Starting phenix.real_space_refine on Fri Mar 22 03:13:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycz_33743/03_2024/7ycz_33743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycz_33743/03_2024/7ycz_33743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycz_33743/03_2024/7ycz_33743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycz_33743/03_2024/7ycz_33743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycz_33743/03_2024/7ycz_33743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycz_33743/03_2024/7ycz_33743.pdb" } resolution = 3.24 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= 0.002 sd= 0.031 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 146 5.16 5 C 20495 2.51 5 N 5324 2.21 5 O 6148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32113 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8035 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "E" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "F" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "G" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain breaks: 1 Chain: "I" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 16.86, per 1000 atoms: 0.53 Number of scatterers: 32113 At special positions: 0 Unit cell: (165.984, 208.544, 213.864, 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 146 16.00 O 6148 8.00 N 5324 7.00 C 20495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 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: 11.50 Conformation dependent library (CDL) restraints added in 6.4 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7810 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 66 sheets defined 17.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.537A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.119A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.121A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.817A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.427A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.581A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.503A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.575A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.529A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 5.681A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 778 removed outlier: 3.634A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.710A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 879 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.661A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.668A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 958 removed outlier: 3.743A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.713A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.407A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.968A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.537A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.566A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.968A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.875A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.933A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.330A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.750A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.679A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.113A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.725A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.723A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.940A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.211A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.618A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.425A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1031 removed outlier: 3.556A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.854A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.616A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.644A pdb=" N ASP G 84 " --> pdb=" O GLN G 81 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU G 85 " --> pdb=" O ALA G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 85' Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.648A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.527A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE A 199 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 228 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.159A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.556A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.956A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 134 removed outlier: 8.280A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.514A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.518A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 4.059A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.139A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 removed outlier: 5.754A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.408A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.623A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 96 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 224 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.659A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.598A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 122 removed outlier: 4.093A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.376A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.672A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.578A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.818A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.894A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.853A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.923A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.819A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.557A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 186 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 229 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.648A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.657A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.577A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.066A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.809A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.297A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 727 removed outlier: 7.232A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.026A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.574A pdb=" N SER D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.752A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 93 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.782A pdb=" N TYR D 152 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF7, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.573A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E 89 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.641A pdb=" N SER E 117 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER E 140 " --> pdb=" O SER E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.536A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.742A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 41 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 93 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.829A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.522A pdb=" N VAL G 10 " --> pdb=" O THR G 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AG6, first strand: chain 'G' and resid 47 through 51 removed outlier: 5.468A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 148 through 149 Processing sheet with id=AG8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.754A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 41 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 93 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AH2, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AH3, first strand: chain 'I' and resid 47 through 51 removed outlier: 5.461A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR I 89 " --> pdb=" O TYR I 38 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2493 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: 13.67 Time building geometry restraints manager: 12.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6342 1.33 - 1.45: 8151 1.45 - 1.57: 18200 1.57 - 1.69: 0 1.69 - 1.81: 182 Bond restraints: 32875 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" O PHE B 329 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.05e-02 9.07e+03 7.92e+00 bond pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 1.536 1.503 0.033 1.25e-02 6.40e+03 7.01e+00 bond pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.32e-02 5.74e+03 5.95e+00 bond pdb=" CA PRO B 330 " pdb=" CB PRO B 330 " ideal model delta sigma weight residual 1.533 1.499 0.035 1.42e-02 4.96e+03 5.91e+00 bond pdb=" CA PRO C 330 " pdb=" CB PRO C 330 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.47e-02 4.63e+03 5.27e+00 ... (remaining 32870 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.24: 1195 107.24 - 113.94: 18441 113.94 - 120.63: 12102 120.63 - 127.32: 12731 127.32 - 134.01: 339 Bond angle restraints: 44808 Sorted by residual: angle pdb=" N PHE C 329 " pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 109.82 101.09 8.73 1.68e+00 3.54e-01 2.70e+01 angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 120.98 115.99 4.99 1.07e+00 8.73e-01 2.18e+01 angle pdb=" C ILE A 332 " pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 120.44 126.52 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.34 118.27 -6.93 1.55e+00 4.16e-01 2.00e+01 angle pdb=" N PRO B 330 " pdb=" CA PRO B 330 " pdb=" C PRO B 330 " ideal model delta sigma weight residual 112.47 121.34 -8.87 2.06e+00 2.36e-01 1.86e+01 ... (remaining 44803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 18795 17.33 - 34.66: 687 34.66 - 51.99: 130 51.99 - 69.32: 18 69.32 - 86.65: 6 Dihedral angle restraints: 19636 sinusoidal: 7501 harmonic: 12135 Sorted by residual: dihedral pdb=" CA ASP E 52 " pdb=" C ASP E 52 " pdb=" N VAL E 53 " pdb=" CA VAL E 53 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA SER C 112 " pdb=" C SER C 112 " pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA SER D 120 " pdb=" C SER D 120 " pdb=" N ALA D 121 " pdb=" CA ALA D 121 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 19633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4427 0.057 - 0.113: 689 0.113 - 0.170: 24 0.170 - 0.226: 1 0.226 - 0.283: 2 Chirality restraints: 5143 Sorted by residual: chirality pdb=" CA PRO B 330 " pdb=" N PRO B 330 " pdb=" C PRO B 330 " pdb=" CB PRO B 330 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO C 330 " pdb=" N PRO C 330 " pdb=" C PRO C 330 " pdb=" CB PRO C 330 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 5140 not shown) Planarity restraints: 5765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 328 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C ARG A 328 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG A 328 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 329 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO C 330 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 330 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.027 5.00e-02 4.00e+02 ... (remaining 5762 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3041 2.75 - 3.29: 31491 3.29 - 3.83: 52825 3.83 - 4.36: 62055 4.36 - 4.90: 107184 Nonbonded interactions: 256596 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.214 2.440 nonbonded pdb=" O ILE F 106 " pdb=" OH TYR G 38 " model vdw 2.242 2.440 nonbonded pdb=" O ILE D 106 " pdb=" OH TYR E 38 " model vdw 2.246 2.440 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.247 2.440 nonbonded pdb=" OG SER E 65 " pdb=" OG1 THR E 76 " model vdw 2.248 2.440 ... (remaining 256591 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' and (resid 26 through 243 or resid 262 through 1147)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.520 Check model and map are aligned: 0.450 Set scattering table: 0.300 Process input model: 85.280 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.180 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.002 0.042 32875 Z= 0.136 Angle : 0.541 8.873 44808 Z= 0.329 Chirality : 0.040 0.283 5143 Planarity : 0.004 0.050 5765 Dihedral : 9.011 86.654 11688 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.50 % Favored : 94.45 % Rotamer: Outliers : 4.91 % Allowed : 6.33 % Favored : 88.77 % 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: -4.43 (0.10), residues: 4110 helix: -3.02 (0.13), residues: 634 sheet: -2.50 (0.15), residues: 942 loop : -3.25 (0.10), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.001 0.000 HIS A1064 PHE 0.010 0.001 PHE B 329 TYR 0.005 0.000 TYR C1067 ARG 0.003 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1110 time to evaluate : 3.225 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: 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 32 PHE cc_start: 0.7896 (m-80) cc_final: 0.7649 (m-80) REVERT: A 49 HIS cc_start: 0.7920 (t-90) cc_final: 0.7704 (t-170) REVERT: A 81 ASN cc_start: 0.7754 (m110) cc_final: 0.7530 (m-40) REVERT: A 90 VAL cc_start: 0.8692 (p) cc_final: 0.8361 (t) REVERT: A 97 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8010 (ttpp) REVERT: A 99 ASN cc_start: 0.7695 (m-40) cc_final: 0.7171 (t0) REVERT: A 129 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7467 (ttpp) REVERT: A 193 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7962 (ptmt) REVERT: A 208 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8276 (pt) REVERT: A 269 TYR cc_start: 0.7961 (m-10) cc_final: 0.7484 (m-80) REVERT: A 331 ASN cc_start: 0.6165 (OUTLIER) cc_final: 0.5325 (m-40) REVERT: A 335 LEU cc_start: 0.8429 (tp) cc_final: 0.8115 (mm) REVERT: A 349 SER cc_start: 0.8234 (m) cc_final: 0.7971 (t) REVERT: A 378 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7532 (mtpt) REVERT: A 403 ARG cc_start: 0.7053 (ttp-170) cc_final: 0.6734 (ttp80) REVERT: A 420 ASP cc_start: 0.6803 (m-30) cc_final: 0.6552 (m-30) REVERT: A 421 TYR cc_start: 0.7113 (m-10) cc_final: 0.6265 (m-80) REVERT: A 439 ASN cc_start: 0.7484 (t0) cc_final: 0.7145 (t0) REVERT: A 440 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7275 (ttpp) REVERT: A 461 LEU cc_start: 0.8434 (tp) cc_final: 0.8022 (tp) REVERT: A 467 ASP cc_start: 0.7118 (t0) cc_final: 0.6750 (p0) REVERT: A 496 SER cc_start: 0.8342 (m) cc_final: 0.8079 (t) REVERT: A 512 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 514 SER cc_start: 0.7628 (m) cc_final: 0.7338 (t) REVERT: A 547 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7790 (mtmm) REVERT: A 551 VAL cc_start: 0.8574 (t) cc_final: 0.8369 (t) REVERT: A 572 THR cc_start: 0.8161 (m) cc_final: 0.7407 (p) REVERT: A 573 THR cc_start: 0.8739 (m) cc_final: 0.8494 (p) REVERT: A 578 ASP cc_start: 0.7501 (t0) cc_final: 0.7108 (t70) REVERT: A 588 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 616 ASN cc_start: 0.5434 (t0) cc_final: 0.5034 (t0) REVERT: A 755 GLN cc_start: 0.7167 (mp-120) cc_final: 0.6712 (mp-120) REVERT: A 776 LYS cc_start: 0.8263 (tmmt) cc_final: 0.7898 (ttmt) REVERT: A 955 ASN cc_start: 0.7158 (m-40) cc_final: 0.6849 (m-40) REVERT: A 990 GLU cc_start: 0.7031 (mp0) cc_final: 0.6358 (mp0) REVERT: A 993 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 998 THR cc_start: 0.8449 (m) cc_final: 0.8135 (p) REVERT: A 1017 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 1028 LYS cc_start: 0.8378 (mttt) cc_final: 0.8023 (mtpt) REVERT: A 1029 MET cc_start: 0.8620 (tpp) cc_final: 0.8413 (tpp) REVERT: A 1081 ILE cc_start: 0.7945 (pt) cc_final: 0.7592 (mt) REVERT: A 1097 SER cc_start: 0.8593 (t) cc_final: 0.8297 (p) REVERT: B 104 TRP cc_start: 0.8449 (m-90) cc_final: 0.7775 (m-90) REVERT: B 105 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7563 (mm) REVERT: B 117 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 221 SER cc_start: 0.8174 (p) cc_final: 0.7970 (p) REVERT: B 277 LEU cc_start: 0.8359 (mt) cc_final: 0.8120 (mp) REVERT: B 331 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6668 (m-40) REVERT: B 356 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8191 (mmmt) REVERT: B 383 SER cc_start: 0.8030 (m) cc_final: 0.7541 (p) REVERT: B 394 ASN cc_start: 0.7552 (p0) cc_final: 0.6645 (p0) REVERT: B 434 ILE cc_start: 0.8486 (mt) cc_final: 0.8261 (mm) REVERT: B 437 ASN cc_start: 0.7960 (t0) cc_final: 0.7456 (t0) REVERT: B 440 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8197 (tppt) REVERT: B 456 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6809 (p90) REVERT: B 532 ASN cc_start: 0.7936 (m-40) cc_final: 0.7728 (m-40) REVERT: B 541 PHE cc_start: 0.7803 (p90) cc_final: 0.7567 (p90) REVERT: B 586 ASP cc_start: 0.7590 (t0) cc_final: 0.7187 (t0) REVERT: B 616 ASN cc_start: 0.7154 (t0) cc_final: 0.6271 (t0) REVERT: B 707 TYR cc_start: 0.8092 (t80) cc_final: 0.7706 (t80) REVERT: B 711 SER cc_start: 0.8153 (t) cc_final: 0.7908 (p) REVERT: B 762 GLN cc_start: 0.7658 (pt0) cc_final: 0.7351 (pt0) REVERT: B 787 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7474 (mm-40) REVERT: B 854 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8103 (ttmm) REVERT: B 868 GLU cc_start: 0.7337 (tp30) cc_final: 0.6927 (tp30) REVERT: B 888 PHE cc_start: 0.8653 (p90) cc_final: 0.8369 (p90) REVERT: B 921 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7755 (mmmt) REVERT: B 922 LEU cc_start: 0.8812 (tp) cc_final: 0.8601 (tp) REVERT: B 933 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8175 (mtmm) REVERT: B 964 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7932 (ttmm) REVERT: B 968 SER cc_start: 0.8367 (m) cc_final: 0.8026 (p) REVERT: B 1017 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6554 (tm-30) REVERT: B 1019 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6755 (ttp80) REVERT: B 1111 GLU cc_start: 0.7791 (tt0) cc_final: 0.7564 (tt0) REVERT: B 1118 ASP cc_start: 0.7394 (t70) cc_final: 0.7183 (t0) REVERT: B 1136 THR cc_start: 0.8461 (t) cc_final: 0.8197 (t) REVERT: B 1141 LEU cc_start: 0.8423 (tp) cc_final: 0.7969 (tp) REVERT: C 47 VAL cc_start: 0.8808 (m) cc_final: 0.8566 (p) REVERT: C 81 ASN cc_start: 0.7904 (p0) cc_final: 0.7369 (p0) REVERT: C 85 PRO cc_start: 0.7684 (Cg_endo) cc_final: 0.6539 (Cg_exo) REVERT: C 121 ASN cc_start: 0.6742 (t0) cc_final: 0.6374 (t0) REVERT: C 132 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6635 (tp30) REVERT: C 224 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6477 (mm-30) REVERT: C 281 GLU cc_start: 0.6623 (pp20) cc_final: 0.6024 (pp20) REVERT: C 287 ASP cc_start: 0.7428 (p0) cc_final: 0.7056 (p0) REVERT: C 290 ASP cc_start: 0.7446 (t0) cc_final: 0.7220 (t0) REVERT: C 362 VAL cc_start: 0.8278 (t) cc_final: 0.7961 (p) REVERT: C 366 SER cc_start: 0.8662 (m) cc_final: 0.8195 (p) REVERT: C 429 PHE cc_start: 0.7871 (t80) cc_final: 0.7667 (t80) REVERT: C 433 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8621 (t) REVERT: C 454 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.6839 (ttm-80) REVERT: C 456 PHE cc_start: 0.6957 (m-80) cc_final: 0.6484 (m-80) REVERT: C 461 LEU cc_start: 0.7237 (tp) cc_final: 0.6941 (tp) REVERT: C 462 LYS cc_start: 0.7724 (ptpp) cc_final: 0.7451 (ptpp) REVERT: C 465 GLU cc_start: 0.6760 (tt0) cc_final: 0.6251 (tt0) REVERT: C 470 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.6890 (p) REVERT: C 511 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8120 (t) REVERT: C 514 SER cc_start: 0.8363 (m) cc_final: 0.8010 (p) REVERT: C 616 ASN cc_start: 0.4976 (t0) cc_final: 0.4399 (t0) REVERT: C 654 GLU cc_start: 0.7243 (pm20) cc_final: 0.6869 (pm20) REVERT: C 742 ILE cc_start: 0.8727 (mm) cc_final: 0.8448 (mt) REVERT: C 762 GLN cc_start: 0.7655 (tt0) cc_final: 0.7376 (tt0) REVERT: C 776 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7923 (ttpt) REVERT: C 823 PHE cc_start: 0.7325 (m-80) cc_final: 0.7091 (m-80) REVERT: C 868 GLU cc_start: 0.7315 (tp30) cc_final: 0.6766 (tp30) REVERT: C 922 LEU cc_start: 0.8757 (tp) cc_final: 0.8501 (tt) REVERT: C 927 PHE cc_start: 0.8314 (t80) cc_final: 0.8038 (t80) REVERT: C 964 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7810 (ttpp) REVERT: C 990 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7313 (mm-30) REVERT: C 993 ILE cc_start: 0.9037 (tp) cc_final: 0.8763 (tt) REVERT: C 1002 GLN cc_start: 0.7031 (tp-100) cc_final: 0.6731 (tp-100) REVERT: C 1017 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 1038 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7944 (mtmm) REVERT: C 1072 GLU cc_start: 0.7722 (pm20) cc_final: 0.7462 (pm20) REVERT: C 1084 ASP cc_start: 0.7826 (m-30) cc_final: 0.7623 (m-30) REVERT: C 1118 ASP cc_start: 0.6793 (t0) cc_final: 0.6551 (t0) REVERT: C 1123 SER cc_start: 0.8698 (t) cc_final: 0.8192 (p) REVERT: C 1134 ASN cc_start: 0.5488 (m-40) cc_final: 0.5225 (m-40) REVERT: D 3 THR cc_start: 0.7272 (p) cc_final: 0.7021 (p) REVERT: D 15 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6568 (mmtm) REVERT: D 59 LYS cc_start: 0.7689 (mttp) cc_final: 0.7325 (mttp) REVERT: D 78 ASN cc_start: 0.6614 (m110) cc_final: 0.6375 (m110) REVERT: D 182 LEU cc_start: 0.7751 (mt) cc_final: 0.7402 (pp) REVERT: E 104 THR cc_start: 0.7862 (m) cc_final: 0.7510 (p) REVERT: E 120 LEU cc_start: 0.1108 (OUTLIER) cc_final: 0.0836 (pp) REVERT: F 2 VAL cc_start: 0.8244 (t) cc_final: 0.7938 (p) REVERT: F 23 THR cc_start: 0.7825 (m) cc_final: 0.7585 (p) REVERT: H 29 LEU cc_start: 0.9150 (tp) cc_final: 0.8842 (tp) outliers start: 176 outliers final: 74 residues processed: 1229 average time/residue: 0.4338 time to fit residues: 841.3149 Evaluate side-chains 977 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 888 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 10.0000 chunk 313 optimal weight: 0.0070 chunk 174 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 241 optimal weight: 0.0970 chunk 375 optimal weight: 6.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 81 ASN A 121 ASN A 125 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 331 ASN A 343 ASN A 388 ASN A 417 ASN A 540 ASN A 644 GLN A 709 ASN A 784 GLN A 895 GLN A 914 ASN A 965 GLN A1011 GLN A1048 HIS A1074 ASN B 52 GLN B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 165 ASN B 173 GLN B 186 ASN B 194 ASN B 205 HIS B 218 GLN B 271 GLN B 331 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 703 ASN B 762 GLN B 784 GLN B 853 GLN B 901 GLN B 913 GLN B 965 GLN B 992 GLN B1002 GLN B1005 GLN B1011 GLN B1048 HIS B1054 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 81 ASN C 87 ASN C 165 ASN C 173 GLN C 186 ASN C 194 ASN C 370 ASN C 409 GLN C 505 HIS C 540 ASN C 563 GLN C 710 ASN C 762 GLN C 853 GLN C 901 GLN C 913 GLN C 914 ASN C1011 GLN C1048 HIS C1125 ASN D 41 GLN D 199 GLN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 39 GLN E 41 HIS E 111 GLN E 197 GLN F 41 GLN F 199 GLN G 39 GLN G 71 ASN G 81 GLN G 111 GLN G 197 GLN H 41 GLN I 39 GLN I 40 GLN I 41 HIS I 81 GLN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 32875 Z= 0.279 Angle : 0.618 15.790 44808 Z= 0.315 Chirality : 0.046 0.371 5143 Planarity : 0.005 0.047 5765 Dihedral : 6.551 76.142 4638 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.82 % Allowed : 12.88 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.26 (0.12), residues: 4110 helix: -0.57 (0.19), residues: 648 sheet: -1.97 (0.15), residues: 982 loop : -2.82 (0.11), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 55 HIS 0.005 0.001 HIS C 505 PHE 0.028 0.002 PHE C 55 TYR 0.024 0.002 TYR C 265 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 870 time to evaluate : 3.541 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8592 (m-10) cc_final: 0.8142 (m-80) REVERT: A 87 ASN cc_start: 0.7485 (p0) cc_final: 0.6908 (p0) REVERT: A 90 VAL cc_start: 0.8409 (p) cc_final: 0.8180 (t) REVERT: A 105 ILE cc_start: 0.8437 (mt) cc_final: 0.8209 (mt) REVERT: A 121 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.6620 (p0) REVERT: A 190 PHE cc_start: 0.8144 (m-80) cc_final: 0.7905 (m-80) REVERT: A 228 ASP cc_start: 0.7307 (t0) cc_final: 0.6955 (t0) REVERT: A 235 ILE cc_start: 0.8428 (mm) cc_final: 0.8148 (tp) REVERT: A 269 TYR cc_start: 0.8084 (m-10) cc_final: 0.7604 (m-10) REVERT: A 287 ASP cc_start: 0.7612 (p0) cc_final: 0.7321 (p0) REVERT: A 335 LEU cc_start: 0.8566 (tp) cc_final: 0.8330 (mm) REVERT: A 349 SER cc_start: 0.8050 (m) cc_final: 0.7684 (t) REVERT: A 353 TRP cc_start: 0.8722 (p-90) cc_final: 0.8180 (p-90) REVERT: A 378 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7270 (mtpt) REVERT: A 392 PHE cc_start: 0.8415 (m-80) cc_final: 0.8144 (m-10) REVERT: A 398 ASP cc_start: 0.7259 (m-30) cc_final: 0.6756 (m-30) REVERT: A 403 ARG cc_start: 0.7056 (ttp-170) cc_final: 0.6754 (mtp180) REVERT: A 421 TYR cc_start: 0.7276 (m-10) cc_final: 0.6268 (m-80) REVERT: A 440 LYS cc_start: 0.7705 (ttpp) cc_final: 0.7417 (ttpp) REVERT: A 448 ASN cc_start: 0.7939 (t0) cc_final: 0.7018 (t0) REVERT: A 451 TYR cc_start: 0.7130 (m-80) cc_final: 0.6654 (m-80) REVERT: A 465 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6668 (tm-30) REVERT: A 467 ASP cc_start: 0.7659 (t0) cc_final: 0.6739 (p0) REVERT: A 496 SER cc_start: 0.8498 (m) cc_final: 0.8214 (t) REVERT: A 514 SER cc_start: 0.7906 (m) cc_final: 0.7500 (p) REVERT: A 572 THR cc_start: 0.8058 (m) cc_final: 0.7371 (p) REVERT: A 578 ASP cc_start: 0.7434 (t0) cc_final: 0.7178 (t70) REVERT: A 588 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 616 ASN cc_start: 0.6082 (t0) cc_final: 0.5632 (t0) REVERT: A 776 LYS cc_start: 0.8393 (tmmt) cc_final: 0.8064 (ttpp) REVERT: A 790 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7926 (mtmm) REVERT: A 921 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7571 (mtpp) REVERT: A 922 LEU cc_start: 0.8696 (tp) cc_final: 0.8487 (tt) REVERT: A 945 LEU cc_start: 0.8423 (mm) cc_final: 0.8191 (mp) REVERT: A 949 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7581 (mm-40) REVERT: A 957 GLN cc_start: 0.7665 (pt0) cc_final: 0.7365 (pt0) REVERT: A 990 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 1005 GLN cc_start: 0.7808 (tp40) cc_final: 0.7593 (tp40) REVERT: A 1014 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7409 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 1034 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8830 (mt) REVERT: A 1081 ILE cc_start: 0.7966 (pt) cc_final: 0.7759 (mt) REVERT: A 1097 SER cc_start: 0.8274 (t) cc_final: 0.7920 (p) REVERT: B 53 ASP cc_start: 0.6993 (t0) cc_final: 0.6762 (t0) REVERT: B 105 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 158 ARG cc_start: 0.5696 (OUTLIER) cc_final: 0.5462 (tmm160) REVERT: B 189 GLU cc_start: 0.7126 (pt0) cc_final: 0.6824 (pt0) REVERT: B 223 LEU cc_start: 0.8019 (mp) cc_final: 0.7497 (mt) REVERT: B 239 GLN cc_start: 0.7429 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 329 PHE cc_start: 0.8336 (m-10) cc_final: 0.8112 (m-10) REVERT: B 334 ASN cc_start: 0.7620 (t0) cc_final: 0.7394 (t0) REVERT: B 356 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8229 (mmmt) REVERT: B 394 ASN cc_start: 0.7430 (p0) cc_final: 0.6447 (p0) REVERT: B 414 GLN cc_start: 0.7655 (mp10) cc_final: 0.7013 (mp10) REVERT: B 434 ILE cc_start: 0.8612 (mt) cc_final: 0.8398 (mp) REVERT: B 437 ASN cc_start: 0.7586 (t0) cc_final: 0.7298 (t0) REVERT: B 440 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8262 (tppt) REVERT: B 456 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6509 (p90) REVERT: B 541 PHE cc_start: 0.7943 (p90) cc_final: 0.7727 (p90) REVERT: B 557 LYS cc_start: 0.8520 (mttp) cc_final: 0.8249 (mtmm) REVERT: B 586 ASP cc_start: 0.7484 (t0) cc_final: 0.7270 (t0) REVERT: B 615 VAL cc_start: 0.8462 (t) cc_final: 0.8215 (m) REVERT: B 651 ILE cc_start: 0.8741 (pt) cc_final: 0.8465 (pt) REVERT: B 695 TYR cc_start: 0.8212 (p90) cc_final: 0.7412 (p90) REVERT: B 711 SER cc_start: 0.8321 (t) cc_final: 0.7964 (p) REVERT: B 759 PHE cc_start: 0.6861 (t80) cc_final: 0.6514 (t80) REVERT: B 779 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7321 (mm-40) REVERT: B 820 ASP cc_start: 0.7399 (t0) cc_final: 0.7138 (m-30) REVERT: B 854 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8037 (ttmm) REVERT: B 933 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8303 (mtpp) REVERT: B 964 LYS cc_start: 0.8361 (ttpp) cc_final: 0.8061 (ttmm) REVERT: B 965 GLN cc_start: 0.8285 (mm110) cc_final: 0.7939 (mm-40) REVERT: B 968 SER cc_start: 0.8738 (m) cc_final: 0.8308 (p) REVERT: B 985 ASP cc_start: 0.7399 (p0) cc_final: 0.7135 (p0) REVERT: B 990 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6866 (mm-30) REVERT: B 993 ILE cc_start: 0.8385 (tp) cc_final: 0.8114 (tt) REVERT: B 1014 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7486 (mtm-85) REVERT: B 1017 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7045 (tm-30) REVERT: B 1050 MET cc_start: 0.8089 (ptm) cc_final: 0.7885 (ptp) REVERT: B 1104 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 1118 ASP cc_start: 0.7622 (t70) cc_final: 0.7384 (t0) REVERT: B 1141 LEU cc_start: 0.8539 (tp) cc_final: 0.8092 (tp) REVERT: C 52 GLN cc_start: 0.7258 (tp40) cc_final: 0.6969 (tp40) REVERT: C 81 ASN cc_start: 0.7961 (p0) cc_final: 0.7468 (p0) REVERT: C 121 ASN cc_start: 0.6748 (t0) cc_final: 0.6433 (t0) REVERT: C 132 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6441 (tp30) REVERT: C 196 ASP cc_start: 0.7178 (p0) cc_final: 0.6893 (p0) REVERT: C 206 THR cc_start: 0.8487 (t) cc_final: 0.8179 (p) REVERT: C 223 LEU cc_start: 0.8353 (mp) cc_final: 0.8049 (mp) REVERT: C 224 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6973 (mp0) REVERT: C 287 ASP cc_start: 0.7516 (p0) cc_final: 0.7221 (p0) REVERT: C 310 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8218 (ttpt) REVERT: C 327 VAL cc_start: 0.8688 (p) cc_final: 0.8466 (m) REVERT: C 356 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8214 (tttp) REVERT: C 362 VAL cc_start: 0.8295 (t) cc_final: 0.8054 (p) REVERT: C 388 ASN cc_start: 0.8175 (m110) cc_final: 0.7970 (m110) REVERT: C 395 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8261 (t) REVERT: C 417 ASN cc_start: 0.7294 (t0) cc_final: 0.7040 (t0) REVERT: C 462 LYS cc_start: 0.7649 (ptpp) cc_final: 0.7439 (ptpp) REVERT: C 468 ILE cc_start: 0.7986 (tp) cc_final: 0.7715 (tt) REVERT: C 503 VAL cc_start: 0.8538 (t) cc_final: 0.8243 (m) REVERT: C 511 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8208 (t) REVERT: C 514 SER cc_start: 0.8348 (m) cc_final: 0.8131 (p) REVERT: C 532 ASN cc_start: 0.8429 (t0) cc_final: 0.8154 (m-40) REVERT: C 553 THR cc_start: 0.8163 (t) cc_final: 0.7934 (p) REVERT: C 578 ASP cc_start: 0.7303 (t0) cc_final: 0.7004 (t70) REVERT: C 599 THR cc_start: 0.8345 (m) cc_final: 0.8105 (t) REVERT: C 615 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7639 (t) REVERT: C 654 GLU cc_start: 0.7335 (pm20) cc_final: 0.7064 (pm20) REVERT: C 737 ASP cc_start: 0.6521 (t70) cc_final: 0.6270 (t0) REVERT: C 765 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7274 (ttp80) REVERT: C 776 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8022 (ttpt) REVERT: C 859 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7889 (p) REVERT: C 868 GLU cc_start: 0.6971 (tp30) cc_final: 0.6555 (tp30) REVERT: C 902 MET cc_start: 0.7862 (tpp) cc_final: 0.7339 (mmm) REVERT: C 936 ASP cc_start: 0.7495 (m-30) cc_final: 0.7196 (m-30) REVERT: C 960 ASN cc_start: 0.8168 (t0) cc_final: 0.7788 (t0) REVERT: C 993 ILE cc_start: 0.9034 (tp) cc_final: 0.8783 (tp) REVERT: C 1002 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6854 (tp-100) REVERT: C 1005 GLN cc_start: 0.7960 (tp40) cc_final: 0.7496 (tp40) REVERT: C 1017 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 1018 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7867 (mp) REVERT: C 1031 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 1123 SER cc_start: 0.8872 (t) cc_final: 0.8342 (p) REVERT: C 1127 ASP cc_start: 0.6807 (p0) cc_final: 0.6488 (p0) REVERT: D 4 LEU cc_start: 0.8063 (mt) cc_final: 0.7829 (mt) REVERT: D 15 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6626 (mmtm) REVERT: D 59 LYS cc_start: 0.7847 (mttp) cc_final: 0.7456 (mttp) REVERT: E 44 GLN cc_start: 0.7250 (mp10) cc_final: 0.6794 (mp10) REVERT: E 104 THR cc_start: 0.7939 (m) cc_final: 0.7612 (p) REVERT: F 2 VAL cc_start: 0.8360 (t) cc_final: 0.8041 (p) REVERT: H 84 MET cc_start: 0.3294 (pmm) cc_final: 0.1368 (tpt) outliers start: 209 outliers final: 114 residues processed: 995 average time/residue: 0.4505 time to fit residues: 706.3444 Evaluate side-chains 918 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 787 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 312 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 376 optimal weight: 0.3980 chunk 406 optimal weight: 7.9990 chunk 335 optimal weight: 0.3980 chunk 373 optimal weight: 0.0270 chunk 128 optimal weight: 2.9990 chunk 302 optimal weight: 0.1980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 121 ASN A 125 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 895 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1101 HIS A1119 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 321 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 544 ASN B 580 GLN B 913 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1083 HIS B1106 GLN C 505 HIS C 616 ASN C 824 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 32875 Z= 0.155 Angle : 0.578 15.957 44808 Z= 0.286 Chirality : 0.044 0.303 5143 Planarity : 0.004 0.065 5765 Dihedral : 6.191 76.216 4600 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.71 % Allowed : 15.89 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.72 (0.12), residues: 4110 helix: 0.25 (0.20), residues: 662 sheet: -1.64 (0.16), residues: 980 loop : -2.59 (0.11), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 37 HIS 0.009 0.001 HIS A1101 PHE 0.025 0.001 PHE D 24 TYR 0.038 0.001 TYR A 170 ARG 0.009 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 809 time to evaluate : 3.567 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: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7454 (p0) cc_final: 0.6708 (p0) REVERT: A 90 VAL cc_start: 0.8347 (p) cc_final: 0.8123 (t) REVERT: A 105 ILE cc_start: 0.8422 (mt) cc_final: 0.8172 (mt) REVERT: A 121 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 228 ASP cc_start: 0.7232 (t0) cc_final: 0.6833 (t0) REVERT: A 235 ILE cc_start: 0.8420 (mm) cc_final: 0.8087 (tp) REVERT: A 269 TYR cc_start: 0.8021 (m-10) cc_final: 0.7508 (m-10) REVERT: A 287 ASP cc_start: 0.7637 (p0) cc_final: 0.7313 (p0) REVERT: A 335 LEU cc_start: 0.8513 (tp) cc_final: 0.8306 (mm) REVERT: A 349 SER cc_start: 0.7994 (m) cc_final: 0.7655 (t) REVERT: A 353 TRP cc_start: 0.8651 (p-90) cc_final: 0.7968 (p-90) REVERT: A 378 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7398 (mtpt) REVERT: A 392 PHE cc_start: 0.8384 (m-80) cc_final: 0.8160 (m-80) REVERT: A 421 TYR cc_start: 0.7251 (m-10) cc_final: 0.6310 (m-80) REVERT: A 440 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7328 (ttpp) REVERT: A 448 ASN cc_start: 0.7882 (t0) cc_final: 0.7183 (t0) REVERT: A 451 TYR cc_start: 0.7077 (m-80) cc_final: 0.6648 (m-80) REVERT: A 467 ASP cc_start: 0.7372 (t0) cc_final: 0.6576 (p0) REVERT: A 496 SER cc_start: 0.8480 (m) cc_final: 0.8179 (t) REVERT: A 514 SER cc_start: 0.7907 (m) cc_final: 0.7390 (p) REVERT: A 573 THR cc_start: 0.8713 (m) cc_final: 0.8401 (p) REVERT: A 578 ASP cc_start: 0.7395 (t0) cc_final: 0.7124 (t70) REVERT: A 588 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 616 ASN cc_start: 0.6547 (t0) cc_final: 0.6112 (t0) REVERT: A 719 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7827 (p) REVERT: A 752 LEU cc_start: 0.8093 (mm) cc_final: 0.7861 (mm) REVERT: A 755 GLN cc_start: 0.7357 (mp-120) cc_final: 0.6898 (mp-120) REVERT: A 790 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7752 (mtmm) REVERT: A 902 MET cc_start: 0.8101 (mmm) cc_final: 0.7847 (mmt) REVERT: A 921 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7539 (mtpp) REVERT: A 945 LEU cc_start: 0.8393 (mm) cc_final: 0.8140 (mp) REVERT: A 949 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7490 (mm-40) REVERT: A 990 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: A 1014 ARG cc_start: 0.7597 (ttm110) cc_final: 0.7314 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6938 (tm-30) REVERT: A 1081 ILE cc_start: 0.7970 (pt) cc_final: 0.7765 (mt) REVERT: A 1097 SER cc_start: 0.8179 (t) cc_final: 0.7838 (p) REVERT: B 96 GLU cc_start: 0.6174 (pt0) cc_final: 0.5966 (pt0) REVERT: B 105 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7624 (mp) REVERT: B 189 GLU cc_start: 0.7103 (pt0) cc_final: 0.6801 (pt0) REVERT: B 223 LEU cc_start: 0.8022 (mp) cc_final: 0.7573 (mt) REVERT: B 237 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7780 (mtp85) REVERT: B 239 GLN cc_start: 0.7443 (tm-30) cc_final: 0.7019 (tm-30) REVERT: B 386 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7614 (mmmt) REVERT: B 394 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.6886 (p0) REVERT: B 395 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7497 (m) REVERT: B 396 TYR cc_start: 0.7897 (m-10) cc_final: 0.7678 (m-80) REVERT: B 414 GLN cc_start: 0.7669 (mp10) cc_final: 0.6867 (mp10) REVERT: B 434 ILE cc_start: 0.8580 (mt) cc_final: 0.8310 (mp) REVERT: B 440 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8193 (tppt) REVERT: B 456 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6728 (p90) REVERT: B 557 LYS cc_start: 0.8407 (mttp) cc_final: 0.8169 (mtmm) REVERT: B 581 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7710 (p) REVERT: B 651 ILE cc_start: 0.8725 (pt) cc_final: 0.8500 (pt) REVERT: B 711 SER cc_start: 0.8293 (t) cc_final: 0.7940 (p) REVERT: B 759 PHE cc_start: 0.6816 (t80) cc_final: 0.6415 (t80) REVERT: B 779 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7534 (tp40) REVERT: B 803 SER cc_start: 0.8490 (m) cc_final: 0.8184 (p) REVERT: B 854 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8003 (ttmm) REVERT: B 868 GLU cc_start: 0.7021 (tp30) cc_final: 0.6658 (tp30) REVERT: B 933 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8160 (mtpp) REVERT: B 964 LYS cc_start: 0.8370 (ttpp) cc_final: 0.8017 (ttmm) REVERT: B 965 GLN cc_start: 0.8272 (mm110) cc_final: 0.7956 (mm-40) REVERT: B 968 SER cc_start: 0.8692 (m) cc_final: 0.8269 (p) REVERT: B 985 ASP cc_start: 0.7460 (p0) cc_final: 0.7146 (p0) REVERT: B 990 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7050 (mm-30) REVERT: B 993 ILE cc_start: 0.8311 (tp) cc_final: 0.8082 (tp) REVERT: B 994 ASP cc_start: 0.7414 (m-30) cc_final: 0.7144 (t0) REVERT: B 1005 GLN cc_start: 0.7535 (tp-100) cc_final: 0.7032 (tp40) REVERT: B 1050 MET cc_start: 0.7971 (ptm) cc_final: 0.7757 (ptp) REVERT: B 1118 ASP cc_start: 0.7559 (t70) cc_final: 0.7301 (t0) REVERT: B 1141 LEU cc_start: 0.8531 (tp) cc_final: 0.8123 (tp) REVERT: C 121 ASN cc_start: 0.6775 (t0) cc_final: 0.6502 (t0) REVERT: C 132 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6382 (tp30) REVERT: C 196 ASP cc_start: 0.7079 (p0) cc_final: 0.6833 (p0) REVERT: C 206 THR cc_start: 0.8509 (t) cc_final: 0.8284 (p) REVERT: C 223 LEU cc_start: 0.8345 (mp) cc_final: 0.8064 (mp) REVERT: C 224 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6970 (mp0) REVERT: C 310 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8181 (ttpp) REVERT: C 327 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8438 (m) REVERT: C 356 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8182 (tttp) REVERT: C 386 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7863 (ptpp) REVERT: C 417 ASN cc_start: 0.7271 (t0) cc_final: 0.6449 (t0) REVERT: C 503 VAL cc_start: 0.8434 (t) cc_final: 0.8138 (m) REVERT: C 511 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (t) REVERT: C 532 ASN cc_start: 0.8376 (t0) cc_final: 0.8125 (m-40) REVERT: C 537 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7917 (mttp) REVERT: C 559 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7905 (t80) REVERT: C 599 THR cc_start: 0.8350 (m) cc_final: 0.8104 (t) REVERT: C 615 VAL cc_start: 0.7828 (t) cc_final: 0.7583 (t) REVERT: C 654 GLU cc_start: 0.7319 (pm20) cc_final: 0.7063 (pm20) REVERT: C 737 ASP cc_start: 0.6351 (t70) cc_final: 0.6121 (t0) REVERT: C 776 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7810 (ttpp) REVERT: C 859 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7882 (p) REVERT: C 868 GLU cc_start: 0.6872 (tp30) cc_final: 0.6482 (tp30) REVERT: C 933 LYS cc_start: 0.8236 (mttt) cc_final: 0.7935 (mtpt) REVERT: C 936 ASP cc_start: 0.7476 (m-30) cc_final: 0.7095 (m-30) REVERT: C 960 ASN cc_start: 0.8126 (t0) cc_final: 0.7798 (t0) REVERT: C 993 ILE cc_start: 0.8957 (tp) cc_final: 0.8627 (tp) REVERT: C 1002 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6721 (tp-100) REVERT: C 1005 GLN cc_start: 0.7879 (tp40) cc_final: 0.7457 (tp40) REVERT: C 1017 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6886 (tm-30) REVERT: C 1018 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7793 (mp) REVERT: C 1072 GLU cc_start: 0.7755 (pm20) cc_final: 0.7482 (pm20) REVERT: C 1123 SER cc_start: 0.8835 (t) cc_final: 0.8374 (m) REVERT: C 1127 ASP cc_start: 0.6946 (p0) cc_final: 0.6656 (p0) REVERT: D 4 LEU cc_start: 0.8068 (mt) cc_final: 0.7842 (mt) REVERT: D 15 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6532 (mmtm) REVERT: D 59 LYS cc_start: 0.7798 (mttp) cc_final: 0.7396 (mttp) REVERT: E 47 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8406 (ptmm) REVERT: E 104 THR cc_start: 0.7958 (m) cc_final: 0.7578 (p) REVERT: F 2 VAL cc_start: 0.8386 (t) cc_final: 0.8057 (p) REVERT: H 84 MET cc_start: 0.3861 (pmm) cc_final: 0.1294 (tpp) outliers start: 169 outliers final: 115 residues processed: 914 average time/residue: 0.4597 time to fit residues: 660.4021 Evaluate side-chains 911 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 778 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 0.0010 chunk 283 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 377 optimal weight: 6.9990 chunk 400 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 358 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 218 GLN A 394 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 580 GLN B 913 GLN B 954 HIS ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 239 GLN C 460 ASN C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN E 33 ASN E 39 GLN E 81 GLN G 39 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32875 Z= 0.185 Angle : 0.571 13.395 44808 Z= 0.285 Chirality : 0.044 0.383 5143 Planarity : 0.004 0.096 5765 Dihedral : 6.043 75.999 4593 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.43 % Allowed : 16.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.39 (0.12), residues: 4110 helix: 0.65 (0.21), residues: 660 sheet: -1.36 (0.16), residues: 985 loop : -2.43 (0.11), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 55 HIS 0.006 0.001 HIS C 505 PHE 0.030 0.001 PHE C 429 TYR 0.029 0.001 TYR C 421 ARG 0.014 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 806 time to evaluate : 3.531 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: symmetry clash REVERT: A 87 ASN cc_start: 0.7458 (p0) cc_final: 0.6731 (p0) REVERT: A 90 VAL cc_start: 0.8350 (p) cc_final: 0.8123 (t) REVERT: A 105 ILE cc_start: 0.8451 (mt) cc_final: 0.8181 (mt) REVERT: A 121 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6635 (p0) REVERT: A 205 HIS cc_start: 0.6881 (t-90) cc_final: 0.6641 (t-90) REVERT: A 228 ASP cc_start: 0.7314 (t0) cc_final: 0.6823 (t0) REVERT: A 231 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8046 (pt) REVERT: A 269 TYR cc_start: 0.8032 (m-10) cc_final: 0.7515 (m-10) REVERT: A 287 ASP cc_start: 0.7649 (p0) cc_final: 0.7283 (p0) REVERT: A 332 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7035 (mp) REVERT: A 335 LEU cc_start: 0.8546 (tp) cc_final: 0.8331 (mm) REVERT: A 349 SER cc_start: 0.8009 (m) cc_final: 0.7645 (t) REVERT: A 353 TRP cc_start: 0.8745 (p-90) cc_final: 0.8045 (p-90) REVERT: A 355 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7121 (ttm-80) REVERT: A 378 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7233 (mtpt) REVERT: A 392 PHE cc_start: 0.8448 (m-80) cc_final: 0.8108 (m-80) REVERT: A 396 TYR cc_start: 0.7959 (m-10) cc_final: 0.7374 (m-10) REVERT: A 398 ASP cc_start: 0.7389 (m-30) cc_final: 0.7140 (m-30) REVERT: A 421 TYR cc_start: 0.7314 (m-10) cc_final: 0.6314 (m-80) REVERT: A 440 LYS cc_start: 0.7600 (ttpp) cc_final: 0.7278 (ttpp) REVERT: A 448 ASN cc_start: 0.7902 (t0) cc_final: 0.7244 (t0) REVERT: A 451 TYR cc_start: 0.7130 (m-80) cc_final: 0.6705 (m-80) REVERT: A 467 ASP cc_start: 0.7381 (t0) cc_final: 0.6671 (p0) REVERT: A 496 SER cc_start: 0.8481 (m) cc_final: 0.8126 (t) REVERT: A 514 SER cc_start: 0.7872 (m) cc_final: 0.7492 (p) REVERT: A 572 THR cc_start: 0.8600 (t) cc_final: 0.8085 (p) REVERT: A 573 THR cc_start: 0.8701 (m) cc_final: 0.8460 (p) REVERT: A 578 ASP cc_start: 0.7415 (t0) cc_final: 0.7127 (t70) REVERT: A 588 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 599 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8247 (p) REVERT: A 671 CYS cc_start: 0.5292 (m) cc_final: 0.5045 (m) REVERT: A 902 MET cc_start: 0.8133 (mmm) cc_final: 0.7928 (mmt) REVERT: A 921 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7551 (mtpp) REVERT: A 949 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7590 (mm-40) REVERT: A 965 GLN cc_start: 0.8188 (mt0) cc_final: 0.7847 (mt0) REVERT: A 1014 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7312 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6900 (tm-30) REVERT: A 1028 LYS cc_start: 0.7963 (mttt) cc_final: 0.7743 (mtpt) REVERT: A 1081 ILE cc_start: 0.7973 (pt) cc_final: 0.7769 (mt) REVERT: A 1097 SER cc_start: 0.8175 (t) cc_final: 0.7859 (p) REVERT: A 1101 HIS cc_start: 0.8208 (m-70) cc_final: 0.7939 (m-70) REVERT: A 1107 ARG cc_start: 0.6823 (mtm-85) cc_final: 0.6286 (mtm-85) REVERT: B 96 GLU cc_start: 0.6285 (pt0) cc_final: 0.6055 (pt0) REVERT: B 105 ILE cc_start: 0.8021 (mm) cc_final: 0.7647 (mp) REVERT: B 189 GLU cc_start: 0.7096 (pt0) cc_final: 0.6832 (pt0) REVERT: B 223 LEU cc_start: 0.8009 (mp) cc_final: 0.7581 (mt) REVERT: B 239 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 386 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7707 (mmmt) REVERT: B 394 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.6694 (p0) REVERT: B 395 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7503 (m) REVERT: B 414 GLN cc_start: 0.7736 (mp10) cc_final: 0.6913 (mp10) REVERT: B 434 ILE cc_start: 0.8624 (mt) cc_final: 0.8385 (mp) REVERT: B 440 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8198 (tppt) REVERT: B 651 ILE cc_start: 0.8728 (pt) cc_final: 0.8511 (pt) REVERT: B 655 TYR cc_start: 0.8252 (t80) cc_final: 0.7758 (t80) REVERT: B 711 SER cc_start: 0.8333 (t) cc_final: 0.7967 (p) REVERT: B 779 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7570 (tp40) REVERT: B 803 SER cc_start: 0.8540 (m) cc_final: 0.8305 (p) REVERT: B 854 LYS cc_start: 0.8345 (ttpt) cc_final: 0.8024 (ttmm) REVERT: B 868 GLU cc_start: 0.7057 (tp30) cc_final: 0.6646 (tp30) REVERT: B 933 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8171 (mtpp) REVERT: B 964 LYS cc_start: 0.8361 (ttpp) cc_final: 0.7944 (ttmm) REVERT: B 965 GLN cc_start: 0.8298 (mm110) cc_final: 0.8000 (mm-40) REVERT: B 968 SER cc_start: 0.8749 (m) cc_final: 0.8329 (p) REVERT: B 976 VAL cc_start: 0.8464 (t) cc_final: 0.8188 (m) REVERT: B 985 ASP cc_start: 0.7421 (p0) cc_final: 0.7143 (p0) REVERT: B 990 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 993 ILE cc_start: 0.8326 (tp) cc_final: 0.8068 (tp) REVERT: B 994 ASP cc_start: 0.7413 (m-30) cc_final: 0.7110 (t0) REVERT: B 1005 GLN cc_start: 0.7597 (tp40) cc_final: 0.7170 (tp40) REVERT: C 81 ASN cc_start: 0.8209 (p0) cc_final: 0.7985 (p0) REVERT: C 102 ARG cc_start: 0.6036 (mtp85) cc_final: 0.5705 (mtp85) REVERT: C 121 ASN cc_start: 0.6794 (t0) cc_final: 0.5977 (t0) REVERT: C 132 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6379 (tp30) REVERT: C 196 ASP cc_start: 0.7087 (p0) cc_final: 0.6854 (p0) REVERT: C 206 THR cc_start: 0.8600 (t) cc_final: 0.8374 (p) REVERT: C 223 LEU cc_start: 0.8367 (mp) cc_final: 0.8081 (mp) REVERT: C 224 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6986 (mp0) REVERT: C 310 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8190 (ttpt) REVERT: C 385 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (p) REVERT: C 503 VAL cc_start: 0.8457 (t) cc_final: 0.8193 (m) REVERT: C 511 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8168 (t) REVERT: C 532 ASN cc_start: 0.8397 (t0) cc_final: 0.8159 (m-40) REVERT: C 537 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7801 (mtpp) REVERT: C 559 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7929 (t80) REVERT: C 599 THR cc_start: 0.8437 (m) cc_final: 0.8157 (t) REVERT: C 615 VAL cc_start: 0.7909 (t) cc_final: 0.7683 (t) REVERT: C 654 GLU cc_start: 0.7335 (pm20) cc_final: 0.7096 (pm20) REVERT: C 752 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8544 (mp) REVERT: C 776 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7785 (ttpp) REVERT: C 859 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7874 (p) REVERT: C 868 GLU cc_start: 0.6941 (tp30) cc_final: 0.6545 (tp30) REVERT: C 904 TYR cc_start: 0.7393 (m-10) cc_final: 0.6568 (m-10) REVERT: C 933 LYS cc_start: 0.8244 (mttt) cc_final: 0.7987 (mtpt) REVERT: C 960 ASN cc_start: 0.8140 (t0) cc_final: 0.7855 (t0) REVERT: C 993 ILE cc_start: 0.8946 (tp) cc_final: 0.8628 (tp) REVERT: C 1002 GLN cc_start: 0.7241 (tp-100) cc_final: 0.6734 (tp-100) REVERT: C 1005 GLN cc_start: 0.7902 (tp40) cc_final: 0.7447 (tp40) REVERT: C 1017 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6865 (tm-30) REVERT: C 1018 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 1072 GLU cc_start: 0.7754 (pm20) cc_final: 0.7515 (pm20) REVERT: C 1123 SER cc_start: 0.8799 (t) cc_final: 0.8362 (m) REVERT: C 1136 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8316 (p) REVERT: C 1141 LEU cc_start: 0.8505 (mm) cc_final: 0.8242 (mm) REVERT: D 4 LEU cc_start: 0.8091 (mt) cc_final: 0.7888 (mt) REVERT: D 15 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6568 (mmtm) REVERT: E 44 GLN cc_start: 0.7271 (mp10) cc_final: 0.6834 (mp10) REVERT: E 47 LYS cc_start: 0.8633 (ptmm) cc_final: 0.8427 (ptmm) REVERT: E 104 THR cc_start: 0.7925 (m) cc_final: 0.7548 (p) REVERT: F 2 VAL cc_start: 0.8429 (t) cc_final: 0.8101 (p) REVERT: H 84 MET cc_start: 0.3754 (pmm) cc_final: 0.1420 (tpp) outliers start: 195 outliers final: 138 residues processed: 922 average time/residue: 0.4546 time to fit residues: 659.0490 Evaluate side-chains 948 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 793 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 297 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 276 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 359 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 505 HIS ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN G 41 HIS H 79 GLN I 33 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32875 Z= 0.232 Angle : 0.583 12.366 44808 Z= 0.292 Chirality : 0.045 0.392 5143 Planarity : 0.004 0.052 5765 Dihedral : 5.994 75.553 4585 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.52 % Allowed : 16.92 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.18 (0.13), residues: 4110 helix: 0.78 (0.21), residues: 658 sheet: -1.19 (0.16), residues: 993 loop : -2.31 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.004 0.001 HIS B1064 PHE 0.032 0.002 PHE C 429 TYR 0.017 0.001 TYR A1067 ARG 0.010 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 803 time to evaluate : 3.745 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: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7524 (p0) cc_final: 0.6899 (p0) REVERT: A 90 VAL cc_start: 0.8365 (p) cc_final: 0.8132 (t) REVERT: A 116 SER cc_start: 0.8641 (p) cc_final: 0.8373 (m) REVERT: A 121 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.6741 (p0) REVERT: A 205 HIS cc_start: 0.6922 (t-90) cc_final: 0.6705 (t-90) REVERT: A 215 ASP cc_start: 0.7223 (t0) cc_final: 0.6968 (t0) REVERT: A 228 ASP cc_start: 0.7385 (t0) cc_final: 0.6924 (t0) REVERT: A 231 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7974 (pt) REVERT: A 235 ILE cc_start: 0.8432 (mm) cc_final: 0.8118 (tp) REVERT: A 269 TYR cc_start: 0.8076 (m-10) cc_final: 0.7580 (m-10) REVERT: A 287 ASP cc_start: 0.7651 (p0) cc_final: 0.7288 (p0) REVERT: A 332 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 349 SER cc_start: 0.8053 (m) cc_final: 0.7681 (t) REVERT: A 353 TRP cc_start: 0.8749 (p-90) cc_final: 0.8149 (p-90) REVERT: A 355 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7113 (ttm-80) REVERT: A 378 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7376 (mtpt) REVERT: A 392 PHE cc_start: 0.8521 (m-80) cc_final: 0.8121 (m-80) REVERT: A 396 TYR cc_start: 0.7975 (m-10) cc_final: 0.7466 (m-10) REVERT: A 421 TYR cc_start: 0.7418 (m-10) cc_final: 0.6388 (m-80) REVERT: A 440 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7360 (ttpp) REVERT: A 448 ASN cc_start: 0.7885 (t0) cc_final: 0.7354 (t0) REVERT: A 451 TYR cc_start: 0.7166 (m-80) cc_final: 0.6745 (m-80) REVERT: A 465 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6455 (tm-30) REVERT: A 467 ASP cc_start: 0.7516 (t0) cc_final: 0.6598 (p0) REVERT: A 473 TYR cc_start: 0.6957 (t80) cc_final: 0.6529 (t80) REVERT: A 496 SER cc_start: 0.8417 (m) cc_final: 0.8061 (t) REVERT: A 514 SER cc_start: 0.7932 (m) cc_final: 0.7566 (p) REVERT: A 572 THR cc_start: 0.8615 (t) cc_final: 0.8348 (p) REVERT: A 573 THR cc_start: 0.8720 (m) cc_final: 0.8483 (p) REVERT: A 588 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 599 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8296 (p) REVERT: A 649 CYS cc_start: 0.4768 (p) cc_final: 0.4479 (p) REVERT: A 671 CYS cc_start: 0.5436 (m) cc_final: 0.5124 (m) REVERT: A 790 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7873 (mtmm) REVERT: A 921 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7577 (mtpp) REVERT: A 949 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7686 (mm-40) REVERT: A 1010 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7970 (mm-40) REVERT: A 1014 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7341 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 1097 SER cc_start: 0.8179 (t) cc_final: 0.7882 (p) REVERT: A 1107 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6570 (mtm-85) REVERT: B 105 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 189 GLU cc_start: 0.7138 (pt0) cc_final: 0.6825 (pt0) REVERT: B 223 LEU cc_start: 0.8040 (mp) cc_final: 0.7641 (mt) REVERT: B 239 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7038 (tm-30) REVERT: B 241 LEU cc_start: 0.7623 (mt) cc_final: 0.6759 (mp) REVERT: B 273 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7751 (tpp80) REVERT: B 378 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7235 (ptpp) REVERT: B 380 TYR cc_start: 0.7255 (m-10) cc_final: 0.6937 (m-10) REVERT: B 386 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7738 (mmmt) REVERT: B 394 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.6933 (p0) REVERT: B 395 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7513 (m) REVERT: B 414 GLN cc_start: 0.7776 (mp10) cc_final: 0.7021 (mp10) REVERT: B 434 ILE cc_start: 0.8684 (mt) cc_final: 0.8417 (mp) REVERT: B 440 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8137 (tppt) REVERT: B 643 PHE cc_start: 0.8200 (t80) cc_final: 0.7856 (t80) REVERT: B 655 TYR cc_start: 0.8239 (t80) cc_final: 0.7838 (t80) REVERT: B 711 SER cc_start: 0.8425 (t) cc_final: 0.8015 (p) REVERT: B 740 MET cc_start: 0.7398 (tpp) cc_final: 0.7177 (tpp) REVERT: B 751 ASN cc_start: 0.8407 (m-40) cc_final: 0.8198 (m-40) REVERT: B 779 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7540 (tp40) REVERT: B 803 SER cc_start: 0.8561 (m) cc_final: 0.8338 (p) REVERT: B 854 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8059 (ttmm) REVERT: B 868 GLU cc_start: 0.7050 (tp30) cc_final: 0.6666 (tp30) REVERT: B 933 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8145 (mtpp) REVERT: B 964 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7981 (ttmm) REVERT: B 965 GLN cc_start: 0.8275 (mm110) cc_final: 0.7960 (mm-40) REVERT: B 976 VAL cc_start: 0.8516 (t) cc_final: 0.8226 (m) REVERT: B 985 ASP cc_start: 0.7421 (p0) cc_final: 0.7142 (p0) REVERT: B 990 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 993 ILE cc_start: 0.8348 (tp) cc_final: 0.8122 (tp) REVERT: B 994 ASP cc_start: 0.7443 (m-30) cc_final: 0.6986 (t0) REVERT: C 81 ASN cc_start: 0.8269 (p0) cc_final: 0.8021 (p0) REVERT: C 102 ARG cc_start: 0.6107 (mtp85) cc_final: 0.5772 (mtp85) REVERT: C 121 ASN cc_start: 0.6845 (t0) cc_final: 0.6037 (t0) REVERT: C 132 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6333 (tp30) REVERT: C 196 ASP cc_start: 0.7125 (p0) cc_final: 0.6895 (p0) REVERT: C 224 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6986 (mp0) REVERT: C 310 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8230 (ttpt) REVERT: C 324 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6695 (tm-30) REVERT: C 385 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 503 VAL cc_start: 0.8507 (t) cc_final: 0.8268 (m) REVERT: C 511 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8189 (t) REVERT: C 532 ASN cc_start: 0.8462 (t0) cc_final: 0.8194 (m-40) REVERT: C 537 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7874 (mtpp) REVERT: C 599 THR cc_start: 0.8530 (m) cc_final: 0.8240 (t) REVERT: C 654 GLU cc_start: 0.7333 (pm20) cc_final: 0.7084 (pm20) REVERT: C 698 SER cc_start: 0.9012 (t) cc_final: 0.8548 (p) REVERT: C 752 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8569 (mp) REVERT: C 776 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7782 (ttpp) REVERT: C 859 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7883 (p) REVERT: C 868 GLU cc_start: 0.6958 (tp30) cc_final: 0.6557 (tp30) REVERT: C 933 LYS cc_start: 0.8254 (mttt) cc_final: 0.8000 (mtpt) REVERT: C 960 ASN cc_start: 0.8160 (t0) cc_final: 0.7876 (t0) REVERT: C 969 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7881 (ptpp) REVERT: C 993 ILE cc_start: 0.8906 (tp) cc_final: 0.8590 (tp) REVERT: C 1005 GLN cc_start: 0.7921 (tp40) cc_final: 0.7422 (tp40) REVERT: C 1017 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6852 (tm-30) REVERT: C 1018 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7822 (mp) REVERT: C 1072 GLU cc_start: 0.7753 (pm20) cc_final: 0.7514 (pm20) REVERT: C 1123 SER cc_start: 0.8789 (t) cc_final: 0.8333 (m) REVERT: C 1136 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8340 (p) REVERT: D 15 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6333 (mmtm) REVERT: E 44 GLN cc_start: 0.7311 (mp10) cc_final: 0.6853 (mp10) REVERT: E 47 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8426 (ptmm) REVERT: E 104 THR cc_start: 0.7892 (m) cc_final: 0.7537 (p) REVERT: F 2 VAL cc_start: 0.8452 (t) cc_final: 0.8118 (p) REVERT: H 84 MET cc_start: 0.3711 (pmm) cc_final: 0.1255 (tpp) outliers start: 198 outliers final: 148 residues processed: 915 average time/residue: 0.4473 time to fit residues: 646.5095 Evaluate side-chains 946 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 779 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 2.9990 chunk 360 optimal weight: 0.0170 chunk 79 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 132 optimal weight: 0.1980 chunk 210 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 137 ASN A1002 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 607 GLN B 913 GLN B1002 GLN C 505 HIS C 616 ASN C 824 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1134 ASN G 173 ASN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32875 Z= 0.197 Angle : 0.573 15.460 44808 Z= 0.286 Chirality : 0.044 0.389 5143 Planarity : 0.004 0.048 5765 Dihedral : 5.978 75.425 4583 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.49 % Allowed : 17.81 % Favored : 76.70 % 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: -1.99 (0.13), residues: 4110 helix: 1.07 (0.22), residues: 648 sheet: -1.05 (0.16), residues: 997 loop : -2.21 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.013 0.001 HIS C 505 PHE 0.033 0.002 PHE C 429 TYR 0.017 0.001 TYR C 380 ARG 0.010 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 807 time to evaluate : 3.670 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.7532 (p0) cc_final: 0.6888 (p0) REVERT: A 90 VAL cc_start: 0.8359 (p) cc_final: 0.8111 (t) REVERT: A 116 SER cc_start: 0.8666 (p) cc_final: 0.8406 (m) REVERT: A 121 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6691 (p0) REVERT: A 231 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7866 (pt) REVERT: A 269 TYR cc_start: 0.8074 (m-10) cc_final: 0.7582 (m-10) REVERT: A 287 ASP cc_start: 0.7666 (p0) cc_final: 0.7300 (p0) REVERT: A 335 LEU cc_start: 0.8563 (mm) cc_final: 0.8348 (mm) REVERT: A 353 TRP cc_start: 0.8769 (p-90) cc_final: 0.8338 (p-90) REVERT: A 355 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7176 (ttm-80) REVERT: A 378 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7439 (mtpt) REVERT: A 392 PHE cc_start: 0.8556 (m-80) cc_final: 0.8164 (m-80) REVERT: A 421 TYR cc_start: 0.7466 (m-10) cc_final: 0.6481 (m-80) REVERT: A 440 LYS cc_start: 0.7559 (ttpp) cc_final: 0.7268 (ttpp) REVERT: A 448 ASN cc_start: 0.7902 (t0) cc_final: 0.7356 (t0) REVERT: A 451 TYR cc_start: 0.7181 (m-80) cc_final: 0.6672 (m-80) REVERT: A 465 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6644 (tm-30) REVERT: A 473 TYR cc_start: 0.6949 (t80) cc_final: 0.6517 (t80) REVERT: A 514 SER cc_start: 0.7900 (m) cc_final: 0.7495 (p) REVERT: A 573 THR cc_start: 0.8712 (m) cc_final: 0.8429 (p) REVERT: A 588 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8283 (p) REVERT: A 599 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 616 ASN cc_start: 0.6687 (t0) cc_final: 0.6437 (t0) REVERT: A 921 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7576 (mtpp) REVERT: A 947 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8082 (mtpp) REVERT: A 949 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7744 (mm-40) REVERT: A 1014 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7330 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6906 (tm-30) REVERT: A 1097 SER cc_start: 0.8116 (t) cc_final: 0.7828 (p) REVERT: A 1107 ARG cc_start: 0.6950 (mtm-85) cc_final: 0.6650 (mtt-85) REVERT: B 105 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7653 (mp) REVERT: B 189 GLU cc_start: 0.7109 (pt0) cc_final: 0.6789 (pt0) REVERT: B 223 LEU cc_start: 0.8069 (mp) cc_final: 0.7666 (mt) REVERT: B 239 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 273 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7717 (tpp80) REVERT: B 386 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7724 (mmmt) REVERT: B 394 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.6957 (p0) REVERT: B 395 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7557 (m) REVERT: B 414 GLN cc_start: 0.7809 (mp10) cc_final: 0.7142 (mp10) REVERT: B 434 ILE cc_start: 0.8666 (mt) cc_final: 0.8422 (mp) REVERT: B 440 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8120 (tppt) REVERT: B 558 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8402 (mmmm) REVERT: B 643 PHE cc_start: 0.8202 (t80) cc_final: 0.7891 (t80) REVERT: B 655 TYR cc_start: 0.8232 (t80) cc_final: 0.7911 (t80) REVERT: B 711 SER cc_start: 0.8419 (t) cc_final: 0.7995 (p) REVERT: B 751 ASN cc_start: 0.8378 (m-40) cc_final: 0.8166 (m-40) REVERT: B 773 GLU cc_start: 0.6863 (tt0) cc_final: 0.6622 (tt0) REVERT: B 779 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7589 (tp40) REVERT: B 803 SER cc_start: 0.8563 (m) cc_final: 0.8346 (p) REVERT: B 854 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8060 (ttmm) REVERT: B 868 GLU cc_start: 0.7051 (tp30) cc_final: 0.6671 (tp30) REVERT: B 933 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8096 (mtpp) REVERT: B 964 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7986 (ttmm) REVERT: B 965 GLN cc_start: 0.8264 (mm110) cc_final: 0.7936 (mm-40) REVERT: B 976 VAL cc_start: 0.8504 (t) cc_final: 0.8196 (m) REVERT: B 985 ASP cc_start: 0.7419 (p0) cc_final: 0.7133 (p0) REVERT: B 990 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6884 (mm-30) REVERT: B 993 ILE cc_start: 0.8334 (tp) cc_final: 0.8127 (tp) REVERT: B 994 ASP cc_start: 0.7431 (m-30) cc_final: 0.6962 (t0) REVERT: B 1005 GLN cc_start: 0.7684 (tp40) cc_final: 0.7087 (tp40) REVERT: B 1014 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7574 (mtm-85) REVERT: B 1141 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8059 (mp) REVERT: C 29 THR cc_start: 0.8731 (t) cc_final: 0.7606 (p) REVERT: C 81 ASN cc_start: 0.8235 (p0) cc_final: 0.8022 (p0) REVERT: C 102 ARG cc_start: 0.6092 (mtp85) cc_final: 0.5757 (mtp85) REVERT: C 121 ASN cc_start: 0.6872 (t0) cc_final: 0.6092 (t0) REVERT: C 132 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6437 (tp30) REVERT: C 196 ASP cc_start: 0.7096 (p0) cc_final: 0.6874 (p0) REVERT: C 224 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6738 (mm-30) REVERT: C 281 GLU cc_start: 0.7039 (pp20) cc_final: 0.6690 (pp20) REVERT: C 310 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8226 (ttpt) REVERT: C 340 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6916 (mm-30) REVERT: C 385 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8450 (p) REVERT: C 417 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7239 (m-40) REVERT: C 503 VAL cc_start: 0.8369 (t) cc_final: 0.8085 (m) REVERT: C 511 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8166 (t) REVERT: C 532 ASN cc_start: 0.8465 (t0) cc_final: 0.8236 (m-40) REVERT: C 537 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7880 (mtpp) REVERT: C 543 PHE cc_start: 0.8064 (m-10) cc_final: 0.7789 (m-10) REVERT: C 599 THR cc_start: 0.8530 (m) cc_final: 0.8250 (t) REVERT: C 654 GLU cc_start: 0.7332 (pm20) cc_final: 0.7125 (pm20) REVERT: C 698 SER cc_start: 0.9018 (t) cc_final: 0.8556 (p) REVERT: C 752 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8536 (mp) REVERT: C 776 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7810 (ttpp) REVERT: C 859 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7900 (p) REVERT: C 868 GLU cc_start: 0.6950 (tp30) cc_final: 0.6544 (tp30) REVERT: C 933 LYS cc_start: 0.8274 (mttt) cc_final: 0.7990 (mtpt) REVERT: C 960 ASN cc_start: 0.8165 (t0) cc_final: 0.7895 (t0) REVERT: C 969 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7872 (ptpp) REVERT: C 993 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8553 (tp) REVERT: C 1005 GLN cc_start: 0.7898 (tp40) cc_final: 0.7390 (tp40) REVERT: C 1017 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6891 (tm-30) REVERT: C 1018 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7832 (mp) REVERT: C 1123 SER cc_start: 0.8750 (t) cc_final: 0.8333 (m) REVERT: C 1136 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8336 (p) REVERT: C 1144 GLU cc_start: 0.7088 (pp20) cc_final: 0.6765 (pp20) REVERT: D 15 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6444 (mmtm) REVERT: D 59 LYS cc_start: 0.7992 (mttp) cc_final: 0.7523 (mttp) REVERT: E 44 GLN cc_start: 0.7301 (mp10) cc_final: 0.6852 (mp10) REVERT: E 104 THR cc_start: 0.7902 (m) cc_final: 0.7564 (p) REVERT: F 2 VAL cc_start: 0.8468 (t) cc_final: 0.8140 (p) REVERT: F 105 THR cc_start: 0.6660 (t) cc_final: 0.6381 (m) REVERT: H 84 MET cc_start: 0.3774 (pmm) cc_final: 0.1169 (tpp) REVERT: I 18 ILE cc_start: 0.6824 (mm) cc_final: 0.6467 (mt) outliers start: 197 outliers final: 145 residues processed: 920 average time/residue: 0.4466 time to fit residues: 647.3879 Evaluate side-chains 953 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 788 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 317 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 616 ASN C 824 ASN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32875 Z= 0.330 Angle : 0.625 13.953 44808 Z= 0.315 Chirality : 0.046 0.367 5143 Planarity : 0.004 0.050 5765 Dihedral : 6.139 74.758 4577 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.46 % Allowed : 18.51 % Favored : 76.03 % 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: -2.02 (0.13), residues: 4110 helix: 0.75 (0.21), residues: 672 sheet: -1.11 (0.15), residues: 1061 loop : -2.15 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 64 HIS 0.007 0.001 HIS B1064 PHE 0.036 0.002 PHE C 429 TYR 0.025 0.002 TYR A 495 ARG 0.009 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 805 time to evaluate : 3.618 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: A 87 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7103 (p0) REVERT: A 90 VAL cc_start: 0.8402 (p) cc_final: 0.8101 (t) REVERT: A 116 SER cc_start: 0.8554 (p) cc_final: 0.8353 (m) REVERT: A 120 VAL cc_start: 0.7556 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 121 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6883 (p0) REVERT: A 235 ILE cc_start: 0.8446 (mm) cc_final: 0.8180 (tp) REVERT: A 269 TYR cc_start: 0.8123 (m-10) cc_final: 0.7681 (m-10) REVERT: A 287 ASP cc_start: 0.7692 (p0) cc_final: 0.7300 (p0) REVERT: A 301 CYS cc_start: 0.7622 (m) cc_final: 0.7320 (m) REVERT: A 335 LEU cc_start: 0.8682 (mm) cc_final: 0.8449 (mm) REVERT: A 353 TRP cc_start: 0.8796 (p-90) cc_final: 0.8344 (p-90) REVERT: A 355 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7224 (ttm-80) REVERT: A 378 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7499 (mtpt) REVERT: A 392 PHE cc_start: 0.8622 (m-80) cc_final: 0.8138 (m-80) REVERT: A 408 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7220 (ttp80) REVERT: A 421 TYR cc_start: 0.7628 (m-10) cc_final: 0.6592 (m-80) REVERT: A 440 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7427 (ttpp) REVERT: A 448 ASN cc_start: 0.7831 (t0) cc_final: 0.7370 (t0) REVERT: A 451 TYR cc_start: 0.7275 (m-80) cc_final: 0.6696 (m-80) REVERT: A 465 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6662 (tm-30) REVERT: A 473 TYR cc_start: 0.7022 (t80) cc_final: 0.6620 (t80) REVERT: A 514 SER cc_start: 0.8007 (m) cc_final: 0.7590 (p) REVERT: A 588 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8416 (p) REVERT: A 697 MET cc_start: 0.7660 (ttm) cc_final: 0.7380 (mtp) REVERT: A 921 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7647 (mtpp) REVERT: A 947 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8082 (mtpp) REVERT: A 949 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7737 (mm-40) REVERT: A 1014 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7327 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 1097 SER cc_start: 0.8162 (t) cc_final: 0.7887 (p) REVERT: A 1107 ARG cc_start: 0.7016 (mtm-85) cc_final: 0.6766 (mtt-85) REVERT: B 105 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 189 GLU cc_start: 0.7128 (pt0) cc_final: 0.6833 (pt0) REVERT: B 223 LEU cc_start: 0.8123 (mp) cc_final: 0.7696 (mt) REVERT: B 239 GLN cc_start: 0.7529 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 273 ARG cc_start: 0.8000 (tpp80) cc_final: 0.7751 (tpp80) REVERT: B 360 ASN cc_start: 0.7792 (m110) cc_final: 0.7547 (m110) REVERT: B 386 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7863 (mmmt) REVERT: B 394 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7024 (p0) REVERT: B 395 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7622 (m) REVERT: B 400 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6398 (p90) REVERT: B 414 GLN cc_start: 0.7817 (mp10) cc_final: 0.7195 (mp10) REVERT: B 433 VAL cc_start: 0.8732 (t) cc_final: 0.8282 (p) REVERT: B 434 ILE cc_start: 0.8698 (mt) cc_final: 0.8415 (mp) REVERT: B 440 LYS cc_start: 0.8447 (ttpp) cc_final: 0.8170 (tppt) REVERT: B 581 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 643 PHE cc_start: 0.8264 (t80) cc_final: 0.7906 (t80) REVERT: B 711 SER cc_start: 0.8510 (t) cc_final: 0.8063 (p) REVERT: B 751 ASN cc_start: 0.8428 (m-40) cc_final: 0.8218 (m-40) REVERT: B 773 GLU cc_start: 0.6918 (tt0) cc_final: 0.6674 (tt0) REVERT: B 779 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7759 (tp40) REVERT: B 854 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8127 (ttmm) REVERT: B 868 GLU cc_start: 0.7066 (tp30) cc_final: 0.6709 (tp30) REVERT: B 900 MET cc_start: 0.7799 (mtp) cc_final: 0.7586 (mtm) REVERT: B 933 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8151 (mtpp) REVERT: B 964 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8026 (ttmm) REVERT: B 965 GLN cc_start: 0.8219 (mm110) cc_final: 0.8001 (mm-40) REVERT: B 976 VAL cc_start: 0.8554 (t) cc_final: 0.8219 (m) REVERT: B 985 ASP cc_start: 0.7458 (p0) cc_final: 0.7157 (p0) REVERT: B 990 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6991 (mm-30) REVERT: B 994 ASP cc_start: 0.7472 (m-30) cc_final: 0.7009 (t0) REVERT: B 1005 GLN cc_start: 0.7716 (tp40) cc_final: 0.7016 (tp40) REVERT: B 1014 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7569 (mtm-85) REVERT: C 81 ASN cc_start: 0.8247 (p0) cc_final: 0.8023 (p0) REVERT: C 102 ARG cc_start: 0.6159 (mtp85) cc_final: 0.5833 (mtp85) REVERT: C 121 ASN cc_start: 0.6857 (t0) cc_final: 0.6076 (t0) REVERT: C 196 ASP cc_start: 0.7197 (p0) cc_final: 0.6986 (p0) REVERT: C 281 GLU cc_start: 0.7082 (pp20) cc_final: 0.6738 (pp20) REVERT: C 385 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8606 (p) REVERT: C 467 ASP cc_start: 0.7518 (p0) cc_final: 0.7008 (p0) REVERT: C 511 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8209 (t) REVERT: C 543 PHE cc_start: 0.8119 (m-10) cc_final: 0.7876 (m-10) REVERT: C 698 SER cc_start: 0.9089 (t) cc_final: 0.8593 (p) REVERT: C 752 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8597 (mp) REVERT: C 776 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7846 (ttpp) REVERT: C 859 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7932 (p) REVERT: C 868 GLU cc_start: 0.6981 (tp30) cc_final: 0.6580 (tp30) REVERT: C 933 LYS cc_start: 0.8287 (mttt) cc_final: 0.8015 (mtpt) REVERT: C 960 ASN cc_start: 0.8207 (t0) cc_final: 0.7959 (t0) REVERT: C 969 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7974 (ptpp) REVERT: C 993 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8525 (tp) REVERT: C 1005 GLN cc_start: 0.7976 (tp40) cc_final: 0.7642 (tp40) REVERT: C 1017 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6906 (tm-30) REVERT: C 1018 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7876 (mp) REVERT: C 1123 SER cc_start: 0.8736 (t) cc_final: 0.8387 (m) REVERT: C 1144 GLU cc_start: 0.7232 (pp20) cc_final: 0.6952 (pp20) REVERT: D 15 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6430 (mmtm) REVERT: D 59 LYS cc_start: 0.8176 (mttp) cc_final: 0.7728 (mttp) REVERT: D 182 LEU cc_start: 0.8142 (mt) cc_final: 0.7790 (mt) REVERT: E 19 THR cc_start: 0.8345 (p) cc_final: 0.7983 (p) REVERT: E 44 GLN cc_start: 0.7317 (mp10) cc_final: 0.6870 (mp10) REVERT: E 104 THR cc_start: 0.7970 (m) cc_final: 0.7470 (p) REVERT: F 2 VAL cc_start: 0.8496 (t) cc_final: 0.8169 (p) REVERT: I 18 ILE cc_start: 0.6843 (mm) cc_final: 0.6467 (mt) outliers start: 196 outliers final: 150 residues processed: 910 average time/residue: 0.4538 time to fit residues: 648.4463 Evaluate side-chains 950 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 781 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 253 optimal weight: 0.5980 chunk 271 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 762 GLN A 901 GLN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 954 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 607 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1134 ASN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32875 Z= 0.220 Angle : 0.596 19.283 44808 Z= 0.299 Chirality : 0.045 0.379 5143 Planarity : 0.004 0.051 5765 Dihedral : 6.063 74.979 4576 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.13 % Allowed : 19.62 % Favored : 75.25 % 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: -1.83 (0.13), residues: 4110 helix: 0.89 (0.21), residues: 685 sheet: -0.94 (0.16), residues: 1018 loop : -2.07 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 49 HIS 0.004 0.001 HIS B1064 PHE 0.036 0.002 PHE C 429 TYR 0.016 0.001 TYR A1067 ARG 0.010 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 786 time to evaluate : 3.647 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: symmetry clash REVERT: A 87 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7095 (p0) REVERT: A 90 VAL cc_start: 0.8364 (p) cc_final: 0.8086 (t) REVERT: A 115 GLN cc_start: 0.7603 (mp10) cc_final: 0.7188 (mm-40) REVERT: A 116 SER cc_start: 0.8628 (p) cc_final: 0.8355 (m) REVERT: A 120 VAL cc_start: 0.7581 (t) cc_final: 0.7329 (p) REVERT: A 121 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6873 (p0) REVERT: A 269 TYR cc_start: 0.8109 (m-10) cc_final: 0.7648 (m-10) REVERT: A 287 ASP cc_start: 0.7694 (p0) cc_final: 0.7285 (p0) REVERT: A 301 CYS cc_start: 0.7510 (m) cc_final: 0.7200 (m) REVERT: A 335 LEU cc_start: 0.8633 (mm) cc_final: 0.8387 (mm) REVERT: A 353 TRP cc_start: 0.8778 (p-90) cc_final: 0.8292 (p-90) REVERT: A 355 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7214 (ttm-80) REVERT: A 378 LYS cc_start: 0.7608 (mtpt) cc_final: 0.7260 (mtpt) REVERT: A 392 PHE cc_start: 0.8571 (m-80) cc_final: 0.8168 (m-80) REVERT: A 421 TYR cc_start: 0.7550 (m-10) cc_final: 0.6525 (m-80) REVERT: A 440 LYS cc_start: 0.7558 (ttpp) cc_final: 0.7250 (ttpp) REVERT: A 448 ASN cc_start: 0.7844 (t0) cc_final: 0.7433 (t0) REVERT: A 451 TYR cc_start: 0.7248 (m-80) cc_final: 0.6697 (m-80) REVERT: A 465 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6696 (tm-30) REVERT: A 473 TYR cc_start: 0.6991 (t80) cc_final: 0.6597 (t80) REVERT: A 514 SER cc_start: 0.7969 (m) cc_final: 0.7517 (p) REVERT: A 588 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 599 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 855 PHE cc_start: 0.8396 (m-10) cc_final: 0.8180 (m-80) REVERT: A 921 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7640 (mtpp) REVERT: A 947 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8090 (mtpp) REVERT: A 949 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7761 (mm-40) REVERT: A 1002 GLN cc_start: 0.7072 (mt0) cc_final: 0.6736 (mt0) REVERT: A 1014 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7321 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6924 (tm-30) REVERT: A 1031 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 1034 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8749 (mt) REVERT: A 1097 SER cc_start: 0.8101 (t) cc_final: 0.7806 (p) REVERT: A 1107 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6743 (mtt-85) REVERT: B 105 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7624 (mp) REVERT: B 189 GLU cc_start: 0.7110 (pt0) cc_final: 0.6795 (pt0) REVERT: B 223 LEU cc_start: 0.8108 (mp) cc_final: 0.7672 (mt) REVERT: B 239 GLN cc_start: 0.7558 (tm-30) cc_final: 0.6994 (tm-30) REVERT: B 273 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7745 (tpp80) REVERT: B 334 ASN cc_start: 0.7740 (t0) cc_final: 0.7483 (t0) REVERT: B 386 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7893 (mmmt) REVERT: B 394 ASN cc_start: 0.7602 (p0) cc_final: 0.7053 (p0) REVERT: B 395 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7670 (m) REVERT: B 400 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6408 (p90) REVERT: B 414 GLN cc_start: 0.7916 (mp10) cc_final: 0.7258 (mp10) REVERT: B 433 VAL cc_start: 0.8737 (t) cc_final: 0.8319 (p) REVERT: B 434 ILE cc_start: 0.8655 (mt) cc_final: 0.8378 (mp) REVERT: B 440 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8095 (tppt) REVERT: B 581 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7816 (p) REVERT: B 643 PHE cc_start: 0.8279 (t80) cc_final: 0.7838 (t80) REVERT: B 711 SER cc_start: 0.8463 (t) cc_final: 0.8008 (p) REVERT: B 773 GLU cc_start: 0.6869 (tt0) cc_final: 0.6638 (tt0) REVERT: B 779 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7791 (tp40) REVERT: B 854 LYS cc_start: 0.8311 (ttpt) cc_final: 0.8073 (ttmm) REVERT: B 868 GLU cc_start: 0.7063 (tp30) cc_final: 0.6705 (tp30) REVERT: B 900 MET cc_start: 0.7774 (mtp) cc_final: 0.7568 (mtm) REVERT: B 933 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8082 (mtpp) REVERT: B 964 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8009 (ttmm) REVERT: B 965 GLN cc_start: 0.8214 (mm110) cc_final: 0.8006 (mm-40) REVERT: B 976 VAL cc_start: 0.8550 (t) cc_final: 0.8228 (m) REVERT: B 985 ASP cc_start: 0.7459 (p0) cc_final: 0.7168 (p0) REVERT: B 990 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 994 ASP cc_start: 0.7314 (m-30) cc_final: 0.6910 (t0) REVERT: B 1005 GLN cc_start: 0.7685 (tp40) cc_final: 0.7089 (tp40) REVERT: B 1014 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7578 (mtm-85) REVERT: B 1141 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8235 (mt) REVERT: C 29 THR cc_start: 0.8660 (t) cc_final: 0.7349 (p) REVERT: C 102 ARG cc_start: 0.6135 (mtp85) cc_final: 0.5797 (mtp85) REVERT: C 121 ASN cc_start: 0.6883 (t0) cc_final: 0.6096 (t0) REVERT: C 188 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7114 (mtt90) REVERT: C 189 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6713 (mt-10) REVERT: C 269 TYR cc_start: 0.8018 (m-80) cc_final: 0.7815 (m-80) REVERT: C 281 GLU cc_start: 0.7062 (pp20) cc_final: 0.6745 (pp20) REVERT: C 385 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8591 (p) REVERT: C 511 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8178 (t) REVERT: C 543 PHE cc_start: 0.8077 (m-10) cc_final: 0.7875 (m-10) REVERT: C 654 GLU cc_start: 0.7315 (pm20) cc_final: 0.7024 (pm20) REVERT: C 698 SER cc_start: 0.9063 (t) cc_final: 0.8557 (p) REVERT: C 776 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7848 (ttpp) REVERT: C 859 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7929 (p) REVERT: C 868 GLU cc_start: 0.6948 (tp30) cc_final: 0.6546 (tp30) REVERT: C 933 LYS cc_start: 0.8289 (mttt) cc_final: 0.8017 (mtpt) REVERT: C 960 ASN cc_start: 0.8174 (t0) cc_final: 0.7907 (t0) REVERT: C 993 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8507 (tp) REVERT: C 1005 GLN cc_start: 0.7936 (tp40) cc_final: 0.7408 (tp40) REVERT: C 1017 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6930 (tm-30) REVERT: C 1018 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7860 (mp) REVERT: C 1123 SER cc_start: 0.8672 (t) cc_final: 0.8293 (m) REVERT: C 1144 GLU cc_start: 0.7195 (pp20) cc_final: 0.6938 (pp20) REVERT: D 15 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6487 (mmtm) REVERT: D 59 LYS cc_start: 0.8123 (mttp) cc_final: 0.7677 (mttp) REVERT: E 34 TYR cc_start: 0.8216 (m-80) cc_final: 0.7850 (m-80) REVERT: E 44 GLN cc_start: 0.7339 (mp10) cc_final: 0.6886 (mp10) REVERT: E 84 ASP cc_start: 0.8097 (t0) cc_final: 0.7683 (t0) REVERT: E 104 THR cc_start: 0.7869 (m) cc_final: 0.7468 (p) REVERT: F 2 VAL cc_start: 0.8471 (t) cc_final: 0.8131 (p) REVERT: H 84 MET cc_start: 0.4215 (pmm) cc_final: 0.0937 (tpp) REVERT: I 18 ILE cc_start: 0.6726 (mm) cc_final: 0.6360 (mt) outliers start: 184 outliers final: 144 residues processed: 891 average time/residue: 0.4645 time to fit residues: 652.6073 Evaluate side-chains 937 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 776 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 20.0000 chunk 382 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 chunk 371 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 114 optimal weight: 0.0170 chunk 336 optimal weight: 3.9990 chunk 351 optimal weight: 20.0000 chunk 370 optimal weight: 8.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 762 GLN A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 271 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 751 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1134 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 32875 Z= 0.367 Angle : 0.657 18.630 44808 Z= 0.333 Chirality : 0.047 0.349 5143 Planarity : 0.005 0.057 5765 Dihedral : 6.218 74.509 4572 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.04 % Allowed : 19.76 % Favored : 75.20 % 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: -1.87 (0.13), residues: 4110 helix: 0.75 (0.21), residues: 687 sheet: -1.01 (0.15), residues: 1076 loop : -2.04 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 64 HIS 0.008 0.001 HIS B1064 PHE 0.040 0.002 PHE C 429 TYR 0.022 0.002 TYR C 453 ARG 0.008 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 810 time to evaluate : 3.290 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: symmetry clash REVERT: A 87 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7309 (p0) REVERT: A 90 VAL cc_start: 0.8402 (p) cc_final: 0.8096 (t) REVERT: A 171 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.8008 (t) REVERT: A 188 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6597 (ttm-80) REVERT: A 228 ASP cc_start: 0.7500 (t0) cc_final: 0.6919 (t70) REVERT: A 269 TYR cc_start: 0.8153 (m-10) cc_final: 0.7770 (m-10) REVERT: A 287 ASP cc_start: 0.7725 (p0) cc_final: 0.7303 (p0) REVERT: A 301 CYS cc_start: 0.7587 (m) cc_final: 0.7286 (m) REVERT: A 335 LEU cc_start: 0.8774 (mm) cc_final: 0.8540 (mm) REVERT: A 353 TRP cc_start: 0.8762 (p-90) cc_final: 0.8255 (p-90) REVERT: A 355 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7256 (ttm-80) REVERT: A 378 LYS cc_start: 0.7625 (mtpt) cc_final: 0.7293 (mtpt) REVERT: A 421 TYR cc_start: 0.7661 (m-10) cc_final: 0.6490 (m-80) REVERT: A 440 LYS cc_start: 0.7665 (ttpp) cc_final: 0.7352 (ttpp) REVERT: A 448 ASN cc_start: 0.7859 (t0) cc_final: 0.7378 (t0) REVERT: A 451 TYR cc_start: 0.7279 (m-80) cc_final: 0.6680 (m-80) REVERT: A 465 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6664 (tm-30) REVERT: A 473 TYR cc_start: 0.7039 (t80) cc_final: 0.6645 (t80) REVERT: A 514 SER cc_start: 0.7995 (m) cc_final: 0.7578 (p) REVERT: A 588 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 779 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7762 (tp40) REVERT: A 921 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7727 (mtpp) REVERT: A 947 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8093 (mtpp) REVERT: A 1014 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7338 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6914 (tm-30) REVERT: A 1031 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7262 (mt-10) REVERT: A 1097 SER cc_start: 0.8175 (t) cc_final: 0.7899 (p) REVERT: B 83 VAL cc_start: 0.7525 (t) cc_final: 0.7324 (t) REVERT: B 105 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7510 (mp) REVERT: B 117 LEU cc_start: 0.8495 (tt) cc_final: 0.8102 (tt) REVERT: B 189 GLU cc_start: 0.7141 (pt0) cc_final: 0.6854 (pt0) REVERT: B 223 LEU cc_start: 0.8107 (mp) cc_final: 0.7709 (mt) REVERT: B 226 LEU cc_start: 0.8270 (tp) cc_final: 0.7981 (mt) REVERT: B 237 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7761 (mtp85) REVERT: B 239 GLN cc_start: 0.7571 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 241 LEU cc_start: 0.7650 (mt) cc_final: 0.6660 (mt) REVERT: B 334 ASN cc_start: 0.7785 (t0) cc_final: 0.7337 (t0) REVERT: B 386 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7887 (mmmt) REVERT: B 394 ASN cc_start: 0.7535 (p0) cc_final: 0.7092 (p0) REVERT: B 395 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7665 (m) REVERT: B 400 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6625 (p90) REVERT: B 414 GLN cc_start: 0.7959 (mp10) cc_final: 0.7274 (mp10) REVERT: B 433 VAL cc_start: 0.8788 (t) cc_final: 0.8395 (p) REVERT: B 434 ILE cc_start: 0.8695 (mt) cc_final: 0.8455 (mp) REVERT: B 440 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8153 (tppt) REVERT: B 581 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 643 PHE cc_start: 0.8309 (t80) cc_final: 0.7902 (t80) REVERT: B 711 SER cc_start: 0.8517 (t) cc_final: 0.8080 (p) REVERT: B 759 PHE cc_start: 0.6831 (t80) cc_final: 0.6163 (t80) REVERT: B 773 GLU cc_start: 0.6925 (tt0) cc_final: 0.6679 (tt0) REVERT: B 779 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7795 (tp40) REVERT: B 854 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8095 (ttmm) REVERT: B 868 GLU cc_start: 0.7081 (tp30) cc_final: 0.6754 (tp30) REVERT: B 900 MET cc_start: 0.7805 (mtp) cc_final: 0.7597 (mtm) REVERT: B 933 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8144 (mtpp) REVERT: B 964 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8038 (ttmm) REVERT: B 976 VAL cc_start: 0.8586 (t) cc_final: 0.8230 (m) REVERT: B 985 ASP cc_start: 0.7458 (p0) cc_final: 0.7162 (p0) REVERT: B 994 ASP cc_start: 0.7386 (m-30) cc_final: 0.6964 (t0) REVERT: B 1005 GLN cc_start: 0.7739 (tp40) cc_final: 0.7109 (tp40) REVERT: C 80 ASP cc_start: 0.6388 (p0) cc_final: 0.5648 (p0) REVERT: C 102 ARG cc_start: 0.6215 (mtp85) cc_final: 0.5900 (mtp85) REVERT: C 121 ASN cc_start: 0.6895 (t0) cc_final: 0.6211 (t0) REVERT: C 269 TYR cc_start: 0.8042 (m-80) cc_final: 0.7741 (m-80) REVERT: C 281 GLU cc_start: 0.7075 (pp20) cc_final: 0.6751 (pp20) REVERT: C 385 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8611 (p) REVERT: C 420 ASP cc_start: 0.6865 (p0) cc_final: 0.6547 (p0) REVERT: C 467 ASP cc_start: 0.7511 (p0) cc_final: 0.7027 (p0) REVERT: C 511 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8217 (t) REVERT: C 516 GLU cc_start: 0.6421 (mp0) cc_final: 0.6097 (mp0) REVERT: C 599 THR cc_start: 0.8535 (m) cc_final: 0.8305 (t) REVERT: C 654 GLU cc_start: 0.7282 (pm20) cc_final: 0.6985 (pm20) REVERT: C 698 SER cc_start: 0.9089 (t) cc_final: 0.8560 (p) REVERT: C 776 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7882 (ttpp) REVERT: C 859 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 868 GLU cc_start: 0.6968 (tp30) cc_final: 0.6576 (tp30) REVERT: C 933 LYS cc_start: 0.8318 (mttt) cc_final: 0.8043 (mtpt) REVERT: C 960 ASN cc_start: 0.8225 (t0) cc_final: 0.7961 (t0) REVERT: C 969 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8054 (ptpp) REVERT: C 976 VAL cc_start: 0.8498 (t) cc_final: 0.8153 (m) REVERT: C 984 LEU cc_start: 0.8715 (tp) cc_final: 0.8499 (tp) REVERT: C 993 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8498 (tp) REVERT: C 994 ASP cc_start: 0.7804 (t70) cc_final: 0.7476 (t70) REVERT: C 1017 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6908 (tm-30) REVERT: C 1018 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.7878 (mp) REVERT: C 1091 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7165 (mtt180) REVERT: C 1123 SER cc_start: 0.8675 (t) cc_final: 0.8332 (m) REVERT: C 1144 GLU cc_start: 0.7440 (pp20) cc_final: 0.6955 (pp20) REVERT: D 15 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6449 (mmtm) REVERT: D 56 ASP cc_start: 0.7808 (p0) cc_final: 0.7564 (p0) REVERT: D 59 LYS cc_start: 0.8252 (mttp) cc_final: 0.7957 (mttp) REVERT: D 72 THR cc_start: 0.8259 (t) cc_final: 0.8035 (p) REVERT: D 182 LEU cc_start: 0.8192 (mt) cc_final: 0.7826 (mt) REVERT: E 34 TYR cc_start: 0.8300 (m-80) cc_final: 0.7985 (m-80) REVERT: E 44 GLN cc_start: 0.7358 (mp10) cc_final: 0.6883 (mp10) REVERT: E 104 THR cc_start: 0.7736 (m) cc_final: 0.7385 (p) REVERT: F 2 VAL cc_start: 0.8497 (t) cc_final: 0.8171 (p) REVERT: I 18 ILE cc_start: 0.6714 (mm) cc_final: 0.6391 (mt) outliers start: 181 outliers final: 144 residues processed: 908 average time/residue: 0.4903 time to fit residues: 705.1811 Evaluate side-chains 948 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 789 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 2.9990 chunk 393 optimal weight: 0.7980 chunk 239 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 412 optimal weight: 2.9990 chunk 379 optimal weight: 0.0970 chunk 328 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 201 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 955 ASN B 965 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 901 GLN C 935 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32875 Z= 0.186 Angle : 0.621 16.942 44808 Z= 0.309 Chirality : 0.045 0.256 5143 Planarity : 0.004 0.054 5765 Dihedral : 6.051 75.096 4567 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.10 % Favored : 92.87 % Rotamer: Outliers : 4.12 % Allowed : 21.04 % Favored : 74.83 % 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: -1.66 (0.13), residues: 4110 helix: 1.00 (0.21), residues: 681 sheet: -0.89 (0.15), residues: 1072 loop : -1.92 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 38 HIS 0.004 0.001 HIS C1101 PHE 0.036 0.002 PHE C 429 TYR 0.025 0.001 TYR C 170 ARG 0.007 0.000 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 773 time to evaluate : 3.725 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: symmetry clash REVERT: A 87 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7299 (p0) REVERT: A 90 VAL cc_start: 0.8355 (p) cc_final: 0.8062 (t) REVERT: A 99 ASN cc_start: 0.7686 (m-40) cc_final: 0.7298 (t160) REVERT: A 115 GLN cc_start: 0.7626 (mp10) cc_final: 0.7279 (mm-40) REVERT: A 188 ARG cc_start: 0.6966 (ttm-80) cc_final: 0.6587 (ttm-80) REVERT: A 269 TYR cc_start: 0.8095 (m-10) cc_final: 0.7673 (m-10) REVERT: A 287 ASP cc_start: 0.7697 (p0) cc_final: 0.7266 (p0) REVERT: A 301 CYS cc_start: 0.7476 (m) cc_final: 0.7154 (m) REVERT: A 335 LEU cc_start: 0.8648 (mm) cc_final: 0.8403 (mm) REVERT: A 353 TRP cc_start: 0.8758 (p-90) cc_final: 0.8284 (p-90) REVERT: A 355 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7216 (ttm-80) REVERT: A 378 LYS cc_start: 0.7503 (mtpt) cc_final: 0.7177 (mtpt) REVERT: A 392 PHE cc_start: 0.8410 (m-80) cc_final: 0.8123 (m-80) REVERT: A 421 TYR cc_start: 0.7594 (m-10) cc_final: 0.6568 (m-80) REVERT: A 440 LYS cc_start: 0.7434 (ttpp) cc_final: 0.7122 (ttpp) REVERT: A 448 ASN cc_start: 0.7874 (t0) cc_final: 0.7495 (t0) REVERT: A 451 TYR cc_start: 0.7242 (m-80) cc_final: 0.6688 (m-80) REVERT: A 465 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6666 (tm-30) REVERT: A 473 TYR cc_start: 0.6949 (t80) cc_final: 0.6569 (t80) REVERT: A 514 SER cc_start: 0.7966 (m) cc_final: 0.7524 (p) REVERT: A 725 GLU cc_start: 0.6977 (tt0) cc_final: 0.6743 (tt0) REVERT: A 779 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7749 (tp40) REVERT: A 947 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8067 (mtpp) REVERT: A 949 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7747 (mm-40) REVERT: A 1002 GLN cc_start: 0.7075 (mt0) cc_final: 0.6706 (mt0) REVERT: A 1014 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7312 (mtm-85) REVERT: A 1017 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6937 (tm-30) REVERT: A 1097 SER cc_start: 0.8065 (t) cc_final: 0.7762 (p) REVERT: B 105 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7618 (mp) REVERT: B 189 GLU cc_start: 0.7093 (pt0) cc_final: 0.6770 (pt0) REVERT: B 223 LEU cc_start: 0.8098 (mp) cc_final: 0.7670 (mt) REVERT: B 237 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7765 (mtp85) REVERT: B 239 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7008 (tm-30) REVERT: B 270 LEU cc_start: 0.8715 (mp) cc_final: 0.8504 (mt) REVERT: B 334 ASN cc_start: 0.7736 (t0) cc_final: 0.7082 (t0) REVERT: B 386 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7848 (mmmt) REVERT: B 395 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7698 (m) REVERT: B 400 PHE cc_start: 0.7298 (p90) cc_final: 0.6543 (p90) REVERT: B 414 GLN cc_start: 0.7943 (mp10) cc_final: 0.7451 (mp10) REVERT: B 433 VAL cc_start: 0.8750 (t) cc_final: 0.8373 (p) REVERT: B 434 ILE cc_start: 0.8626 (mt) cc_final: 0.8380 (mp) REVERT: B 437 ASN cc_start: 0.8011 (t0) cc_final: 0.7634 (t0) REVERT: B 440 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8067 (tppt) REVERT: B 581 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7831 (p) REVERT: B 643 PHE cc_start: 0.8291 (t80) cc_final: 0.7911 (t80) REVERT: B 711 SER cc_start: 0.8398 (t) cc_final: 0.7994 (p) REVERT: B 773 GLU cc_start: 0.6847 (tt0) cc_final: 0.6618 (tt0) REVERT: B 779 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7761 (tp40) REVERT: B 825 LYS cc_start: 0.8520 (mttm) cc_final: 0.8186 (mttt) REVERT: B 854 LYS cc_start: 0.8244 (ttpt) cc_final: 0.8012 (ttmm) REVERT: B 868 GLU cc_start: 0.7062 (tp30) cc_final: 0.6720 (tp30) REVERT: B 900 MET cc_start: 0.7743 (mtp) cc_final: 0.7521 (mtm) REVERT: B 933 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8093 (mtpp) REVERT: B 964 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7961 (ttmm) REVERT: B 976 VAL cc_start: 0.8535 (t) cc_final: 0.8185 (m) REVERT: B 985 ASP cc_start: 0.7449 (p0) cc_final: 0.7168 (p0) REVERT: B 994 ASP cc_start: 0.7279 (m-30) cc_final: 0.6875 (t0) REVERT: B 1005 GLN cc_start: 0.7664 (tp40) cc_final: 0.7114 (tp40) REVERT: B 1014 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7553 (mtm-85) REVERT: C 80 ASP cc_start: 0.6340 (p0) cc_final: 0.5620 (p0) REVERT: C 102 ARG cc_start: 0.6140 (mtp85) cc_final: 0.5799 (mtp85) REVERT: C 121 ASN cc_start: 0.6801 (t0) cc_final: 0.6000 (t0) REVERT: C 188 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7102 (mtt90) REVERT: C 189 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6714 (mt-10) REVERT: C 237 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7382 (mtp-110) REVERT: C 269 TYR cc_start: 0.8053 (m-80) cc_final: 0.7783 (m-80) REVERT: C 281 GLU cc_start: 0.7214 (pp20) cc_final: 0.6924 (pp20) REVERT: C 367 VAL cc_start: 0.8889 (p) cc_final: 0.8669 (t) REVERT: C 385 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8554 (p) REVERT: C 420 ASP cc_start: 0.6798 (p0) cc_final: 0.6559 (p0) REVERT: C 467 ASP cc_start: 0.7487 (p0) cc_final: 0.7157 (p0) REVERT: C 503 VAL cc_start: 0.8515 (t) cc_final: 0.8298 (m) REVERT: C 511 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8128 (t) REVERT: C 543 PHE cc_start: 0.8454 (m-10) cc_final: 0.8092 (m-80) REVERT: C 599 THR cc_start: 0.8509 (m) cc_final: 0.8289 (t) REVERT: C 654 GLU cc_start: 0.7257 (pm20) cc_final: 0.6972 (pm20) REVERT: C 698 SER cc_start: 0.9040 (t) cc_final: 0.8548 (p) REVERT: C 776 LYS cc_start: 0.8351 (ttpt) cc_final: 0.7887 (ttpp) REVERT: C 859 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7919 (p) REVERT: C 868 GLU cc_start: 0.6919 (tp30) cc_final: 0.6512 (tp30) REVERT: C 916 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8068 (tp) REVERT: C 933 LYS cc_start: 0.8297 (mttt) cc_final: 0.8018 (mtpt) REVERT: C 960 ASN cc_start: 0.8158 (t0) cc_final: 0.7897 (t0) REVERT: C 969 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7914 (ptpp) REVERT: C 976 VAL cc_start: 0.8417 (t) cc_final: 0.8096 (m) REVERT: C 993 ILE cc_start: 0.8802 (tp) cc_final: 0.8502 (tp) REVERT: C 994 ASP cc_start: 0.7801 (t70) cc_final: 0.7448 (t70) REVERT: C 1005 GLN cc_start: 0.7781 (tp40) cc_final: 0.7372 (tp40) REVERT: C 1017 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6953 (tm-30) REVERT: C 1018 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7834 (mp) REVERT: C 1123 SER cc_start: 0.8623 (t) cc_final: 0.8251 (m) REVERT: C 1144 GLU cc_start: 0.7243 (pp20) cc_final: 0.7029 (pp20) REVERT: D 15 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6455 (mmtm) REVERT: D 59 LYS cc_start: 0.8174 (mttp) cc_final: 0.7711 (mttp) REVERT: D 72 THR cc_start: 0.8251 (t) cc_final: 0.8013 (p) REVERT: D 105 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8077 (p) REVERT: D 182 LEU cc_start: 0.8191 (mt) cc_final: 0.7790 (mt) REVERT: E 13 SER cc_start: 0.8401 (t) cc_final: 0.8200 (m) REVERT: E 44 GLN cc_start: 0.7340 (mp10) cc_final: 0.6855 (mp10) REVERT: E 104 THR cc_start: 0.7726 (m) cc_final: 0.7290 (p) REVERT: F 2 VAL cc_start: 0.8475 (t) cc_final: 0.8137 (p) REVERT: H 23 THR cc_start: 0.6929 (t) cc_final: 0.6688 (m) REVERT: I 18 ILE cc_start: 0.6736 (mm) cc_final: 0.6424 (mt) outliers start: 148 outliers final: 126 residues processed: 859 average time/residue: 0.4790 time to fit residues: 647.6288 Evaluate side-chains 902 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 764 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 0.8980 chunk 349 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 337 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 762 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 417 ASN C 505 HIS C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121718 restraints weight = 53748.259| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.70 r_work: 0.3390 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32875 Z= 0.296 Angle : 0.648 17.046 44808 Z= 0.325 Chirality : 0.046 0.258 5143 Planarity : 0.004 0.060 5765 Dihedral : 6.113 75.207 4565 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.24 % Allowed : 21.15 % Favored : 74.61 % 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: -1.65 (0.13), residues: 4110 helix: 0.94 (0.21), residues: 682 sheet: -0.85 (0.15), residues: 1077 loop : -1.90 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 64 HIS 0.006 0.001 HIS B1064 PHE 0.038 0.002 PHE C 429 TYR 0.019 0.001 TYR C 453 ARG 0.011 0.001 ARG A1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11255.77 seconds wall clock time: 200 minutes 33.46 seconds (12033.46 seconds total)