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR F 498 " --> pdb=" O SER F 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE F 451 " --> pdb=" O TYR F 498 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 458 through 460 Processing sheet with id=AG4, first strand: chain 'F' and resid 517 through 521 removed outlier: 6.418A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU F 674 " --> pdb=" O ILE F 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 678 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL F 680 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE F 663 " --> pdb=" O VAL F 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP F 659 " --> pdb=" O TYR F 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR F 655 " --> pdb=" O ASP F 659 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU F 734 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS F 640 " --> pdb=" O LEU F 734 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG F 793 " --> pdb=" O VAL F 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL F 776 " --> pdb=" O ARG F 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL F 807 " --> pdb=" O ALA F 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 860 " --> pdb=" O GLU F 753 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 2898 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: 17.69 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12305 1.34 - 1.46: 5348 1.46 - 1.57: 20813 1.57 - 1.69: 6 1.69 - 1.81: 144 Bond restraints: 38616 Sorted by residual: bond pdb=" CB TRP C 868 " pdb=" CG TRP C 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.54e+00 bond pdb=" CB TRP D 868 " pdb=" CG TRP D 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB TRP A 868 " pdb=" CG TRP A 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB TRP F 868 " pdb=" CG TRP F 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB TRP E 868 " pdb=" CG TRP E 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 ... (remaining 38611 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.58: 948 105.58 - 112.70: 20413 112.70 - 119.82: 12274 119.82 - 126.94: 18386 126.94 - 134.06: 383 Bond angle restraints: 52404 Sorted by residual: angle pdb=" C PRO C 876 " pdb=" N LYS C 877 " pdb=" CA LYS C 877 " ideal model delta sigma weight residual 121.70 128.30 -6.60 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C PRO F 876 " pdb=" N LYS F 877 " pdb=" CA LYS F 877 " ideal model delta sigma weight residual 121.70 128.27 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO D 876 " pdb=" N LYS D 877 " pdb=" CA LYS D 877 " ideal model delta sigma weight residual 121.70 128.27 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO E 876 " pdb=" N LYS E 877 " pdb=" CA LYS E 877 " ideal model delta sigma weight residual 121.70 128.25 -6.55 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO B 876 " pdb=" N LYS B 877 " pdb=" CA LYS B 877 " ideal model delta sigma weight residual 121.70 128.25 -6.55 1.80e+00 3.09e-01 1.33e+01 ... (remaining 52399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 22125 15.20 - 30.41: 837 30.41 - 45.61: 240 45.61 - 60.82: 6 60.82 - 76.02: 48 Dihedral angle restraints: 23256 sinusoidal: 9180 harmonic: 14076 Sorted by residual: dihedral pdb=" CA ALA E 471 " pdb=" C ALA E 471 " pdb=" N SER E 472 " pdb=" CA SER E 472 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA ALA A 471 " pdb=" C ALA A 471 " pdb=" N SER A 472 " pdb=" CA SER A 472 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ALA D 471 " pdb=" C ALA D 471 " pdb=" N SER D 472 " pdb=" CA SER D 472 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.33e+01 ... (remaining 23253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3414 0.035 - 0.071: 1610 0.071 - 0.106: 625 0.106 - 0.142: 331 0.142 - 0.177: 80 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CB ILE C 622 " pdb=" CA ILE C 622 " pdb=" CG1 ILE C 622 " pdb=" CG2 ILE C 622 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CB ILE B 622 " pdb=" CA ILE B 622 " pdb=" CG1 ILE B 622 " pdb=" CG2 ILE B 622 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CB ILE F 622 " pdb=" CA ILE F 622 " pdb=" CG1 ILE F 622 " pdb=" CG2 ILE F 622 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 6057 not shown) Planarity restraints: 6822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 846 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO E 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 847 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 846 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 847 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 847 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 847 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 846 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 847 " 0.036 5.00e-02 4.00e+02 ... (remaining 6819 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 11073 2.83 - 3.35: 30658 3.35 - 3.86: 58722 3.86 - 4.38: 64967 4.38 - 4.90: 115733 Nonbonded interactions: 281153 Sorted by model distance: nonbonded pdb=" OG1 THR A 740 " pdb=" O VAL A 776 " model vdw 2.311 2.440 nonbonded pdb=" OG1 THR E 740 " pdb=" O VAL E 776 " model vdw 2.311 2.440 nonbonded pdb=" OG1 THR F 740 " pdb=" O VAL F 776 " model vdw 2.311 2.440 nonbonded pdb=" OG1 THR C 740 " pdb=" O VAL C 776 " model vdw 2.311 2.440 nonbonded pdb=" OG1 THR B 740 " pdb=" O VAL B 776 " model vdw 2.311 2.440 ... (remaining 281148 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.030 Extract box with map and model: 6.940 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 96.040 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.049 38616 Z= 0.313 Angle : 0.868 11.965 52404 Z= 0.465 Chirality : 0.054 0.177 6060 Planarity : 0.007 0.064 6822 Dihedral : 9.835 76.021 14292 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.27 (0.10), residues: 4980 helix: -3.89 (0.12), residues: 528 sheet: -1.63 (0.11), residues: 1728 loop : -2.17 (0.10), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 574 HIS 0.005 0.001 HIS F 441 PHE 0.029 0.003 PHE F 605 TYR 0.025 0.002 TYR F 814 ARG 0.005 0.001 ARG E 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 881 time to evaluate : 3.992 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8106 (m-80) cc_final: 0.7618 (m-80) REVERT: A 239 LYS cc_start: 0.5960 (ttmt) cc_final: 0.5547 (tttp) REVERT: A 240 LEU cc_start: 0.7887 (tt) cc_final: 0.7586 (tp) REVERT: A 716 GLN cc_start: 0.8641 (tt0) cc_final: 0.8207 (pt0) REVERT: A 795 SER cc_start: 0.8535 (m) cc_final: 0.8315 (t) REVERT: B 51 ILE cc_start: 0.8426 (mt) cc_final: 0.8118 (mt) REVERT: B 145 PHE cc_start: 0.8133 (m-80) cc_final: 0.7664 (m-80) REVERT: B 158 ASN cc_start: 0.8017 (t0) cc_final: 0.7526 (t0) REVERT: B 174 ASN cc_start: 0.7842 (m-40) cc_final: 0.7640 (m-40) REVERT: B 240 LEU cc_start: 0.7928 (tt) cc_final: 0.7572 (tp) REVERT: B 518 SER cc_start: 0.9019 (m) cc_final: 0.8678 (t) REVERT: C 158 ASN cc_start: 0.8207 (t0) cc_final: 0.7877 (t0) REVERT: C 239 LYS cc_start: 0.6575 (ttmt) cc_final: 0.5914 (tttm) REVERT: C 240 LEU cc_start: 0.8169 (tt) cc_final: 0.7793 (tp) REVERT: C 383 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 503 LYS cc_start: 0.8912 (mttt) cc_final: 0.8704 (mtpp) REVERT: C 518 SER cc_start: 0.8966 (m) cc_final: 0.8694 (t) REVERT: C 716 GLN cc_start: 0.8333 (tt0) cc_final: 0.8132 (pt0) REVERT: C 795 SER cc_start: 0.8350 (m) cc_final: 0.7960 (t) REVERT: D 145 PHE cc_start: 0.8065 (m-80) cc_final: 0.7857 (m-80) REVERT: D 158 ASN cc_start: 0.8007 (t0) cc_final: 0.7167 (t0) REVERT: D 239 LYS cc_start: 0.6108 (ttmt) cc_final: 0.5692 (tttp) REVERT: D 240 LEU cc_start: 0.7978 (tt) cc_final: 0.7662 (tp) REVERT: D 354 ASN cc_start: 0.6782 (p0) cc_final: 0.6513 (p0) REVERT: D 701 PRO cc_start: 0.7757 (Cg_exo) cc_final: 0.7441 (Cg_endo) REVERT: D 716 GLN cc_start: 0.8682 (tt0) cc_final: 0.8244 (pt0) REVERT: D 795 SER cc_start: 0.8608 (m) cc_final: 0.8396 (t) REVERT: E 51 ILE cc_start: 0.8424 (mt) cc_final: 0.8135 (mt) REVERT: E 145 PHE cc_start: 0.8139 (m-80) cc_final: 0.7651 (m-80) REVERT: E 158 ASN cc_start: 0.7991 (t0) cc_final: 0.7488 (t0) REVERT: E 240 LEU cc_start: 0.7960 (tt) cc_final: 0.7538 (tp) REVERT: E 383 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7019 (mm-30) REVERT: E 503 LYS cc_start: 0.8914 (mttt) cc_final: 0.8710 (mtpp) REVERT: E 518 SER cc_start: 0.9005 (m) cc_final: 0.8657 (t) REVERT: E 795 SER cc_start: 0.8482 (m) cc_final: 0.8247 (t) REVERT: F 158 ASN cc_start: 0.8170 (t0) cc_final: 0.7868 (t0) REVERT: F 239 LYS cc_start: 0.6968 (ttmt) cc_final: 0.6192 (tttp) REVERT: F 240 LEU cc_start: 0.8164 (tt) cc_final: 0.7817 (tp) REVERT: F 383 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7089 (mm-30) REVERT: F 503 LYS cc_start: 0.8861 (mttt) cc_final: 0.8602 (mtpp) REVERT: F 518 SER cc_start: 0.9020 (m) cc_final: 0.8752 (t) REVERT: F 795 SER cc_start: 0.8402 (m) cc_final: 0.8073 (t) outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.5188 time to fit residues: 720.9825 Evaluate side-chains 521 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 201 optimal weight: 0.8980 chunk 390 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 290 optimal weight: 0.7980 chunk 452 optimal weight: 0.0170 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 164 HIS A 316 ASN A 345 ASN A 409 GLN A 441 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 640 HIS A 662 GLN A 804 ASN A 832 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS B 316 ASN B 345 ASN B 409 GLN B 441 HIS ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 HIS ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 HIS B 662 GLN ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 164 HIS C 316 ASN C 345 ASN C 409 GLN C 441 HIS ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 HIS C 662 GLN ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 164 HIS D 316 ASN D 345 ASN D 409 GLN D 441 HIS ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN D 640 HIS D 662 GLN ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 316 ASN E 345 ASN E 409 GLN E 441 HIS ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 HIS E 662 GLN E 804 ASN ** E 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 164 HIS F 316 ASN F 345 ASN F 409 GLN F 441 HIS ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 HIS F 662 GLN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 38616 Z= 0.295 Angle : 0.656 9.710 52404 Z= 0.343 Chirality : 0.047 0.181 6060 Planarity : 0.006 0.052 6822 Dihedral : 5.480 30.203 5358 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.59 % Allowed : 9.81 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.69 (0.10), residues: 4980 helix: -3.09 (0.16), residues: 552 sheet: -1.34 (0.11), residues: 1800 loop : -1.76 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 574 HIS 0.006 0.001 HIS F 441 PHE 0.030 0.002 PHE A 364 TYR 0.013 0.002 TYR B 744 ARG 0.006 0.001 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 534 time to evaluate : 4.470 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LYS cc_start: 0.5822 (ttmt) cc_final: 0.5511 (tttp) REVERT: A 240 LEU cc_start: 0.7987 (tt) cc_final: 0.7642 (tp) REVERT: A 716 GLN cc_start: 0.8692 (tt0) cc_final: 0.8269 (pt0) REVERT: A 804 ASN cc_start: 0.7277 (m110) cc_final: 0.6783 (m110) REVERT: B 51 ILE cc_start: 0.8344 (mt) cc_final: 0.7987 (mt) REVERT: B 120 VAL cc_start: 0.8627 (p) cc_final: 0.8371 (m) REVERT: B 145 PHE cc_start: 0.8111 (m-80) cc_final: 0.7188 (m-80) REVERT: B 240 LEU cc_start: 0.8031 (tt) cc_final: 0.7663 (tp) REVERT: B 518 SER cc_start: 0.9015 (m) cc_final: 0.8799 (t) REVERT: B 556 ASP cc_start: 0.8270 (m-30) cc_final: 0.7914 (m-30) REVERT: C 135 MET cc_start: 0.7033 (ttp) cc_final: 0.6790 (ptp) REVERT: C 158 ASN cc_start: 0.8423 (t0) cc_final: 0.8118 (t0) REVERT: C 239 LYS cc_start: 0.6961 (ttmt) cc_final: 0.6200 (tttm) REVERT: C 240 LEU cc_start: 0.8141 (tt) cc_final: 0.7841 (tp) REVERT: C 383 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7158 (mm-30) REVERT: C 518 SER cc_start: 0.8940 (m) cc_final: 0.8722 (t) REVERT: C 716 GLN cc_start: 0.8349 (tt0) cc_final: 0.8145 (pt0) REVERT: C 795 SER cc_start: 0.8317 (m) cc_final: 0.8011 (t) REVERT: D 145 PHE cc_start: 0.8066 (m-80) cc_final: 0.7774 (m-80) REVERT: D 239 LYS cc_start: 0.5980 (ttmt) cc_final: 0.5690 (tttp) REVERT: D 240 LEU cc_start: 0.8091 (tt) cc_final: 0.7711 (tp) REVERT: D 716 GLN cc_start: 0.8757 (tt0) cc_final: 0.8303 (pt0) REVERT: E 114 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7639 (tttm) REVERT: E 145 PHE cc_start: 0.8098 (m-80) cc_final: 0.7258 (m-80) REVERT: E 240 LEU cc_start: 0.7989 (tt) cc_final: 0.7656 (tp) REVERT: E 503 LYS cc_start: 0.8859 (mttt) cc_final: 0.8637 (mtpp) REVERT: E 518 SER cc_start: 0.9025 (m) cc_final: 0.8768 (p) REVERT: E 678 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8393 (ttmm) REVERT: E 687 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7884 (tm-30) REVERT: E 795 SER cc_start: 0.8367 (m) cc_final: 0.8159 (t) REVERT: E 804 ASN cc_start: 0.7291 (m110) cc_final: 0.6888 (m110) REVERT: F 239 LYS cc_start: 0.6762 (ttmt) cc_final: 0.6154 (tttm) REVERT: F 240 LEU cc_start: 0.8158 (tt) cc_final: 0.7856 (tp) REVERT: F 383 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7234 (mm-30) REVERT: F 491 MET cc_start: 0.8042 (tpp) cc_final: 0.7786 (mmt) REVERT: F 503 LYS cc_start: 0.8849 (mttt) cc_final: 0.8548 (mtpp) REVERT: F 518 SER cc_start: 0.8972 (m) cc_final: 0.8707 (t) REVERT: F 785 SER cc_start: 0.8555 (m) cc_final: 0.8275 (p) REVERT: F 795 SER cc_start: 0.8307 (m) cc_final: 0.8038 (t) outliers start: 65 outliers final: 40 residues processed: 569 average time/residue: 0.5055 time to fit residues: 461.3947 Evaluate side-chains 511 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 471 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 605 PHE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 792 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 376 optimal weight: 0.4980 chunk 307 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 453 optimal weight: 1.9990 chunk 489 optimal weight: 6.9990 chunk 403 optimal weight: 10.0000 chunk 449 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 363 optimal weight: 0.0870 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS B 832 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN E 158 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN E 800 HIS E 832 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN F 804 ASN F 832 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 38616 Z= 0.243 Angle : 0.589 9.317 52404 Z= 0.307 Chirality : 0.046 0.172 6060 Planarity : 0.005 0.040 6822 Dihedral : 5.093 25.806 5358 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.12 % Allowed : 9.79 % Favored : 87.09 % 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: -2.32 (0.11), residues: 4980 helix: -2.48 (0.20), residues: 558 sheet: -1.17 (0.11), residues: 1794 loop : -1.52 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 574 HIS 0.007 0.001 HIS B 800 PHE 0.019 0.002 PHE C 364 TYR 0.013 0.002 TYR D 154 ARG 0.005 0.001 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 525 time to evaluate : 4.181 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: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8504 (m-80) cc_final: 0.8279 (m-10) REVERT: A 195 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7927 (p0) REVERT: A 239 LYS cc_start: 0.5774 (ttmt) cc_final: 0.5521 (tttp) REVERT: A 240 LEU cc_start: 0.7818 (tt) cc_final: 0.7502 (tp) REVERT: A 354 ASN cc_start: 0.7149 (p0) cc_final: 0.6671 (p0) REVERT: A 716 GLN cc_start: 0.8735 (tt0) cc_final: 0.8448 (pt0) REVERT: A 731 ASP cc_start: 0.8205 (t0) cc_final: 0.7515 (p0) REVERT: A 804 ASN cc_start: 0.7032 (m110) cc_final: 0.6631 (m110) REVERT: B 51 ILE cc_start: 0.8359 (mt) cc_final: 0.8003 (mt) REVERT: B 145 PHE cc_start: 0.8048 (m-80) cc_final: 0.7157 (m-80) REVERT: B 224 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8053 (m) REVERT: B 240 LEU cc_start: 0.8007 (tt) cc_final: 0.7648 (tp) REVERT: B 518 SER cc_start: 0.9050 (m) cc_final: 0.8653 (p) REVERT: B 556 ASP cc_start: 0.8373 (m-30) cc_final: 0.7954 (m-30) REVERT: B 642 PHE cc_start: 0.7760 (m-10) cc_final: 0.7332 (m-10) REVERT: B 687 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 98 MET cc_start: 0.7866 (mmt) cc_final: 0.7622 (mmp) REVERT: C 174 ASN cc_start: 0.7932 (p0) cc_final: 0.7666 (p0) REVERT: C 239 LYS cc_start: 0.6624 (ttmt) cc_final: 0.6050 (tttp) REVERT: C 240 LEU cc_start: 0.8162 (tt) cc_final: 0.7849 (tp) REVERT: C 383 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 491 MET cc_start: 0.8489 (mmt) cc_final: 0.8238 (mmt) REVERT: C 518 SER cc_start: 0.8957 (m) cc_final: 0.8689 (t) REVERT: C 564 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7119 (ttp-170) REVERT: C 588 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7134 (pp) REVERT: C 795 SER cc_start: 0.8277 (m) cc_final: 0.7930 (t) REVERT: C 804 ASN cc_start: 0.7066 (m110) cc_final: 0.6643 (m110) REVERT: C 830 PHE cc_start: 0.6290 (p90) cc_final: 0.5776 (p90) REVERT: C 832 GLN cc_start: 0.8183 (mp10) cc_final: 0.7707 (mp10) REVERT: D 145 PHE cc_start: 0.7900 (m-80) cc_final: 0.7647 (m-80) REVERT: D 195 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8018 (p0) REVERT: D 239 LYS cc_start: 0.5945 (ttmt) cc_final: 0.5724 (tttp) REVERT: D 240 LEU cc_start: 0.8012 (tt) cc_final: 0.7640 (tp) REVERT: D 716 GLN cc_start: 0.8816 (tt0) cc_final: 0.8502 (pt0) REVERT: D 731 ASP cc_start: 0.8388 (t0) cc_final: 0.7810 (p0) REVERT: E 114 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7496 (tmtt) REVERT: E 145 PHE cc_start: 0.8069 (m-80) cc_final: 0.7257 (m-80) REVERT: E 224 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8201 (m) REVERT: E 240 LEU cc_start: 0.8007 (tt) cc_final: 0.7656 (tp) REVERT: E 503 LYS cc_start: 0.8786 (mttt) cc_final: 0.8583 (mtpp) REVERT: E 518 SER cc_start: 0.9127 (m) cc_final: 0.8698 (p) REVERT: E 547 ARG cc_start: 0.7048 (ttp-110) cc_final: 0.6740 (ttp-110) REVERT: E 556 ASP cc_start: 0.8197 (m-30) cc_final: 0.7816 (m-30) REVERT: E 678 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8415 (ttmm) REVERT: E 687 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7896 (tm-30) REVERT: E 795 SER cc_start: 0.8356 (m) cc_final: 0.8147 (t) REVERT: E 804 ASN cc_start: 0.7142 (m110) cc_final: 0.6828 (m110) REVERT: F 239 LYS cc_start: 0.6761 (ttmt) cc_final: 0.6016 (tttp) REVERT: F 240 LEU cc_start: 0.8187 (tt) cc_final: 0.7876 (tp) REVERT: F 383 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7283 (mm-30) REVERT: F 503 LYS cc_start: 0.8810 (mttt) cc_final: 0.8518 (mtpp) REVERT: F 518 SER cc_start: 0.8984 (m) cc_final: 0.8690 (t) REVERT: F 588 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7012 (pp) REVERT: F 795 SER cc_start: 0.8294 (m) cc_final: 0.7986 (t) REVERT: F 804 ASN cc_start: 0.7244 (m110) cc_final: 0.6693 (m110) outliers start: 128 outliers final: 68 residues processed: 607 average time/residue: 0.4833 time to fit residues: 476.0068 Evaluate side-chains 546 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 471 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 chunk 235 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 chunk 454 optimal weight: 0.6980 chunk 481 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 430 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 38616 Z= 0.206 Angle : 0.566 9.533 52404 Z= 0.292 Chirality : 0.045 0.160 6060 Planarity : 0.004 0.044 6822 Dihedral : 4.854 24.027 5358 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.93 % Allowed : 11.71 % Favored : 85.36 % 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: -2.15 (0.11), residues: 4980 helix: -2.23 (0.21), residues: 558 sheet: -0.97 (0.11), residues: 1746 loop : -1.51 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 574 HIS 0.003 0.001 HIS F 558 PHE 0.018 0.001 PHE E 858 TYR 0.012 0.001 TYR D 154 ARG 0.009 0.000 ARG E 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 512 time to evaluate : 4.122 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 195 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.7903 (p0) REVERT: A 239 LYS cc_start: 0.5686 (ttmt) cc_final: 0.5432 (tttp) REVERT: A 240 LEU cc_start: 0.7847 (tt) cc_final: 0.7557 (tp) REVERT: A 354 ASN cc_start: 0.7149 (p0) cc_final: 0.6754 (p0) REVERT: A 397 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8845 (pp) REVERT: A 716 GLN cc_start: 0.8744 (tt0) cc_final: 0.8484 (pt0) REVERT: A 731 ASP cc_start: 0.8060 (t0) cc_final: 0.7456 (p0) REVERT: A 798 TYR cc_start: 0.8697 (m-10) cc_final: 0.8082 (m-10) REVERT: A 804 ASN cc_start: 0.6992 (m110) cc_final: 0.6560 (m-40) REVERT: B 51 ILE cc_start: 0.8361 (mt) cc_final: 0.8001 (mt) REVERT: B 54 MET cc_start: 0.4860 (ttt) cc_final: 0.4622 (ttm) REVERT: B 145 PHE cc_start: 0.8024 (m-80) cc_final: 0.7174 (m-80) REVERT: B 224 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 240 LEU cc_start: 0.8047 (tt) cc_final: 0.7677 (tp) REVERT: B 518 SER cc_start: 0.8902 (m) cc_final: 0.8542 (p) REVERT: B 556 ASP cc_start: 0.8378 (m-30) cc_final: 0.7999 (m-30) REVERT: B 687 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 804 ASN cc_start: 0.7153 (m110) cc_final: 0.6846 (m110) REVERT: C 98 MET cc_start: 0.7856 (mmt) cc_final: 0.7599 (mmp) REVERT: C 195 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7356 (p0) REVERT: C 239 LYS cc_start: 0.6705 (ttmt) cc_final: 0.6018 (tttp) REVERT: C 240 LEU cc_start: 0.8169 (tt) cc_final: 0.7851 (tp) REVERT: C 383 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7287 (mm-30) REVERT: C 491 MET cc_start: 0.8318 (mmt) cc_final: 0.8117 (mmt) REVERT: C 518 SER cc_start: 0.8911 (m) cc_final: 0.8624 (p) REVERT: C 588 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6873 (pp) REVERT: C 665 THR cc_start: 0.8877 (t) cc_final: 0.8668 (p) REVERT: C 795 SER cc_start: 0.8296 (m) cc_final: 0.7987 (t) REVERT: C 804 ASN cc_start: 0.7042 (m110) cc_final: 0.6581 (m110) REVERT: D 108 PHE cc_start: 0.8552 (m-10) cc_final: 0.8252 (m-10) REVERT: D 195 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8008 (p0) REVERT: D 239 LYS cc_start: 0.5870 (ttmt) cc_final: 0.5650 (tttp) REVERT: D 240 LEU cc_start: 0.7987 (tt) cc_final: 0.7642 (tp) REVERT: D 354 ASN cc_start: 0.7134 (p0) cc_final: 0.6721 (p0) REVERT: D 397 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8864 (pp) REVERT: D 716 GLN cc_start: 0.8780 (tt0) cc_final: 0.8479 (pt0) REVERT: D 731 ASP cc_start: 0.8208 (t0) cc_final: 0.7454 (p0) REVERT: E 145 PHE cc_start: 0.8052 (m-80) cc_final: 0.7259 (m-80) REVERT: E 240 LEU cc_start: 0.7983 (tt) cc_final: 0.7657 (tp) REVERT: E 503 LYS cc_start: 0.8777 (mttt) cc_final: 0.8566 (mtpp) REVERT: E 518 SER cc_start: 0.9003 (m) cc_final: 0.8579 (p) REVERT: E 547 ARG cc_start: 0.6941 (ttp-110) cc_final: 0.6648 (ttp-110) REVERT: E 556 ASP cc_start: 0.8122 (m-30) cc_final: 0.7764 (m-30) REVERT: E 687 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 795 SER cc_start: 0.8602 (m) cc_final: 0.8241 (t) REVERT: E 804 ASN cc_start: 0.7016 (m110) cc_final: 0.6754 (m-40) REVERT: F 239 LYS cc_start: 0.7045 (ttmt) cc_final: 0.6503 (tttp) REVERT: F 240 LEU cc_start: 0.8192 (tt) cc_final: 0.7893 (tp) REVERT: F 383 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7288 (mm-30) REVERT: F 503 LYS cc_start: 0.8775 (mttt) cc_final: 0.8522 (mtpp) REVERT: F 518 SER cc_start: 0.8984 (m) cc_final: 0.8729 (p) REVERT: F 588 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6829 (pp) REVERT: F 795 SER cc_start: 0.8273 (m) cc_final: 0.7986 (t) REVERT: F 804 ASN cc_start: 0.7050 (m110) cc_final: 0.6549 (m110) outliers start: 120 outliers final: 73 residues processed: 590 average time/residue: 0.4967 time to fit residues: 475.1002 Evaluate side-chains 558 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 477 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 358 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 410 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 432 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN D 832 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38616 Z= 0.243 Angle : 0.579 10.262 52404 Z= 0.296 Chirality : 0.046 0.206 6060 Planarity : 0.004 0.050 6822 Dihedral : 4.804 22.842 5358 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.37 % Allowed : 13.06 % Favored : 83.58 % 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: -2.00 (0.11), residues: 4980 helix: -2.06 (0.21), residues: 552 sheet: -0.92 (0.12), residues: 1746 loop : -1.40 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 574 HIS 0.003 0.001 HIS F 558 PHE 0.017 0.001 PHE C 145 TYR 0.015 0.001 TYR B 154 ARG 0.007 0.000 ARG B 729 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 501 time to evaluate : 4.327 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: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8651 (m-80) cc_final: 0.8305 (m-10) REVERT: A 195 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7945 (p0) REVERT: A 239 LYS cc_start: 0.5681 (ttmt) cc_final: 0.5366 (tttp) REVERT: A 240 LEU cc_start: 0.7806 (tt) cc_final: 0.7476 (tp) REVERT: A 354 ASN cc_start: 0.7167 (p0) cc_final: 0.6710 (p0) REVERT: A 397 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8881 (pp) REVERT: A 716 GLN cc_start: 0.8697 (tt0) cc_final: 0.8401 (pt0) REVERT: A 731 ASP cc_start: 0.8083 (t0) cc_final: 0.7467 (p0) REVERT: A 798 TYR cc_start: 0.8597 (m-10) cc_final: 0.8090 (m-10) REVERT: A 804 ASN cc_start: 0.6896 (m110) cc_final: 0.6459 (m-40) REVERT: B 51 ILE cc_start: 0.8306 (mt) cc_final: 0.7966 (mt) REVERT: B 145 PHE cc_start: 0.8071 (m-80) cc_final: 0.7184 (m-80) REVERT: B 224 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8056 (m) REVERT: B 240 LEU cc_start: 0.8031 (tt) cc_final: 0.7722 (tp) REVERT: B 397 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8567 (pp) REVERT: B 518 SER cc_start: 0.8923 (m) cc_final: 0.8554 (p) REVERT: B 556 ASP cc_start: 0.8414 (m-30) cc_final: 0.8130 (m-30) REVERT: B 687 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 804 ASN cc_start: 0.7040 (m110) cc_final: 0.6751 (m-40) REVERT: C 98 MET cc_start: 0.7869 (mmt) cc_final: 0.7613 (mmp) REVERT: C 240 LEU cc_start: 0.8075 (tt) cc_final: 0.7785 (tp) REVERT: C 325 MET cc_start: 0.8497 (ttm) cc_final: 0.7964 (ttm) REVERT: C 352 ASP cc_start: 0.5982 (m-30) cc_final: 0.5535 (t0) REVERT: C 383 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7241 (mm-30) REVERT: C 518 SER cc_start: 0.8906 (m) cc_final: 0.8588 (p) REVERT: C 588 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6890 (pp) REVERT: C 687 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7708 (tm-30) REVERT: C 785 SER cc_start: 0.8448 (m) cc_final: 0.8093 (p) REVERT: C 795 SER cc_start: 0.8338 (m) cc_final: 0.8022 (t) REVERT: C 804 ASN cc_start: 0.6979 (m110) cc_final: 0.6531 (m110) REVERT: D 108 PHE cc_start: 0.8558 (m-10) cc_final: 0.8072 (m-10) REVERT: D 195 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8039 (p0) REVERT: D 239 LYS cc_start: 0.5972 (ttmt) cc_final: 0.5737 (tttp) REVERT: D 240 LEU cc_start: 0.7992 (tt) cc_final: 0.7645 (tp) REVERT: D 354 ASN cc_start: 0.7171 (p0) cc_final: 0.6621 (p0) REVERT: D 397 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8893 (pp) REVERT: D 646 LYS cc_start: 0.8563 (mptt) cc_final: 0.8167 (mtmm) REVERT: D 716 GLN cc_start: 0.8679 (tt0) cc_final: 0.8321 (pt0) REVERT: D 731 ASP cc_start: 0.8194 (t0) cc_final: 0.7478 (p0) REVERT: E 145 PHE cc_start: 0.8063 (m-80) cc_final: 0.7255 (m-80) REVERT: E 240 LEU cc_start: 0.8069 (tt) cc_final: 0.7678 (tp) REVERT: E 397 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8535 (pp) REVERT: E 503 LYS cc_start: 0.8763 (mttt) cc_final: 0.8551 (mtpp) REVERT: E 518 SER cc_start: 0.9023 (m) cc_final: 0.8585 (p) REVERT: E 687 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 795 SER cc_start: 0.8425 (m) cc_final: 0.8188 (t) REVERT: E 804 ASN cc_start: 0.7104 (m110) cc_final: 0.6844 (m-40) REVERT: F 239 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6526 (tttp) REVERT: F 240 LEU cc_start: 0.8086 (tt) cc_final: 0.7827 (tp) REVERT: F 503 LYS cc_start: 0.8707 (mttt) cc_final: 0.8487 (mtpp) REVERT: F 518 SER cc_start: 0.8989 (m) cc_final: 0.8718 (p) REVERT: F 588 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6847 (pp) REVERT: F 687 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7637 (tm-30) REVERT: F 795 SER cc_start: 0.8298 (m) cc_final: 0.8016 (t) REVERT: F 804 ASN cc_start: 0.7001 (m110) cc_final: 0.6439 (m110) outliers start: 138 outliers final: 98 residues processed: 590 average time/residue: 0.4781 time to fit residues: 460.7399 Evaluate side-chains 585 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 478 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 672 ARG Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 749 SER Chi-restraints excluded: chain E residue 799 GLN Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 0.9990 chunk 433 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 481 optimal weight: 10.0000 chunk 399 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 584 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 584 ASN E 636 GLN E 673 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 584 ASN F 673 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38616 Z= 0.298 Angle : 0.604 12.314 52404 Z= 0.308 Chirality : 0.046 0.188 6060 Planarity : 0.004 0.053 6822 Dihedral : 4.885 21.647 5358 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.78 % Allowed : 13.59 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.11), residues: 4980 helix: -1.89 (0.23), residues: 468 sheet: -0.95 (0.12), residues: 1782 loop : -1.16 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 222 HIS 0.003 0.001 HIS F 558 PHE 0.023 0.002 PHE E 858 TYR 0.015 0.001 TYR E 154 ARG 0.006 0.001 ARG D 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 502 time to evaluate : 4.165 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8639 (m-80) cc_final: 0.8290 (m-10) REVERT: A 195 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8029 (p0) REVERT: A 239 LYS cc_start: 0.5639 (ttmt) cc_final: 0.5320 (tttp) REVERT: A 240 LEU cc_start: 0.7758 (tt) cc_final: 0.7401 (tp) REVERT: A 354 ASN cc_start: 0.7123 (p0) cc_final: 0.6726 (p0) REVERT: A 397 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8884 (pp) REVERT: A 716 GLN cc_start: 0.8693 (tt0) cc_final: 0.8367 (pt0) REVERT: A 731 ASP cc_start: 0.8101 (t0) cc_final: 0.7476 (p0) REVERT: A 804 ASN cc_start: 0.6913 (m110) cc_final: 0.6486 (m-40) REVERT: B 51 ILE cc_start: 0.8370 (mt) cc_final: 0.8041 (mt) REVERT: B 145 PHE cc_start: 0.8128 (m-80) cc_final: 0.7201 (m-80) REVERT: B 224 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8052 (m) REVERT: B 240 LEU cc_start: 0.7947 (tt) cc_final: 0.7619 (tp) REVERT: B 397 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8609 (pp) REVERT: B 411 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 518 SER cc_start: 0.8965 (m) cc_final: 0.8575 (p) REVERT: B 556 ASP cc_start: 0.8444 (m-30) cc_final: 0.7991 (m-30) REVERT: B 687 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 804 ASN cc_start: 0.6957 (m110) cc_final: 0.6729 (m-40) REVERT: B 830 PHE cc_start: 0.6884 (p90) cc_final: 0.6477 (p90) REVERT: C 98 MET cc_start: 0.7884 (mmt) cc_final: 0.7627 (mmp) REVERT: C 240 LEU cc_start: 0.8099 (tt) cc_final: 0.7807 (tp) REVERT: C 518 SER cc_start: 0.8861 (m) cc_final: 0.8516 (p) REVERT: C 588 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6919 (pp) REVERT: C 687 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7861 (tm-30) REVERT: C 785 SER cc_start: 0.8480 (m) cc_final: 0.8106 (p) REVERT: C 795 SER cc_start: 0.8429 (m) cc_final: 0.8116 (t) REVERT: C 804 ASN cc_start: 0.6905 (m110) cc_final: 0.6560 (m110) REVERT: D 108 PHE cc_start: 0.8550 (m-10) cc_final: 0.8089 (m-10) REVERT: D 195 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8101 (p0) REVERT: D 239 LYS cc_start: 0.5733 (ttmt) cc_final: 0.5487 (tttp) REVERT: D 240 LEU cc_start: 0.7950 (tt) cc_final: 0.7563 (tp) REVERT: D 354 ASN cc_start: 0.7000 (p0) cc_final: 0.6568 (p0) REVERT: D 397 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8886 (pp) REVERT: D 477 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7186 (pt) REVERT: D 646 LYS cc_start: 0.8568 (mptt) cc_final: 0.8190 (mtmm) REVERT: D 716 GLN cc_start: 0.8703 (tt0) cc_final: 0.8326 (pt0) REVERT: D 731 ASP cc_start: 0.8138 (t0) cc_final: 0.7475 (p0) REVERT: D 798 TYR cc_start: 0.8613 (m-10) cc_final: 0.7625 (m-10) REVERT: D 832 GLN cc_start: 0.7862 (tt0) cc_final: 0.7653 (tm-30) REVERT: E 145 PHE cc_start: 0.8170 (m-80) cc_final: 0.7350 (m-80) REVERT: E 240 LEU cc_start: 0.7950 (tt) cc_final: 0.7565 (tp) REVERT: E 397 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8569 (pp) REVERT: E 411 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8183 (mt) REVERT: E 503 LYS cc_start: 0.8705 (mttt) cc_final: 0.8476 (mtpp) REVERT: E 518 SER cc_start: 0.9017 (m) cc_final: 0.8582 (p) REVERT: E 687 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8214 (tm-30) REVERT: E 795 SER cc_start: 0.8399 (m) cc_final: 0.8148 (t) REVERT: E 804 ASN cc_start: 0.7123 (m110) cc_final: 0.6852 (m-40) REVERT: E 830 PHE cc_start: 0.6910 (p90) cc_final: 0.6534 (p90) REVERT: F 195 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7423 (p0) REVERT: F 239 LYS cc_start: 0.7181 (ttmt) cc_final: 0.6559 (tttp) REVERT: F 240 LEU cc_start: 0.8120 (tt) cc_final: 0.7839 (tp) REVERT: F 491 MET cc_start: 0.8255 (mmt) cc_final: 0.7959 (mmt) REVERT: F 518 SER cc_start: 0.8929 (m) cc_final: 0.8616 (p) REVERT: F 588 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6824 (pp) REVERT: F 687 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7630 (tm-30) REVERT: F 795 SER cc_start: 0.8467 (m) cc_final: 0.8183 (t) REVERT: F 804 ASN cc_start: 0.6980 (m110) cc_final: 0.6432 (m110) outliers start: 155 outliers final: 111 residues processed: 602 average time/residue: 0.4824 time to fit residues: 474.2255 Evaluate side-chains 606 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 482 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 672 ARG Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 SER Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 749 SER Chi-restraints excluded: chain E residue 799 GLN Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 chunk 272 optimal weight: 0.9980 chunk 405 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 479 optimal weight: 9.9990 chunk 300 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38616 Z= 0.221 Angle : 0.580 13.565 52404 Z= 0.292 Chirality : 0.045 0.181 6060 Planarity : 0.004 0.052 6822 Dihedral : 4.733 19.574 5358 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.56 % Allowed : 14.47 % Favored : 81.97 % 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: -1.75 (0.11), residues: 4980 helix: -1.86 (0.23), residues: 468 sheet: -0.98 (0.12), residues: 1710 loop : -1.09 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 222 HIS 0.003 0.001 HIS F 558 PHE 0.017 0.001 PHE F 858 TYR 0.019 0.001 TYR A 798 ARG 0.012 0.000 ARG E 725 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 493 time to evaluate : 4.173 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8602 (m-80) cc_final: 0.8232 (m-10) REVERT: A 195 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 239 LYS cc_start: 0.5644 (ttmt) cc_final: 0.5311 (tttp) REVERT: A 240 LEU cc_start: 0.7732 (tt) cc_final: 0.7398 (tp) REVERT: A 354 ASN cc_start: 0.7346 (p0) cc_final: 0.6972 (p0) REVERT: A 397 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8885 (pp) REVERT: A 716 GLN cc_start: 0.8698 (tt0) cc_final: 0.8356 (pt0) REVERT: A 731 ASP cc_start: 0.7990 (t0) cc_final: 0.7431 (p0) REVERT: A 785 SER cc_start: 0.7713 (m) cc_final: 0.7505 (p) REVERT: A 804 ASN cc_start: 0.6920 (m110) cc_final: 0.6495 (m-40) REVERT: B 51 ILE cc_start: 0.8369 (mt) cc_final: 0.8042 (mt) REVERT: B 145 PHE cc_start: 0.8116 (m-80) cc_final: 0.7233 (m-80) REVERT: B 224 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8044 (m) REVERT: B 240 LEU cc_start: 0.8090 (tt) cc_final: 0.7759 (tp) REVERT: B 518 SER cc_start: 0.8938 (m) cc_final: 0.8559 (p) REVERT: B 556 ASP cc_start: 0.8426 (m-30) cc_final: 0.8071 (m-30) REVERT: B 687 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 722 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 804 ASN cc_start: 0.6937 (m110) cc_final: 0.6709 (m-40) REVERT: B 858 PHE cc_start: 0.7161 (m-10) cc_final: 0.6930 (m-80) REVERT: C 98 MET cc_start: 0.7852 (mmt) cc_final: 0.7596 (mmp) REVERT: C 240 LEU cc_start: 0.7979 (tt) cc_final: 0.7640 (tp) REVERT: C 518 SER cc_start: 0.8859 (m) cc_final: 0.8522 (p) REVERT: C 588 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6880 (pp) REVERT: C 785 SER cc_start: 0.8489 (m) cc_final: 0.8154 (p) REVERT: C 795 SER cc_start: 0.8302 (m) cc_final: 0.8046 (t) REVERT: C 804 ASN cc_start: 0.6873 (m110) cc_final: 0.6549 (m110) REVERT: C 832 GLN cc_start: 0.6757 (pp30) cc_final: 0.6452 (tm-30) REVERT: D 195 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8088 (p0) REVERT: D 239 LYS cc_start: 0.5773 (ttmt) cc_final: 0.5491 (tttp) REVERT: D 240 LEU cc_start: 0.8002 (tt) cc_final: 0.7645 (tp) REVERT: D 354 ASN cc_start: 0.7162 (p0) cc_final: 0.6743 (p0) REVERT: D 397 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8872 (pp) REVERT: D 468 PHE cc_start: 0.7482 (t80) cc_final: 0.7275 (t80) REVERT: D 646 LYS cc_start: 0.8534 (mptt) cc_final: 0.8142 (mtmm) REVERT: D 716 GLN cc_start: 0.8651 (tt0) cc_final: 0.8236 (pt0) REVERT: D 731 ASP cc_start: 0.8112 (t0) cc_final: 0.7446 (p0) REVERT: D 798 TYR cc_start: 0.8483 (m-10) cc_final: 0.7702 (m-10) REVERT: E 145 PHE cc_start: 0.8139 (m-80) cc_final: 0.7360 (m-80) REVERT: E 240 LEU cc_start: 0.7919 (tt) cc_final: 0.7538 (tp) REVERT: E 397 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8455 (pp) REVERT: E 503 LYS cc_start: 0.8701 (mttt) cc_final: 0.8476 (mtpp) REVERT: E 518 SER cc_start: 0.8979 (m) cc_final: 0.8544 (p) REVERT: E 687 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8217 (tm-30) REVERT: E 725 ARG cc_start: 0.6782 (mmm160) cc_final: 0.6430 (mmp80) REVERT: E 795 SER cc_start: 0.8351 (m) cc_final: 0.7985 (t) REVERT: E 804 ASN cc_start: 0.7123 (m110) cc_final: 0.6840 (m-40) REVERT: E 830 PHE cc_start: 0.6890 (p90) cc_final: 0.6440 (p90) REVERT: F 195 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7343 (p0) REVERT: F 239 LYS cc_start: 0.7218 (ttmt) cc_final: 0.6486 (tttm) REVERT: F 240 LEU cc_start: 0.7978 (tt) cc_final: 0.7649 (tp) REVERT: F 491 MET cc_start: 0.8403 (mmt) cc_final: 0.8116 (mmt) REVERT: F 518 SER cc_start: 0.8927 (m) cc_final: 0.8622 (p) REVERT: F 588 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6832 (pp) REVERT: F 687 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7676 (tm-30) REVERT: F 795 SER cc_start: 0.8267 (m) cc_final: 0.8019 (t) REVERT: F 804 ASN cc_start: 0.6956 (m110) cc_final: 0.6419 (m110) REVERT: F 830 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5508 (p90) outliers start: 146 outliers final: 113 residues processed: 590 average time/residue: 0.4868 time to fit residues: 467.3391 Evaluate side-chains 593 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 470 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 672 ARG Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 749 SER Chi-restraints excluded: chain E residue 752 VAL Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Chi-restraints excluded: chain F residue 830 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.0970 chunk 191 optimal weight: 2.9990 chunk 286 optimal weight: 0.0870 chunk 144 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 overall best weight: 2.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 584 ASN ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN B 151 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN D 130 ASN D 584 ASN ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 ASN E 151 GLN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 38616 Z= 0.371 Angle : 0.650 15.448 52404 Z= 0.328 Chirality : 0.047 0.171 6060 Planarity : 0.005 0.055 6822 Dihedral : 5.022 22.570 5358 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.86 % Allowed : 14.40 % Favored : 81.75 % 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: -1.80 (0.11), residues: 4980 helix: -1.93 (0.23), residues: 468 sheet: -0.99 (0.12), residues: 1788 loop : -1.13 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 222 HIS 0.003 0.001 HIS F 710 PHE 0.029 0.002 PHE E 858 TYR 0.022 0.002 TYR A 798 ARG 0.016 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 492 time to evaluate : 4.137 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8639 (m-80) cc_final: 0.8258 (m-10) REVERT: A 195 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8138 (p0) REVERT: A 239 LYS cc_start: 0.5660 (ttmt) cc_final: 0.5306 (tttp) REVERT: A 240 LEU cc_start: 0.7848 (tt) cc_final: 0.7423 (tp) REVERT: A 354 ASN cc_start: 0.7182 (p0) cc_final: 0.6734 (p0) REVERT: A 397 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8923 (pp) REVERT: A 716 GLN cc_start: 0.8810 (tt0) cc_final: 0.8457 (pt0) REVERT: A 731 ASP cc_start: 0.7976 (t0) cc_final: 0.7339 (p0) REVERT: A 785 SER cc_start: 0.7770 (m) cc_final: 0.7559 (p) REVERT: A 804 ASN cc_start: 0.7032 (m110) cc_final: 0.6619 (m-40) REVERT: B 145 PHE cc_start: 0.8214 (m-80) cc_final: 0.7466 (m-80) REVERT: B 224 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (m) REVERT: B 240 LEU cc_start: 0.7978 (tt) cc_final: 0.7610 (tp) REVERT: B 397 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 411 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 477 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6672 (pp) REVERT: B 518 SER cc_start: 0.9104 (m) cc_final: 0.8743 (p) REVERT: B 687 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 722 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 804 ASN cc_start: 0.7031 (m110) cc_final: 0.6792 (m-40) REVERT: B 830 PHE cc_start: 0.6900 (p90) cc_final: 0.6446 (p90) REVERT: C 98 MET cc_start: 0.7890 (mmt) cc_final: 0.7649 (mmp) REVERT: C 240 LEU cc_start: 0.8003 (tt) cc_final: 0.7645 (tp) REVERT: C 518 SER cc_start: 0.8887 (m) cc_final: 0.8525 (p) REVERT: C 588 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6911 (pp) REVERT: C 785 SER cc_start: 0.8547 (m) cc_final: 0.8189 (p) REVERT: C 799 GLN cc_start: 0.8866 (tt0) cc_final: 0.8512 (tp40) REVERT: C 804 ASN cc_start: 0.6908 (m110) cc_final: 0.6599 (m-40) REVERT: C 832 GLN cc_start: 0.6918 (pp30) cc_final: 0.6620 (tm-30) REVERT: D 195 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8181 (p0) REVERT: D 239 LYS cc_start: 0.5893 (ttmt) cc_final: 0.5573 (tttp) REVERT: D 354 ASN cc_start: 0.7037 (p0) cc_final: 0.6569 (p0) REVERT: D 397 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8898 (pp) REVERT: D 646 LYS cc_start: 0.8493 (mptt) cc_final: 0.8159 (mtmm) REVERT: D 716 GLN cc_start: 0.8839 (tt0) cc_final: 0.8413 (pt0) REVERT: D 731 ASP cc_start: 0.8191 (t0) cc_final: 0.7694 (p0) REVERT: D 785 SER cc_start: 0.8078 (m) cc_final: 0.7826 (p) REVERT: E 240 LEU cc_start: 0.7963 (tt) cc_final: 0.7510 (tp) REVERT: E 397 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8697 (pp) REVERT: E 411 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8254 (mt) REVERT: E 503 LYS cc_start: 0.8718 (mttt) cc_final: 0.8509 (mtpp) REVERT: E 518 SER cc_start: 0.9118 (m) cc_final: 0.8658 (p) REVERT: E 687 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8196 (tm-30) REVERT: E 725 ARG cc_start: 0.6974 (mmm160) cc_final: 0.6572 (mmp80) REVERT: E 795 SER cc_start: 0.8505 (m) cc_final: 0.8192 (t) REVERT: E 804 ASN cc_start: 0.7087 (m110) cc_final: 0.6859 (m-40) REVERT: E 830 PHE cc_start: 0.7057 (p90) cc_final: 0.6549 (p90) REVERT: F 195 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7473 (p0) REVERT: F 239 LYS cc_start: 0.7175 (ttmt) cc_final: 0.6566 (tttp) REVERT: F 240 LEU cc_start: 0.8012 (tt) cc_final: 0.7674 (tp) REVERT: F 518 SER cc_start: 0.8956 (m) cc_final: 0.8623 (p) REVERT: F 588 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6864 (pp) REVERT: F 687 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7733 (tm-30) REVERT: F 795 SER cc_start: 0.8320 (m) cc_final: 0.7831 (t) REVERT: F 799 GLN cc_start: 0.8794 (tt0) cc_final: 0.8436 (tp40) REVERT: F 804 ASN cc_start: 0.6964 (m110) cc_final: 0.6448 (m110) outliers start: 158 outliers final: 119 residues processed: 597 average time/residue: 0.4871 time to fit residues: 475.0900 Evaluate side-chains 599 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 467 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 672 ARG Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 749 SER Chi-restraints excluded: chain E residue 752 VAL Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Chi-restraints excluded: chain F residue 830 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 4.9990 chunk 459 optimal weight: 8.9990 chunk 419 optimal weight: 5.9990 chunk 447 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 351 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 404 optimal weight: 3.9990 chunk 423 optimal weight: 0.0770 chunk 445 optimal weight: 8.9990 overall best weight: 1.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN D 158 ASN ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38616 Z= 0.242 Angle : 0.604 15.834 52404 Z= 0.301 Chirality : 0.046 0.174 6060 Planarity : 0.004 0.056 6822 Dihedral : 4.803 20.048 5358 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.47 % Allowed : 15.30 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 4980 helix: -2.04 (0.22), residues: 468 sheet: -0.93 (0.12), residues: 1776 loop : -1.11 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 574 HIS 0.003 0.001 HIS F 558 PHE 0.016 0.001 PHE D 830 TYR 0.019 0.001 TYR D 798 ARG 0.022 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 482 time to evaluate : 4.129 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: symmetry clash REVERT: A 108 PHE cc_start: 0.8581 (m-80) cc_final: 0.8276 (m-10) REVERT: A 195 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8067 (p0) REVERT: A 239 LYS cc_start: 0.5814 (ttmt) cc_final: 0.5425 (tttp) REVERT: A 240 LEU cc_start: 0.7770 (tt) cc_final: 0.7431 (tp) REVERT: A 354 ASN cc_start: 0.7448 (p0) cc_final: 0.7044 (p0) REVERT: A 397 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8892 (pp) REVERT: A 716 GLN cc_start: 0.8678 (tt0) cc_final: 0.8278 (pt0) REVERT: A 731 ASP cc_start: 0.7952 (t0) cc_final: 0.7347 (p0) REVERT: A 785 SER cc_start: 0.7697 (m) cc_final: 0.7495 (p) REVERT: A 804 ASN cc_start: 0.7001 (m110) cc_final: 0.6600 (m-40) REVERT: B 145 PHE cc_start: 0.8199 (m-80) cc_final: 0.7405 (m-80) REVERT: B 224 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (m) REVERT: B 240 LEU cc_start: 0.7983 (tt) cc_final: 0.7625 (tp) REVERT: B 397 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8510 (pp) REVERT: B 411 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8160 (mt) REVERT: B 518 SER cc_start: 0.8966 (m) cc_final: 0.8577 (p) REVERT: B 556 ASP cc_start: 0.8372 (m-30) cc_final: 0.8066 (m-30) REVERT: B 687 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 722 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7355 (mt-10) REVERT: B 804 ASN cc_start: 0.7035 (m110) cc_final: 0.6785 (m-40) REVERT: C 240 LEU cc_start: 0.7999 (tt) cc_final: 0.7644 (tp) REVERT: C 352 ASP cc_start: 0.6006 (m-30) cc_final: 0.5459 (t0) REVERT: C 518 SER cc_start: 0.8859 (m) cc_final: 0.8501 (p) REVERT: C 785 SER cc_start: 0.8500 (m) cc_final: 0.8151 (p) REVERT: C 804 ASN cc_start: 0.6866 (m110) cc_final: 0.6536 (m-40) REVERT: C 832 GLN cc_start: 0.6981 (pp30) cc_final: 0.6674 (tm-30) REVERT: D 195 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8129 (p0) REVERT: D 239 LYS cc_start: 0.5927 (ttmt) cc_final: 0.5599 (tttp) REVERT: D 240 LEU cc_start: 0.7897 (tt) cc_final: 0.7522 (tp) REVERT: D 354 ASN cc_start: 0.7074 (p0) cc_final: 0.6622 (p0) REVERT: D 397 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8902 (pp) REVERT: D 646 LYS cc_start: 0.8462 (mptt) cc_final: 0.8136 (mtmm) REVERT: D 716 GLN cc_start: 0.8811 (tt0) cc_final: 0.8372 (pt0) REVERT: D 731 ASP cc_start: 0.8183 (t0) cc_final: 0.7699 (p0) REVERT: D 785 SER cc_start: 0.7908 (m) cc_final: 0.7697 (p) REVERT: D 797 ARG cc_start: 0.8759 (ppt170) cc_final: 0.8456 (ppt170) REVERT: E 240 LEU cc_start: 0.7854 (tt) cc_final: 0.7414 (tp) REVERT: E 324 GLU cc_start: 0.7249 (pt0) cc_final: 0.6985 (pt0) REVERT: E 397 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8474 (pp) REVERT: E 411 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8160 (mt) REVERT: E 503 LYS cc_start: 0.8721 (mttt) cc_final: 0.8512 (mtpp) REVERT: E 518 SER cc_start: 0.8886 (m) cc_final: 0.8509 (p) REVERT: E 687 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8177 (tm-30) REVERT: E 795 SER cc_start: 0.8482 (m) cc_final: 0.8166 (t) REVERT: E 804 ASN cc_start: 0.7176 (m110) cc_final: 0.6930 (m-40) REVERT: F 195 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7355 (p0) REVERT: F 239 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6624 (tttp) REVERT: F 240 LEU cc_start: 0.7997 (tt) cc_final: 0.7672 (tp) REVERT: F 352 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5222 (t0) REVERT: F 491 MET cc_start: 0.8457 (mmt) cc_final: 0.8185 (mmt) REVERT: F 518 SER cc_start: 0.8939 (m) cc_final: 0.8621 (p) REVERT: F 687 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 795 SER cc_start: 0.8288 (m) cc_final: 0.7805 (t) REVERT: F 804 ASN cc_start: 0.6923 (m110) cc_final: 0.6476 (m110) outliers start: 142 outliers final: 115 residues processed: 573 average time/residue: 0.4833 time to fit residues: 451.4195 Evaluate side-chains 590 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 464 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 672 ARG Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 749 SER Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 4.9990 chunk 472 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 496 optimal weight: 20.0000 chunk 456 optimal weight: 4.9990 chunk 395 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 305 optimal weight: 9.9990 chunk 242 optimal weight: 0.0770 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 38616 Z= 0.361 Angle : 0.656 15.834 52404 Z= 0.328 Chirality : 0.047 0.187 6060 Planarity : 0.005 0.075 6822 Dihedral : 5.020 29.308 5358 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.37 % Allowed : 15.45 % Favored : 81.19 % 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: -1.84 (0.11), residues: 4980 helix: -2.14 (0.22), residues: 468 sheet: -1.01 (0.12), residues: 1788 loop : -1.12 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 222 HIS 0.005 0.001 HIS F 800 PHE 0.017 0.002 PHE D 253 TYR 0.015 0.002 TYR C 154 ARG 0.022 0.001 ARG E 725 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 471 time to evaluate : 3.957 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: symmetry clash REVERT: A 98 MET cc_start: 0.8244 (mmt) cc_final: 0.7950 (mmp) REVERT: A 108 PHE cc_start: 0.8632 (m-80) cc_final: 0.8272 (m-10) REVERT: A 195 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8173 (p0) REVERT: A 239 LYS cc_start: 0.6254 (ttmt) cc_final: 0.5722 (tttp) REVERT: A 240 LEU cc_start: 0.7848 (tt) cc_final: 0.7413 (tp) REVERT: A 354 ASN cc_start: 0.7164 (p0) cc_final: 0.6722 (p0) REVERT: A 397 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8905 (pp) REVERT: A 716 GLN cc_start: 0.8846 (tt0) cc_final: 0.8429 (pt0) REVERT: A 731 ASP cc_start: 0.8062 (t0) cc_final: 0.7430 (p0) REVERT: A 804 ASN cc_start: 0.7004 (m110) cc_final: 0.6606 (m-40) REVERT: B 145 PHE cc_start: 0.8258 (m-80) cc_final: 0.7474 (m-80) REVERT: B 224 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8079 (m) REVERT: B 240 LEU cc_start: 0.7972 (tt) cc_final: 0.7603 (tp) REVERT: B 397 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8693 (pp) REVERT: B 411 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 518 SER cc_start: 0.9102 (m) cc_final: 0.8735 (p) REVERT: B 687 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 722 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 804 ASN cc_start: 0.7065 (m110) cc_final: 0.6813 (m-40) REVERT: B 830 PHE cc_start: 0.6796 (p90) cc_final: 0.6449 (p90) REVERT: B 832 GLN cc_start: 0.8099 (tt0) cc_final: 0.7847 (tt0) REVERT: C 98 MET cc_start: 0.7696 (mmt) cc_final: 0.7487 (mmp) REVERT: C 240 LEU cc_start: 0.7994 (tt) cc_final: 0.7631 (tp) REVERT: C 518 SER cc_start: 0.8873 (m) cc_final: 0.8492 (p) REVERT: C 785 SER cc_start: 0.8538 (m) cc_final: 0.8172 (p) REVERT: C 804 ASN cc_start: 0.6907 (m110) cc_final: 0.6561 (m-40) REVERT: C 832 GLN cc_start: 0.7025 (pp30) cc_final: 0.6691 (tm-30) REVERT: D 195 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8131 (p0) REVERT: D 239 LYS cc_start: 0.6213 (ttmt) cc_final: 0.5932 (tttp) REVERT: D 354 ASN cc_start: 0.7015 (p0) cc_final: 0.6557 (p0) REVERT: D 397 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8889 (pp) REVERT: D 646 LYS cc_start: 0.8469 (mptt) cc_final: 0.8141 (mtmm) REVERT: D 716 GLN cc_start: 0.8840 (tt0) cc_final: 0.8408 (pt0) REVERT: D 785 SER cc_start: 0.7943 (m) cc_final: 0.7731 (p) REVERT: E 145 PHE cc_start: 0.8303 (m-80) cc_final: 0.8011 (m-80) REVERT: E 240 LEU cc_start: 0.7935 (tt) cc_final: 0.7466 (tp) REVERT: E 397 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8662 (pp) REVERT: E 411 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8233 (mt) REVERT: E 477 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6662 (pp) REVERT: E 503 LYS cc_start: 0.8719 (mttt) cc_final: 0.8511 (mtpp) REVERT: E 518 SER cc_start: 0.9010 (m) cc_final: 0.8629 (p) REVERT: E 687 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8225 (tm-30) REVERT: E 795 SER cc_start: 0.8486 (m) cc_final: 0.8179 (t) REVERT: E 804 ASN cc_start: 0.7174 (m110) cc_final: 0.6884 (m-40) REVERT: F 195 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7505 (p0) REVERT: F 239 LYS cc_start: 0.7074 (ttmt) cc_final: 0.6421 (tttp) REVERT: F 240 LEU cc_start: 0.8015 (tt) cc_final: 0.7663 (tp) REVERT: F 352 ASP cc_start: 0.6127 (OUTLIER) cc_final: 0.5319 (t0) REVERT: F 518 SER cc_start: 0.8945 (m) cc_final: 0.8605 (p) REVERT: F 687 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8046 (tm-30) REVERT: F 795 SER cc_start: 0.8000 (m) cc_final: 0.7784 (t) REVERT: F 804 ASN cc_start: 0.6974 (m110) cc_final: 0.6551 (m110) outliers start: 138 outliers final: 115 residues processed: 558 average time/residue: 0.4931 time to fit residues: 450.3106 Evaluate side-chains 592 residues out of total 4098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 465 time to evaluate : 3.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 672 ARG Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 749 SER Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 352 ASP Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 364 optimal weight: 5.9990 chunk 58 optimal weight: 0.0070 chunk 109 optimal weight: 0.6980 chunk 395 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 chunk 406 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 151 GLN ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN ** E 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134423 restraints weight = 49236.693| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.19 r_work: 0.3204 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38616 Z= 0.283 Angle : 0.632 16.627 52404 Z= 0.313 Chirality : 0.046 0.208 6060 Planarity : 0.004 0.059 6822 Dihedral : 4.919 34.059 5358 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.32 % Allowed : 15.86 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.85 (0.11), residues: 4980 helix: -2.16 (0.21), residues: 468 sheet: -1.04 (0.12), residues: 1770 loop : -1.10 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 222 HIS 0.003 0.001 HIS F 558 PHE 0.026 0.002 PHE B 858 TYR 0.014 0.001 TYR B 154 ARG 0.015 0.001 ARG E 725 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9302.37 seconds wall clock time: 167 minutes 2.44 seconds (10022.44 seconds total)