Starting phenix.real_space_refine on Tue Feb 20 23:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycy_33742/02_2024/7ycy_33742.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycy_33742/02_2024/7ycy_33742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycy_33742/02_2024/7ycy_33742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycy_33742/02_2024/7ycy_33742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycy_33742/02_2024/7ycy_33742.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ycy_33742/02_2024/7ycy_33742.pdb" } resolution = 3.74 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 135 5.16 5 C 18653 2.51 5 N 4836 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" 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 PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" 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 "D ARG 60": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 60": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29175 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: 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: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "I" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 15.23, per 1000 atoms: 0.52 Number of scatterers: 29175 At special positions: 0 Unit cell: (142.576, 177.688, 200.032, 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 135 16.00 O 5551 8.00 N 4836 7.00 C 18653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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 291 " - pdb=" SG CYS B 301 " 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 291 " - pdb=" SG CYS C 301 " 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 E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " 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: 11.26 Conformation dependent library (CDL) restraints added in 5.2 seconds 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 59 sheets defined 18.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.568A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 543 through 546 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.925A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.524A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.541A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 901 through 907 removed outlier: 3.562A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.519A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.887A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.680A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.516A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.731A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.807A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.915A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.356A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.792A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 890' Processing helix chain 'B' and resid 897 through 910 removed outlier: 4.059A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.782A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.530A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.870A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.525A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.595A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.516A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.837A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.606A 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 883 Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.515A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.803A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.838A 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 984 removed outlier: 3.684A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.657A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.597A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.061A 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 'I' and resid 81 through 85 removed outlier: 3.656A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 4.028A 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 42 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.581A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 96 removed outlier: 3.885A pdb=" N SER A 94 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 96 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 186 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 7.579A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.673A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.714A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.554A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.585A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.569A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.402A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.554A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.669A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.831A pdb=" N PHE B 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.770A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.130A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.506A pdb=" N GLU B 189 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 203 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B 224 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.540A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.644A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.582A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.512A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.859A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.715A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.320A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.574A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.772A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.585A pdb=" N TYR C 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 229 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 201 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.611A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 310 through 319 removed outlier: 3.548A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.626A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.914A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.800A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.800A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.436A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.488A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.525A pdb=" N SER D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.680A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 41 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 93 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 114 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AF4, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.584A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.651A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.773A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN F 41 " --> pdb=" O THR F 94 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 94 " --> pdb=" O GLN F 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 93 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 114 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.531A pdb=" N GLY G 12 " --> pdb=" O THR G 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'G' and resid 47 through 51 removed outlier: 5.481A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.601A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.708A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 93 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.189A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 17 through 19 861 hydrogen bonds defined for protein. 2352 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: 12.80 Time building geometry restraints manager: 12.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9307 1.34 - 1.46: 5449 1.46 - 1.58: 14933 1.58 - 1.70: 0 1.70 - 1.81: 171 Bond restraints: 29860 Sorted by residual: bond pdb=" CA ASN C 331 " pdb=" C ASN C 331 " ideal model delta sigma weight residual 1.523 1.476 0.046 1.37e-02 5.33e+03 1.15e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.38e-02 5.25e+03 4.75e+00 bond pdb=" CA GLY C 885 " pdb=" C GLY C 885 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.41e+00 bond pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.42e-02 4.96e+03 2.36e+00 bond pdb=" CA GLY I 30 " pdb=" C GLY I 30 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.28e+00 ... (remaining 29855 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.08: 970 107.08 - 113.81: 16434 113.81 - 120.54: 10810 120.54 - 127.26: 12180 127.26 - 133.99: 284 Bond angle restraints: 40678 Sorted by residual: angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.33 120.14 -8.81 1.43e+00 4.89e-01 3.80e+01 angle pdb=" C PHE C 329 " pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 108.91 117.37 -8.46 1.53e+00 4.27e-01 3.05e+01 angle pdb=" N ILE C 332 " pdb=" CA ILE C 332 " pdb=" C ILE C 332 " ideal model delta sigma weight residual 110.36 115.84 -5.48 1.05e+00 9.07e-01 2.73e+01 angle pdb=" C LEU B 984 " pdb=" N ASP B 985 " pdb=" CA ASP B 985 " ideal model delta sigma weight residual 121.48 131.45 -9.97 2.04e+00 2.40e-01 2.39e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 109.40 4.31 9.50e-01 1.11e+00 2.06e+01 ... (remaining 40673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 17056 17.31 - 34.62: 631 34.62 - 51.93: 96 51.93 - 69.23: 18 69.23 - 86.54: 3 Dihedral angle restraints: 17804 sinusoidal: 6834 harmonic: 10970 Sorted by residual: dihedral pdb=" CA ASP G 52 " pdb=" C ASP G 52 " pdb=" N VAL G 53 " pdb=" CA VAL G 53 " ideal model delta harmonic sigma weight residual 180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP I 52 " pdb=" C ASP I 52 " pdb=" N VAL I 53 " pdb=" CA VAL I 53 " ideal model delta harmonic sigma weight residual 180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA PRO C 330 " pdb=" C PRO C 330 " pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 17801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4116 0.062 - 0.125: 534 0.125 - 0.187: 6 0.187 - 0.249: 0 0.249 - 0.312: 1 Chirality restraints: 4657 Sorted by residual: 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 2.41 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA THR C 333 " pdb=" N THR C 333 " pdb=" C THR C 333 " pdb=" CB THR C 333 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 4654 not shown) Planarity restraints: 5239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO C 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.028 5.00e-02 4.00e+02 ... (remaining 5236 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5297 2.77 - 3.31: 27522 3.31 - 3.84: 48137 3.84 - 4.37: 54826 4.37 - 4.90: 95876 Nonbonded interactions: 231658 Sorted by model distance: nonbonded pdb=" O ILE F 106 " pdb=" OH TYR G 38 " model vdw 2.242 2.440 nonbonded pdb=" OG SER I 65 " pdb=" OG1 THR I 76 " model vdw 2.243 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.246 2.440 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 21 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OG1 THR B 998 " model vdw 2.251 2.440 ... (remaining 231653 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' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.390 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 77.680 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.220 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 0.047 29860 Z= 0.128 Angle : 0.526 9.974 40678 Z= 0.323 Chirality : 0.040 0.312 4657 Planarity : 0.004 0.052 5239 Dihedral : 8.830 86.542 10613 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.56 % Allowed : 5.98 % Favored : 89.45 % 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: -4.39 (0.11), residues: 3713 helix: -1.38 (0.18), residues: 628 sheet: -2.81 (0.16), residues: 780 loop : -3.60 (0.10), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 886 HIS 0.002 0.000 HIS B 49 PHE 0.008 0.001 PHE C 329 TYR 0.005 0.000 TYR A1138 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 901 time to evaluate : 3.367 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8239 (t) cc_final: 0.7987 (t) REVERT: A 47 VAL cc_start: 0.8978 (m) cc_final: 0.8706 (p) REVERT: A 67 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6513 (t) REVERT: A 87 ASN cc_start: 0.7359 (p0) cc_final: 0.6444 (p0) REVERT: A 188 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6149 (mmt-90) REVERT: A 190 PHE cc_start: 0.7157 (m-80) cc_final: 0.6452 (m-80) REVERT: A 192 PHE cc_start: 0.6940 (m-10) cc_final: 0.6568 (m-10) REVERT: A 276 LEU cc_start: 0.8199 (tp) cc_final: 0.7885 (tt) REVERT: A 281 GLU cc_start: 0.7101 (pp20) cc_final: 0.6853 (pp20) REVERT: A 297 SER cc_start: 0.8419 (m) cc_final: 0.8109 (p) REVERT: A 403 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7503 (ttm-80) REVERT: A 534 VAL cc_start: 0.8672 (t) cc_final: 0.8332 (m) REVERT: A 541 PHE cc_start: 0.7716 (p90) cc_final: 0.7451 (p90) REVERT: A 578 ASP cc_start: 0.6140 (t70) cc_final: 0.5524 (t70) REVERT: A 589 PRO cc_start: 0.7722 (Cg_exo) cc_final: 0.7511 (Cg_endo) REVERT: A 599 THR cc_start: 0.8313 (m) cc_final: 0.8056 (t) REVERT: A 644 GLN cc_start: 0.7572 (tp40) cc_final: 0.6193 (tp40) REVERT: A 656 VAL cc_start: 0.8421 (p) cc_final: 0.8199 (m) REVERT: A 659 SER cc_start: 0.8232 (m) cc_final: 0.7967 (p) REVERT: A 666 ILE cc_start: 0.8322 (mm) cc_final: 0.8119 (mt) REVERT: A 674 TYR cc_start: 0.8044 (t80) cc_final: 0.7448 (t80) REVERT: A 698 SER cc_start: 0.8727 (t) cc_final: 0.8193 (p) REVERT: A 705 VAL cc_start: 0.8353 (t) cc_final: 0.8088 (m) REVERT: A 745 ASP cc_start: 0.6037 (m-30) cc_final: 0.5834 (m-30) REVERT: A 754 LEU cc_start: 0.8384 (mt) cc_final: 0.8134 (mt) REVERT: A 763 LEU cc_start: 0.8242 (mt) cc_final: 0.7984 (mt) REVERT: A 773 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5465 (tm-30) REVERT: A 778 THR cc_start: 0.8288 (p) cc_final: 0.7782 (t) REVERT: A 803 SER cc_start: 0.8420 (m) cc_final: 0.8105 (p) REVERT: A 816 SER cc_start: 0.7762 (p) cc_final: 0.7412 (m) REVERT: A 854 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8042 (tmtt) REVERT: A 868 GLU cc_start: 0.7369 (tp30) cc_final: 0.7048 (tp30) REVERT: A 869 MET cc_start: 0.8161 (mtt) cc_final: 0.7952 (mtm) REVERT: A 878 LEU cc_start: 0.8316 (mt) cc_final: 0.7809 (mp) REVERT: A 921 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8092 (mmmm) REVERT: A 922 LEU cc_start: 0.8327 (tp) cc_final: 0.8065 (tp) REVERT: A 925 ASN cc_start: 0.8499 (m-40) cc_final: 0.8072 (m-40) REVERT: A 933 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7586 (mtmm) REVERT: A 934 ILE cc_start: 0.8242 (mm) cc_final: 0.7962 (mm) REVERT: A 945 LEU cc_start: 0.8691 (mm) cc_final: 0.8369 (mp) REVERT: A 949 GLN cc_start: 0.8166 (mm110) cc_final: 0.7276 (mm-40) REVERT: A 953 ASN cc_start: 0.8293 (m-40) cc_final: 0.7773 (m110) REVERT: A 960 ASN cc_start: 0.7764 (m110) cc_final: 0.7522 (m-40) REVERT: A 979 ASP cc_start: 0.7167 (m-30) cc_final: 0.6880 (m-30) REVERT: A 994 ASP cc_start: 0.7304 (m-30) cc_final: 0.6909 (m-30) REVERT: A 1019 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7306 (ttp80) REVERT: A 1028 LYS cc_start: 0.8193 (mttt) cc_final: 0.7944 (mttt) REVERT: A 1050 MET cc_start: 0.7045 (ttm) cc_final: 0.6653 (mtp) REVERT: A 1084 ASP cc_start: 0.8411 (m-30) cc_final: 0.8110 (m-30) REVERT: A 1117 THR cc_start: 0.8159 (p) cc_final: 0.7946 (t) REVERT: A 1129 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8196 (m) REVERT: A 1141 LEU cc_start: 0.8343 (tp) cc_final: 0.7994 (tt) REVERT: B 41 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7871 (mtpt) REVERT: B 50 SER cc_start: 0.9056 (t) cc_final: 0.8791 (p) REVERT: B 105 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7507 (mm) REVERT: B 106 PHE cc_start: 0.7067 (m-80) cc_final: 0.6591 (m-80) REVERT: B 135 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6682 (p90) REVERT: B 224 GLU cc_start: 0.8040 (pm20) cc_final: 0.7800 (pm20) REVERT: B 265 TYR cc_start: 0.7308 (p90) cc_final: 0.7088 (p90) REVERT: B 267 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 278 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8401 (ttmm) REVERT: B 286 THR cc_start: 0.7867 (p) cc_final: 0.7020 (p) REVERT: B 300 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7765 (mtmt) REVERT: B 307 THR cc_start: 0.7221 (m) cc_final: 0.6887 (p) REVERT: B 332 ILE cc_start: 0.7971 (mm) cc_final: 0.7564 (tp) REVERT: B 340 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 353 TRP cc_start: 0.8258 (p-90) cc_final: 0.8003 (p-90) REVERT: B 354 ASN cc_start: 0.8100 (m110) cc_final: 0.7718 (m110) REVERT: B 380 TYR cc_start: 0.6485 (m-80) cc_final: 0.6150 (m-80) REVERT: B 390 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7400 (tt) REVERT: B 408 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7217 (ttp80) REVERT: B 433 VAL cc_start: 0.8389 (p) cc_final: 0.8107 (m) REVERT: B 513 LEU cc_start: 0.7767 (mp) cc_final: 0.7251 (mm) REVERT: B 514 SER cc_start: 0.7825 (m) cc_final: 0.7507 (t) REVERT: B 516 GLU cc_start: 0.6312 (mm-30) cc_final: 0.6078 (mm-30) REVERT: B 535 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7991 (mtpp) REVERT: B 542 ASN cc_start: 0.7836 (t0) cc_final: 0.7610 (t0) REVERT: B 546 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7918 (tm) REVERT: B 644 GLN cc_start: 0.8054 (tp40) cc_final: 0.7346 (tp40) REVERT: B 645 THR cc_start: 0.7955 (p) cc_final: 0.6895 (m) REVERT: B 651 ILE cc_start: 0.8389 (mt) cc_final: 0.8172 (mt) REVERT: B 659 SER cc_start: 0.8658 (m) cc_final: 0.8150 (p) REVERT: B 703 ASN cc_start: 0.8211 (t0) cc_final: 0.7918 (t0) REVERT: B 705 VAL cc_start: 0.8562 (t) cc_final: 0.8338 (p) REVERT: B 707 TYR cc_start: 0.7790 (t80) cc_final: 0.7574 (t80) REVERT: B 732 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8201 (p) REVERT: B 737 ASP cc_start: 0.7484 (t0) cc_final: 0.7160 (t0) REVERT: B 774 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7347 (mm-40) REVERT: B 776 LYS cc_start: 0.8106 (tmmt) cc_final: 0.7737 (ttmt) REVERT: B 850 ILE cc_start: 0.8258 (mm) cc_final: 0.7871 (tp) REVERT: B 851 CYS cc_start: 0.7867 (t) cc_final: 0.7465 (m) REVERT: B 854 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7950 (tttp) REVERT: B 866 THR cc_start: 0.8152 (p) cc_final: 0.7940 (t) REVERT: B 921 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8491 (mmmt) REVERT: B 933 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7851 (ttmm) REVERT: B 950 ASP cc_start: 0.7113 (t70) cc_final: 0.6275 (t70) REVERT: B 976 VAL cc_start: 0.8945 (t) cc_final: 0.8745 (t) REVERT: B 990 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6890 (mm-30) REVERT: B 993 ILE cc_start: 0.8026 (tp) cc_final: 0.7818 (pt) REVERT: B 994 ASP cc_start: 0.7404 (m-30) cc_final: 0.6811 (m-30) REVERT: B 997 ILE cc_start: 0.8433 (tt) cc_final: 0.8087 (pt) REVERT: B 1002 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7346 (tm-30) REVERT: B 1003 SER cc_start: 0.8636 (m) cc_final: 0.7960 (t) REVERT: B 1010 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: B 1019 ARG cc_start: 0.6619 (ttm110) cc_final: 0.6322 (ttp80) REVERT: B 1061 VAL cc_start: 0.8679 (t) cc_final: 0.8287 (p) REVERT: B 1097 SER cc_start: 0.8689 (t) cc_final: 0.7841 (p) REVERT: C 41 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7175 (mtpp) REVERT: C 54 LEU cc_start: 0.8071 (mt) cc_final: 0.7793 (mt) REVERT: C 65 PHE cc_start: 0.6655 (m-80) cc_final: 0.6342 (m-80) REVERT: C 90 VAL cc_start: 0.8586 (m) cc_final: 0.8362 (p) REVERT: C 106 PHE cc_start: 0.6787 (m-80) cc_final: 0.6473 (m-80) REVERT: C 189 GLU cc_start: 0.7072 (pm20) cc_final: 0.6205 (pm20) REVERT: C 192 PHE cc_start: 0.7976 (m-80) cc_final: 0.7584 (m-80) REVERT: C 199 PHE cc_start: 0.7661 (t80) cc_final: 0.7441 (t80) REVERT: C 267 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7170 (p) REVERT: C 271 GLN cc_start: 0.7472 (mt0) cc_final: 0.7058 (mt0) REVERT: C 289 VAL cc_start: 0.8597 (t) cc_final: 0.8357 (m) REVERT: C 297 SER cc_start: 0.7910 (m) cc_final: 0.7337 (p) REVERT: C 436 TRP cc_start: 0.7755 (p90) cc_final: 0.7267 (p-90) REVERT: C 501 TYR cc_start: 0.7145 (m-10) cc_final: 0.6695 (m-10) REVERT: C 531 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (p) REVERT: C 542 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7462 (t0) REVERT: C 563 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6879 (mm-40) REVERT: C 569 ILE cc_start: 0.8400 (pp) cc_final: 0.8162 (mp) REVERT: C 588 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7784 (p) REVERT: C 619 GLU cc_start: 0.6589 (mp0) cc_final: 0.6074 (mp0) REVERT: C 644 GLN cc_start: 0.7967 (tp40) cc_final: 0.7257 (tp40) REVERT: C 675 GLN cc_start: 0.6533 (mm-40) cc_final: 0.6276 (mm-40) REVERT: C 697 MET cc_start: 0.7797 (ptm) cc_final: 0.7583 (ptm) REVERT: C 718 PHE cc_start: 0.6887 (p90) cc_final: 0.6650 (p90) REVERT: C 725 GLU cc_start: 0.7261 (tt0) cc_final: 0.6905 (tt0) REVERT: C 759 PHE cc_start: 0.7362 (t80) cc_final: 0.6404 (t80) REVERT: C 762 GLN cc_start: 0.7696 (tt0) cc_final: 0.7303 (tt0) REVERT: C 763 LEU cc_start: 0.8173 (mt) cc_final: 0.7499 (mp) REVERT: C 764 LYS cc_start: 0.8336 (tttm) cc_final: 0.7876 (ttpp) REVERT: C 765 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7458 (mtm110) REVERT: C 773 GLU cc_start: 0.7155 (tt0) cc_final: 0.6827 (tt0) REVERT: C 816 SER cc_start: 0.8264 (p) cc_final: 0.7892 (m) REVERT: C 821 LEU cc_start: 0.8594 (tp) cc_final: 0.7911 (tp) REVERT: C 854 LYS cc_start: 0.8258 (tmmt) cc_final: 0.7692 (tptp) REVERT: C 855 PHE cc_start: 0.7727 (m-10) cc_final: 0.7294 (m-80) REVERT: C 869 MET cc_start: 0.8270 (mtt) cc_final: 0.8070 (mtm) REVERT: C 905 ARG cc_start: 0.7514 (mtt-85) cc_final: 0.6694 (mmt180) REVERT: C 950 ASP cc_start: 0.7303 (t70) cc_final: 0.6812 (t70) REVERT: C 1002 GLN cc_start: 0.7502 (tp-100) cc_final: 0.7178 (tp-100) REVERT: C 1014 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7242 (ttm110) REVERT: C 1019 ARG cc_start: 0.7388 (ttm110) cc_final: 0.6613 (ttm110) REVERT: C 1031 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6816 (mt-10) REVERT: C 1039 ARG cc_start: 0.7481 (mtp180) cc_final: 0.6728 (mtp180) REVERT: C 1081 ILE cc_start: 0.8609 (pt) cc_final: 0.8262 (mm) REVERT: C 1111 GLU cc_start: 0.7470 (tt0) cc_final: 0.7152 (tt0) REVERT: C 1125 ASN cc_start: 0.7103 (p0) cc_final: 0.6407 (p0) REVERT: C 1127 ASP cc_start: 0.6959 (p0) cc_final: 0.6188 (p0) REVERT: E 50 ILE cc_start: 0.1574 (OUTLIER) cc_final: 0.1211 (pt) REVERT: E 75 LEU cc_start: 0.0142 (OUTLIER) cc_final: -0.0244 (tt) REVERT: F 84 MET cc_start: 0.2315 (ptp) cc_final: 0.2103 (ptm) REVERT: H 20 LEU cc_start: 0.8257 (tt) cc_final: 0.7964 (tt) REVERT: H 54 TYR cc_start: 0.6959 (m-80) cc_final: 0.6526 (m-80) REVERT: H 78 ASN cc_start: 0.5360 (m110) cc_final: 0.4832 (t0) REVERT: H 83 THR cc_start: 0.6792 (p) cc_final: 0.6517 (p) REVERT: H 114 THR cc_start: 0.3704 (p) cc_final: 0.1779 (m) outliers start: 148 outliers final: 43 residues processed: 1020 average time/residue: 0.4182 time to fit residues: 666.3083 Evaluate side-chains 785 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 724 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 990 GLU 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 B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 8.9990 chunk 281 optimal weight: 3.9990 chunk 156 optimal weight: 0.0980 chunk 96 optimal weight: 0.0270 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 112 optimal weight: 0.0970 chunk 176 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 271 GLN A 334 ASN A 370 ASN A 409 GLN A 460 ASN A 542 ASN A 644 GLN A 690 GLN A 784 GLN A 907 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1005 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1101 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 52 GLN B 121 ASN B 173 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 784 GLN B 853 GLN B 901 GLN B 913 GLN B 949 GLN B 954 HIS B 965 GLN B1002 GLN B1010 GLN B1011 GLN B1106 GLN B1119 ASN B1125 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 181 GLN C 245 HIS C 370 ASN C 409 GLN C 437 ASN C 519 HIS C 540 ASN C 613 GLN C 710 ASN C 901 GLN C 913 GLN C1002 GLN C1005 GLN C1011 GLN C1023 ASN C1048 HIS C1083 HIS D 41 GLN E 39 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 41 GLN G 39 GLN G 40 GLN G 71 ASN G 81 GLN H 41 GLN I 39 GLN I 40 GLN I 71 ASN I 81 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29860 Z= 0.186 Angle : 0.583 13.192 40678 Z= 0.295 Chirality : 0.044 0.309 4657 Planarity : 0.004 0.073 5239 Dihedral : 5.542 60.258 4156 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.41 % Allowed : 12.40 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.12), residues: 3713 helix: 0.12 (0.20), residues: 654 sheet: -2.15 (0.17), residues: 744 loop : -3.23 (0.11), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.012 0.001 HIS B 954 PHE 0.028 0.001 PHE C 190 TYR 0.022 0.001 TYR A 495 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 745 time to evaluate : 3.301 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: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8154 (mtpt) REVERT: A 87 ASN cc_start: 0.7306 (p0) cc_final: 0.7099 (p0) REVERT: A 190 PHE cc_start: 0.7148 (m-80) cc_final: 0.6834 (m-80) REVERT: A 233 ILE cc_start: 0.8524 (tt) cc_final: 0.8122 (pt) REVERT: A 281 GLU cc_start: 0.7348 (pp20) cc_final: 0.7095 (pp20) REVERT: A 297 SER cc_start: 0.8367 (m) cc_final: 0.8085 (p) REVERT: A 326 ILE cc_start: 0.7967 (mp) cc_final: 0.7716 (mt) REVERT: A 478 LYS cc_start: -0.0558 (OUTLIER) cc_final: -0.1677 (ptmt) REVERT: A 505 HIS cc_start: 0.7426 (t-90) cc_final: 0.6968 (t-90) REVERT: A 542 ASN cc_start: 0.8140 (t0) cc_final: 0.7824 (t0) REVERT: A 547 LYS cc_start: 0.8418 (pttm) cc_final: 0.8190 (mtmm) REVERT: A 656 VAL cc_start: 0.8386 (p) cc_final: 0.8153 (m) REVERT: A 666 ILE cc_start: 0.8373 (mm) cc_final: 0.8126 (mt) REVERT: A 674 TYR cc_start: 0.8203 (t80) cc_final: 0.7860 (t80) REVERT: A 697 MET cc_start: 0.7111 (ttp) cc_final: 0.6652 (mtp) REVERT: A 698 SER cc_start: 0.8567 (t) cc_final: 0.8193 (p) REVERT: A 754 LEU cc_start: 0.8404 (mt) cc_final: 0.8131 (mt) REVERT: A 759 PHE cc_start: 0.6776 (m-80) cc_final: 0.6379 (m-80) REVERT: A 763 LEU cc_start: 0.8332 (mt) cc_final: 0.8107 (mt) REVERT: A 773 GLU cc_start: 0.6211 (tm-30) cc_final: 0.5423 (tm-30) REVERT: A 803 SER cc_start: 0.8608 (m) cc_final: 0.8135 (p) REVERT: A 816 SER cc_start: 0.7709 (p) cc_final: 0.7499 (p) REVERT: A 825 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8225 (mmtm) REVERT: A 854 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8049 (tmtt) REVERT: A 855 PHE cc_start: 0.8221 (m-80) cc_final: 0.8007 (m-80) REVERT: A 868 GLU cc_start: 0.7356 (tp30) cc_final: 0.7078 (tp30) REVERT: A 869 MET cc_start: 0.8209 (mtt) cc_final: 0.7931 (mtp) REVERT: A 878 LEU cc_start: 0.8228 (mt) cc_final: 0.7958 (mt) REVERT: A 914 ASN cc_start: 0.7428 (p0) cc_final: 0.7217 (p0) REVERT: A 921 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8128 (mmmm) REVERT: A 922 LEU cc_start: 0.8492 (tp) cc_final: 0.8282 (tp) REVERT: A 925 ASN cc_start: 0.8530 (m-40) cc_final: 0.7974 (m-40) REVERT: A 933 LYS cc_start: 0.8075 (mtmm) cc_final: 0.7736 (mtmm) REVERT: A 945 LEU cc_start: 0.8720 (mm) cc_final: 0.8379 (mp) REVERT: A 949 GLN cc_start: 0.8268 (mm110) cc_final: 0.7302 (mm-40) REVERT: A 953 ASN cc_start: 0.8285 (m-40) cc_final: 0.7774 (m110) REVERT: A 960 ASN cc_start: 0.7977 (m110) cc_final: 0.7692 (m-40) REVERT: A 983 ARG cc_start: 0.8325 (mtm180) cc_final: 0.7704 (mtm180) REVERT: A 996 LEU cc_start: 0.8558 (tp) cc_final: 0.8239 (tt) REVERT: A 1006 THR cc_start: 0.8489 (m) cc_final: 0.8274 (p) REVERT: A 1019 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7375 (ttp80) REVERT: A 1029 MET cc_start: 0.8402 (tpp) cc_final: 0.7534 (ttm) REVERT: A 1038 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8121 (mttt) REVERT: A 1050 MET cc_start: 0.6980 (ttm) cc_final: 0.6731 (mtp) REVERT: A 1112 PRO cc_start: 0.8259 (Cg_exo) cc_final: 0.7924 (Cg_endo) REVERT: A 1117 THR cc_start: 0.8329 (p) cc_final: 0.8090 (t) REVERT: A 1129 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8244 (m) REVERT: A 1141 LEU cc_start: 0.8189 (tp) cc_final: 0.7862 (tt) REVERT: B 105 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7427 (mm) REVERT: B 106 PHE cc_start: 0.7319 (m-80) cc_final: 0.6892 (m-80) REVERT: B 135 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6641 (p90) REVERT: B 224 GLU cc_start: 0.8005 (pm20) cc_final: 0.7790 (pm20) REVERT: B 267 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8143 (p) REVERT: B 278 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8459 (ttmt) REVERT: B 286 THR cc_start: 0.7604 (p) cc_final: 0.7352 (p) REVERT: B 307 THR cc_start: 0.7223 (m) cc_final: 0.6840 (p) REVERT: B 329 PHE cc_start: 0.7561 (m-10) cc_final: 0.7140 (m-10) REVERT: B 340 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 353 TRP cc_start: 0.8291 (p-90) cc_final: 0.7974 (p-90) REVERT: B 354 ASN cc_start: 0.8057 (m110) cc_final: 0.7667 (m110) REVERT: B 357 ARG cc_start: 0.7596 (mtp-110) cc_final: 0.7351 (mtp-110) REVERT: B 380 TYR cc_start: 0.6692 (m-80) cc_final: 0.6323 (m-80) REVERT: B 402 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8243 (tp) REVERT: B 408 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7665 (ptm-80) REVERT: B 429 PHE cc_start: 0.8262 (t80) cc_final: 0.7895 (t80) REVERT: B 433 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8120 (m) REVERT: B 515 PHE cc_start: 0.7249 (m-80) cc_final: 0.7046 (m-80) REVERT: B 517 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7235 (tt) REVERT: B 546 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7879 (tm) REVERT: B 547 LYS cc_start: 0.8444 (tptp) cc_final: 0.8090 (tttm) REVERT: B 651 ILE cc_start: 0.8314 (mt) cc_final: 0.8063 (mp) REVERT: B 659 SER cc_start: 0.8648 (m) cc_final: 0.8177 (p) REVERT: B 705 VAL cc_start: 0.8599 (t) cc_final: 0.8392 (p) REVERT: B 737 ASP cc_start: 0.7550 (t0) cc_final: 0.7163 (t0) REVERT: B 764 LYS cc_start: 0.8444 (mtpp) cc_final: 0.7993 (tttm) REVERT: B 776 LYS cc_start: 0.8184 (tmmt) cc_final: 0.7778 (ttpp) REVERT: B 850 ILE cc_start: 0.8294 (mm) cc_final: 0.7956 (tp) REVERT: B 851 CYS cc_start: 0.8067 (t) cc_final: 0.7583 (m) REVERT: B 854 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8109 (tttp) REVERT: B 913 GLN cc_start: 0.7841 (pt0) cc_final: 0.7587 (pt0) REVERT: B 921 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8453 (mmmm) REVERT: B 933 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7766 (mtmm) REVERT: B 949 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7784 (tp-100) REVERT: B 950 ASP cc_start: 0.7211 (t70) cc_final: 0.6633 (t0) REVERT: B 976 VAL cc_start: 0.8510 (t) cc_final: 0.8239 (t) REVERT: B 990 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 993 ILE cc_start: 0.8136 (tp) cc_final: 0.7623 (tp) REVERT: B 994 ASP cc_start: 0.7372 (m-30) cc_final: 0.6941 (m-30) REVERT: B 1002 GLN cc_start: 0.7860 (tp40) cc_final: 0.7406 (tm-30) REVERT: B 1003 SER cc_start: 0.8399 (m) cc_final: 0.8031 (t) REVERT: B 1050 MET cc_start: 0.7130 (mtp) cc_final: 0.6779 (mtp) REVERT: B 1061 VAL cc_start: 0.8784 (t) cc_final: 0.8441 (p) REVERT: B 1081 ILE cc_start: 0.8405 (pt) cc_final: 0.8192 (mt) REVERT: B 1086 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (ptpp) REVERT: B 1097 SER cc_start: 0.8589 (t) cc_final: 0.7996 (p) REVERT: C 28 TYR cc_start: 0.7648 (m-80) cc_final: 0.7355 (m-80) REVERT: C 40 ASP cc_start: 0.7897 (t70) cc_final: 0.7661 (t70) REVERT: C 41 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7354 (mtmt) REVERT: C 54 LEU cc_start: 0.8364 (mt) cc_final: 0.8150 (mt) REVERT: C 105 ILE cc_start: 0.8296 (mp) cc_final: 0.7627 (pt) REVERT: C 106 PHE cc_start: 0.6818 (m-80) cc_final: 0.6518 (m-80) REVERT: C 188 ARG cc_start: 0.7142 (mtt-85) cc_final: 0.6913 (mtp85) REVERT: C 192 PHE cc_start: 0.8261 (m-80) cc_final: 0.7859 (m-80) REVERT: C 199 PHE cc_start: 0.7796 (t80) cc_final: 0.7331 (t80) REVERT: C 201 ILE cc_start: 0.8750 (mt) cc_final: 0.8488 (mp) REVERT: C 297 SER cc_start: 0.7668 (m) cc_final: 0.7034 (p) REVERT: C 298 GLU cc_start: 0.7423 (tt0) cc_final: 0.7183 (tt0) REVERT: C 531 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 542 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7352 (t0) REVERT: C 563 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6900 (mm-40) REVERT: C 569 ILE cc_start: 0.8412 (pp) cc_final: 0.8167 (mp) REVERT: C 588 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7991 (p) REVERT: C 619 GLU cc_start: 0.6745 (mp0) cc_final: 0.6159 (mp0) REVERT: C 644 GLN cc_start: 0.7462 (tp40) cc_final: 0.6939 (tp40) REVERT: C 705 VAL cc_start: 0.8184 (t) cc_final: 0.7855 (m) REVERT: C 725 GLU cc_start: 0.7195 (tt0) cc_final: 0.6987 (tt0) REVERT: C 762 GLN cc_start: 0.7651 (tt0) cc_final: 0.7388 (tt0) REVERT: C 763 LEU cc_start: 0.8310 (mt) cc_final: 0.8054 (mp) REVERT: C 764 LYS cc_start: 0.8324 (tttm) cc_final: 0.7851 (ttpp) REVERT: C 765 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7388 (ttp-110) REVERT: C 776 LYS cc_start: 0.8398 (tptp) cc_final: 0.8110 (tptp) REVERT: C 801 ASN cc_start: 0.5528 (t0) cc_final: 0.5324 (t0) REVERT: C 816 SER cc_start: 0.8261 (p) cc_final: 0.7722 (m) REVERT: C 821 LEU cc_start: 0.8809 (tp) cc_final: 0.8566 (tp) REVERT: C 854 LYS cc_start: 0.8281 (tmmt) cc_final: 0.7820 (tptp) REVERT: C 858 LEU cc_start: 0.7841 (mt) cc_final: 0.7587 (mt) REVERT: C 867 ASP cc_start: 0.7639 (m-30) cc_final: 0.7407 (m-30) REVERT: C 896 ILE cc_start: 0.8406 (tt) cc_final: 0.8045 (mt) REVERT: C 902 MET cc_start: 0.7824 (mtp) cc_final: 0.7562 (mmm) REVERT: C 917 TYR cc_start: 0.7728 (m-10) cc_final: 0.7472 (m-10) REVERT: C 1050 MET cc_start: 0.7388 (mtm) cc_final: 0.6842 (mtm) REVERT: C 1072 GLU cc_start: 0.8337 (pm20) cc_final: 0.8003 (pm20) REVERT: C 1127 ASP cc_start: 0.7234 (p0) cc_final: 0.6407 (p0) REVERT: F 55 TRP cc_start: 0.6267 (p-90) cc_final: 0.6064 (p-90) REVERT: G 49 MET cc_start: 0.2494 (OUTLIER) cc_final: 0.2143 (tpt) REVERT: H 54 TYR cc_start: 0.7022 (m-80) cc_final: 0.6781 (m-80) REVERT: H 60 ARG cc_start: 0.5363 (mmm160) cc_final: 0.4809 (mmt90) REVERT: H 78 ASN cc_start: 0.5397 (m110) cc_final: 0.4845 (t0) outliers start: 143 outliers final: 78 residues processed: 845 average time/residue: 0.4195 time to fit residues: 556.3982 Evaluate side-chains 794 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 698 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 0.1980 chunk 104 optimal weight: 0.0670 chunk 280 optimal weight: 3.9990 chunk 229 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 337 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 334 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A1010 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 394 ASN B 949 GLN B1106 GLN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 955 ASN C1048 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1106 GLN E 40 GLN E 71 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29860 Z= 0.195 Angle : 0.572 13.930 40678 Z= 0.286 Chirality : 0.044 0.335 4657 Planarity : 0.004 0.049 5239 Dihedral : 5.309 59.339 4134 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.78 % Allowed : 14.80 % Favored : 80.42 % 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: -2.93 (0.13), residues: 3713 helix: 0.62 (0.21), residues: 652 sheet: -1.76 (0.17), residues: 777 loop : -2.98 (0.11), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 110 HIS 0.009 0.001 HIS B1048 PHE 0.025 0.001 PHE C 759 TYR 0.018 0.001 TYR C 266 ARG 0.005 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 720 time to evaluate : 3.481 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: A 87 ASN cc_start: 0.7361 (p0) cc_final: 0.7093 (p0) REVERT: A 188 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6364 (mmt180) REVERT: A 190 PHE cc_start: 0.7436 (m-80) cc_final: 0.7214 (m-80) REVERT: A 228 ASP cc_start: 0.6608 (t0) cc_final: 0.6371 (t0) REVERT: A 233 ILE cc_start: 0.8521 (tt) cc_final: 0.8089 (pt) REVERT: A 276 LEU cc_start: 0.8302 (tp) cc_final: 0.8000 (tp) REVERT: A 281 GLU cc_start: 0.7364 (pp20) cc_final: 0.7072 (pp20) REVERT: A 297 SER cc_start: 0.8412 (m) cc_final: 0.8122 (p) REVERT: A 326 ILE cc_start: 0.7967 (mp) cc_final: 0.7697 (mt) REVERT: A 478 LYS cc_start: -0.0482 (OUTLIER) cc_final: -0.1287 (ptmt) REVERT: A 542 ASN cc_start: 0.8139 (t0) cc_final: 0.7852 (t0) REVERT: A 547 LYS cc_start: 0.8449 (pttm) cc_final: 0.8203 (mtmm) REVERT: A 592 PHE cc_start: 0.7750 (p90) cc_final: 0.7068 (p90) REVERT: A 663 ASP cc_start: 0.7205 (m-30) cc_final: 0.6997 (p0) REVERT: A 666 ILE cc_start: 0.8487 (mm) cc_final: 0.8222 (mt) REVERT: A 674 TYR cc_start: 0.8152 (t80) cc_final: 0.7894 (t80) REVERT: A 697 MET cc_start: 0.7163 (ttp) cc_final: 0.6848 (mtp) REVERT: A 698 SER cc_start: 0.8671 (t) cc_final: 0.8091 (p) REVERT: A 705 VAL cc_start: 0.8430 (t) cc_final: 0.8204 (m) REVERT: A 759 PHE cc_start: 0.6820 (m-80) cc_final: 0.6373 (m-80) REVERT: A 763 LEU cc_start: 0.8382 (mt) cc_final: 0.8116 (mt) REVERT: A 773 GLU cc_start: 0.6386 (tm-30) cc_final: 0.5911 (tm-30) REVERT: A 803 SER cc_start: 0.8725 (m) cc_final: 0.8208 (p) REVERT: A 816 SER cc_start: 0.7876 (p) cc_final: 0.7608 (t) REVERT: A 825 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8183 (mmtm) REVERT: A 854 LYS cc_start: 0.8285 (ttmm) cc_final: 0.8070 (tmtt) REVERT: A 855 PHE cc_start: 0.8056 (m-80) cc_final: 0.7829 (m-80) REVERT: A 868 GLU cc_start: 0.7384 (tp30) cc_final: 0.7079 (tp30) REVERT: A 869 MET cc_start: 0.8201 (mtt) cc_final: 0.7974 (mtm) REVERT: A 878 LEU cc_start: 0.8251 (mt) cc_final: 0.8047 (mt) REVERT: A 914 ASN cc_start: 0.7602 (p0) cc_final: 0.7349 (p0) REVERT: A 921 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8136 (mmmm) REVERT: A 922 LEU cc_start: 0.8482 (tp) cc_final: 0.8274 (tp) REVERT: A 925 ASN cc_start: 0.8515 (m-40) cc_final: 0.7939 (m-40) REVERT: A 933 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7612 (mtmm) REVERT: A 945 LEU cc_start: 0.8716 (mm) cc_final: 0.8392 (mp) REVERT: A 949 GLN cc_start: 0.8227 (mm110) cc_final: 0.7348 (mm-40) REVERT: A 953 ASN cc_start: 0.8325 (m-40) cc_final: 0.7909 (m110) REVERT: A 960 ASN cc_start: 0.8067 (m-40) cc_final: 0.7739 (m-40) REVERT: A 979 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7078 (t0) REVERT: A 983 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7952 (mtm180) REVERT: A 994 ASP cc_start: 0.7140 (m-30) cc_final: 0.6850 (m-30) REVERT: A 1029 MET cc_start: 0.8374 (tpp) cc_final: 0.7617 (ttm) REVERT: A 1038 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8073 (mtpp) REVERT: A 1050 MET cc_start: 0.7097 (ttm) cc_final: 0.6745 (mtp) REVERT: A 1117 THR cc_start: 0.8427 (p) cc_final: 0.8165 (t) REVERT: A 1129 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 1141 LEU cc_start: 0.8249 (tp) cc_final: 0.7932 (tt) REVERT: B 105 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7528 (mm) REVERT: B 106 PHE cc_start: 0.7366 (m-80) cc_final: 0.6979 (m-80) REVERT: B 135 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6630 (p90) REVERT: B 170 TYR cc_start: 0.8104 (t80) cc_final: 0.7847 (t80) REVERT: B 190 PHE cc_start: 0.8083 (m-80) cc_final: 0.7817 (m-10) REVERT: B 200 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7668 (mmmm) REVERT: B 224 GLU cc_start: 0.8036 (pm20) cc_final: 0.7784 (pm20) REVERT: B 278 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8378 (ttmt) REVERT: B 286 THR cc_start: 0.7657 (p) cc_final: 0.7276 (p) REVERT: B 307 THR cc_start: 0.7232 (m) cc_final: 0.6832 (p) REVERT: B 329 PHE cc_start: 0.7513 (m-10) cc_final: 0.7272 (m-10) REVERT: B 340 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 353 TRP cc_start: 0.8398 (p-90) cc_final: 0.8009 (p-90) REVERT: B 354 ASN cc_start: 0.7974 (m110) cc_final: 0.7556 (m110) REVERT: B 380 TYR cc_start: 0.6730 (m-80) cc_final: 0.6302 (m-80) REVERT: B 394 ASN cc_start: 0.7475 (t0) cc_final: 0.7269 (p0) REVERT: B 408 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7370 (ptm-80) REVERT: B 429 PHE cc_start: 0.8303 (t80) cc_final: 0.7962 (t80) REVERT: B 433 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 515 PHE cc_start: 0.7401 (m-80) cc_final: 0.7163 (m-80) REVERT: B 547 LYS cc_start: 0.8300 (tptp) cc_final: 0.8081 (tttm) REVERT: B 645 THR cc_start: 0.8346 (p) cc_final: 0.7171 (m) REVERT: B 651 ILE cc_start: 0.8374 (mt) cc_final: 0.8085 (mm) REVERT: B 659 SER cc_start: 0.8659 (m) cc_final: 0.8145 (p) REVERT: B 773 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6928 (tp30) REVERT: B 776 LYS cc_start: 0.8234 (tmmt) cc_final: 0.7823 (ttpp) REVERT: B 823 PHE cc_start: 0.7121 (m-10) cc_final: 0.6866 (m-10) REVERT: B 850 ILE cc_start: 0.8344 (mm) cc_final: 0.8059 (tp) REVERT: B 851 CYS cc_start: 0.8180 (t) cc_final: 0.7586 (m) REVERT: B 854 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8026 (tttp) REVERT: B 921 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8454 (mmmm) REVERT: B 933 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7872 (mtmm) REVERT: B 949 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7800 (mm-40) REVERT: B 969 LYS cc_start: 0.7890 (pttm) cc_final: 0.7594 (pttm) REVERT: B 976 VAL cc_start: 0.8518 (t) cc_final: 0.8242 (t) REVERT: B 990 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7019 (mm-30) REVERT: B 993 ILE cc_start: 0.8243 (tp) cc_final: 0.7923 (tp) REVERT: B 994 ASP cc_start: 0.7570 (m-30) cc_final: 0.7080 (m-30) REVERT: B 1002 GLN cc_start: 0.7780 (tp40) cc_final: 0.7375 (tm-30) REVERT: B 1003 SER cc_start: 0.8704 (m) cc_final: 0.8007 (t) REVERT: B 1041 ASP cc_start: 0.7205 (t70) cc_final: 0.6636 (t0) REVERT: B 1061 VAL cc_start: 0.8764 (t) cc_final: 0.8367 (p) REVERT: B 1081 ILE cc_start: 0.8342 (pt) cc_final: 0.8134 (mt) REVERT: B 1086 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8090 (ptpp) REVERT: B 1097 SER cc_start: 0.8593 (t) cc_final: 0.8107 (p) REVERT: C 40 ASP cc_start: 0.7945 (t70) cc_final: 0.7685 (t70) REVERT: C 41 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7366 (mtmt) REVERT: C 54 LEU cc_start: 0.8537 (mt) cc_final: 0.8223 (mt) REVERT: C 105 ILE cc_start: 0.8321 (mp) cc_final: 0.7737 (pt) REVERT: C 106 PHE cc_start: 0.6943 (m-80) cc_final: 0.6716 (m-80) REVERT: C 192 PHE cc_start: 0.8417 (m-80) cc_final: 0.8123 (m-80) REVERT: C 199 PHE cc_start: 0.7815 (t80) cc_final: 0.7338 (t80) REVERT: C 201 ILE cc_start: 0.8784 (mt) cc_final: 0.8498 (mp) REVERT: C 297 SER cc_start: 0.7796 (m) cc_final: 0.7250 (p) REVERT: C 298 GLU cc_start: 0.7417 (tt0) cc_final: 0.7163 (tt0) REVERT: C 301 CYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5602 (m) REVERT: C 324 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7186 (tm-30) REVERT: C 326 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6214 (pt) REVERT: C 332 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6360 (pp) REVERT: C 531 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8160 (p) REVERT: C 542 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7289 (t0) REVERT: C 563 GLN cc_start: 0.7263 (mm-40) cc_final: 0.7037 (mm-40) REVERT: C 588 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7910 (p) REVERT: C 619 GLU cc_start: 0.6839 (mp0) cc_final: 0.6250 (mp0) REVERT: C 642 VAL cc_start: 0.8583 (t) cc_final: 0.8330 (m) REVERT: C 644 GLN cc_start: 0.7515 (tp-100) cc_final: 0.6864 (tp40) REVERT: C 705 VAL cc_start: 0.8214 (t) cc_final: 0.7946 (m) REVERT: C 725 GLU cc_start: 0.7221 (tt0) cc_final: 0.7011 (tt0) REVERT: C 740 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7213 (tpp) REVERT: C 763 LEU cc_start: 0.8394 (mt) cc_final: 0.8186 (mp) REVERT: C 764 LYS cc_start: 0.8313 (tttm) cc_final: 0.7875 (ttpp) REVERT: C 765 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7427 (ttp-110) REVERT: C 768 THR cc_start: 0.8620 (m) cc_final: 0.8362 (p) REVERT: C 776 LYS cc_start: 0.8452 (tptp) cc_final: 0.8102 (tptp) REVERT: C 790 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7891 (mtmm) REVERT: C 801 ASN cc_start: 0.5592 (t0) cc_final: 0.5340 (t0) REVERT: C 854 LYS cc_start: 0.8254 (tmmt) cc_final: 0.7853 (tptp) REVERT: C 858 LEU cc_start: 0.8117 (mt) cc_final: 0.7889 (mm) REVERT: C 867 ASP cc_start: 0.7596 (m-30) cc_final: 0.7384 (m-30) REVERT: C 902 MET cc_start: 0.7925 (mtp) cc_final: 0.7680 (tpp) REVERT: C 945 LEU cc_start: 0.8524 (mm) cc_final: 0.8249 (mt) REVERT: C 964 LYS cc_start: 0.8596 (tppt) cc_final: 0.8200 (ttmm) REVERT: C 990 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7256 (mm-30) REVERT: C 998 THR cc_start: 0.8369 (t) cc_final: 0.8098 (p) REVERT: C 1014 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7400 (ttm110) REVERT: C 1072 GLU cc_start: 0.8365 (pm20) cc_final: 0.8028 (pm20) REVERT: E 39 GLN cc_start: 0.3988 (mm110) cc_final: 0.3526 (mm110) REVERT: G 49 MET cc_start: 0.2935 (ppp) cc_final: 0.2105 (tpt) REVERT: H 54 TYR cc_start: 0.7048 (m-80) cc_final: 0.6820 (m-80) REVERT: H 60 ARG cc_start: 0.5479 (mmm160) cc_final: 0.4982 (mmt90) REVERT: H 78 ASN cc_start: 0.5458 (m110) cc_final: 0.5041 (t0) outliers start: 155 outliers final: 91 residues processed: 826 average time/residue: 0.4198 time to fit residues: 548.1829 Evaluate side-chains 793 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 682 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 0.0170 chunk 253 optimal weight: 0.2980 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 358 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 321 optimal weight: 0.0470 chunk 96 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 949 GLN C 953 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS G 33 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29860 Z= 0.153 Angle : 0.552 13.493 40678 Z= 0.273 Chirality : 0.043 0.222 4657 Planarity : 0.004 0.072 5239 Dihedral : 5.146 60.458 4127 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.96 % Allowed : 15.91 % Favored : 79.12 % 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: -2.64 (0.13), residues: 3713 helix: 0.92 (0.21), residues: 654 sheet: -1.63 (0.17), residues: 799 loop : -2.79 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 436 HIS 0.010 0.001 HIS A 505 PHE 0.027 0.001 PHE A 220 TYR 0.021 0.001 TYR A1067 ARG 0.011 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 697 time to evaluate : 3.278 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: A 87 ASN cc_start: 0.7267 (p0) cc_final: 0.7048 (p0) REVERT: A 188 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6282 (mmt180) REVERT: A 190 PHE cc_start: 0.7495 (m-80) cc_final: 0.7233 (m-80) REVERT: A 228 ASP cc_start: 0.6742 (t0) cc_final: 0.6412 (t0) REVERT: A 233 ILE cc_start: 0.8466 (tt) cc_final: 0.8053 (pt) REVERT: A 276 LEU cc_start: 0.8313 (tp) cc_final: 0.8058 (tp) REVERT: A 281 GLU cc_start: 0.7348 (pp20) cc_final: 0.7085 (pp20) REVERT: A 297 SER cc_start: 0.8441 (m) cc_final: 0.8073 (p) REVERT: A 326 ILE cc_start: 0.7955 (mp) cc_final: 0.7679 (mt) REVERT: A 436 TRP cc_start: 0.6634 (p-90) cc_final: 0.6351 (p90) REVERT: A 478 LYS cc_start: -0.0488 (OUTLIER) cc_final: -0.1057 (ptmt) REVERT: A 542 ASN cc_start: 0.8236 (t0) cc_final: 0.7891 (m-40) REVERT: A 592 PHE cc_start: 0.7691 (p90) cc_final: 0.7144 (p90) REVERT: A 663 ASP cc_start: 0.7252 (m-30) cc_final: 0.7017 (p0) REVERT: A 666 ILE cc_start: 0.8522 (mm) cc_final: 0.8252 (mt) REVERT: A 674 TYR cc_start: 0.8119 (t80) cc_final: 0.7893 (t80) REVERT: A 697 MET cc_start: 0.7121 (ttp) cc_final: 0.6850 (mtp) REVERT: A 698 SER cc_start: 0.8622 (t) cc_final: 0.7922 (p) REVERT: A 751 ASN cc_start: 0.7757 (m-40) cc_final: 0.7462 (p0) REVERT: A 759 PHE cc_start: 0.6799 (m-80) cc_final: 0.6351 (m-80) REVERT: A 763 LEU cc_start: 0.8326 (mt) cc_final: 0.8079 (mt) REVERT: A 773 GLU cc_start: 0.6491 (tm-30) cc_final: 0.6002 (tm-30) REVERT: A 803 SER cc_start: 0.8705 (m) cc_final: 0.8170 (p) REVERT: A 816 SER cc_start: 0.7919 (p) cc_final: 0.7568 (t) REVERT: A 825 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8233 (mmtm) REVERT: A 868 GLU cc_start: 0.7380 (tp30) cc_final: 0.7046 (tp30) REVERT: A 869 MET cc_start: 0.8198 (mtt) cc_final: 0.7963 (mtm) REVERT: A 878 LEU cc_start: 0.8283 (mt) cc_final: 0.8061 (mt) REVERT: A 902 MET cc_start: 0.7804 (tpp) cc_final: 0.7560 (tpp) REVERT: A 914 ASN cc_start: 0.7621 (p0) cc_final: 0.7339 (p0) REVERT: A 921 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8119 (mmmm) REVERT: A 922 LEU cc_start: 0.8457 (tp) cc_final: 0.8251 (tp) REVERT: A 925 ASN cc_start: 0.8476 (m-40) cc_final: 0.7897 (m-40) REVERT: A 933 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7583 (mtmm) REVERT: A 949 GLN cc_start: 0.8174 (mm110) cc_final: 0.7302 (mm-40) REVERT: A 953 ASN cc_start: 0.8389 (m-40) cc_final: 0.7988 (m110) REVERT: A 960 ASN cc_start: 0.8044 (m-40) cc_final: 0.7779 (m-40) REVERT: A 979 ASP cc_start: 0.7437 (t0) cc_final: 0.7101 (t0) REVERT: A 983 ARG cc_start: 0.8297 (mtm180) cc_final: 0.7882 (mtm180) REVERT: A 994 ASP cc_start: 0.7043 (m-30) cc_final: 0.6781 (m-30) REVERT: A 1029 MET cc_start: 0.8315 (tpp) cc_final: 0.7600 (ttm) REVERT: A 1038 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8110 (mtpp) REVERT: A 1050 MET cc_start: 0.7005 (ttm) cc_final: 0.6266 (mtm) REVERT: A 1117 THR cc_start: 0.8475 (p) cc_final: 0.8205 (t) REVERT: A 1129 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8335 (m) REVERT: A 1141 LEU cc_start: 0.8222 (tp) cc_final: 0.7924 (tt) REVERT: B 104 TRP cc_start: 0.7237 (m-90) cc_final: 0.6498 (m-90) REVERT: B 105 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7552 (mm) REVERT: B 106 PHE cc_start: 0.7340 (m-80) cc_final: 0.6938 (m-80) REVERT: B 135 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6654 (p90) REVERT: B 190 PHE cc_start: 0.8110 (m-80) cc_final: 0.7851 (m-10) REVERT: B 193 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7384 (mttp) REVERT: B 224 GLU cc_start: 0.8043 (pm20) cc_final: 0.7575 (pm20) REVERT: B 228 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6895 (t0) REVERT: B 278 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8367 (ttmt) REVERT: B 286 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7152 (p) REVERT: B 307 THR cc_start: 0.7201 (m) cc_final: 0.6931 (p) REVERT: B 317 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.8045 (p0) REVERT: B 319 ARG cc_start: 0.7478 (mtm110) cc_final: 0.6975 (ttm110) REVERT: B 329 PHE cc_start: 0.7536 (m-10) cc_final: 0.7300 (m-10) REVERT: B 340 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7353 (mm-30) REVERT: B 353 TRP cc_start: 0.8399 (p-90) cc_final: 0.8030 (p-90) REVERT: B 354 ASN cc_start: 0.7981 (m110) cc_final: 0.7580 (m110) REVERT: B 356 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8302 (tppp) REVERT: B 380 TYR cc_start: 0.6703 (m-80) cc_final: 0.6281 (m-80) REVERT: B 394 ASN cc_start: 0.7402 (t0) cc_final: 0.7128 (p0) REVERT: B 429 PHE cc_start: 0.8279 (t80) cc_final: 0.7946 (t80) REVERT: B 433 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8129 (m) REVERT: B 439 ASN cc_start: 0.7650 (t0) cc_final: 0.7198 (t0) REVERT: B 515 PHE cc_start: 0.7411 (m-80) cc_final: 0.7209 (m-80) REVERT: B 517 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7236 (tt) REVERT: B 602 THR cc_start: 0.8850 (m) cc_final: 0.8331 (p) REVERT: B 645 THR cc_start: 0.8275 (p) cc_final: 0.6952 (m) REVERT: B 651 ILE cc_start: 0.8377 (mt) cc_final: 0.8117 (mm) REVERT: B 659 SER cc_start: 0.8635 (m) cc_final: 0.8142 (p) REVERT: B 740 MET cc_start: 0.8154 (ttm) cc_final: 0.7805 (ttp) REVERT: B 759 PHE cc_start: 0.7372 (t80) cc_final: 0.6956 (t80) REVERT: B 776 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7827 (ttpp) REVERT: B 850 ILE cc_start: 0.8349 (mm) cc_final: 0.8039 (tp) REVERT: B 851 CYS cc_start: 0.8208 (t) cc_final: 0.7550 (m) REVERT: B 854 LYS cc_start: 0.8319 (ttpp) cc_final: 0.7956 (tttp) REVERT: B 856 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8452 (mmmm) REVERT: B 921 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8412 (mmmm) REVERT: B 933 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7829 (mtmm) REVERT: B 969 LYS cc_start: 0.7880 (pttm) cc_final: 0.7616 (pttm) REVERT: B 976 VAL cc_start: 0.8483 (t) cc_final: 0.8173 (t) REVERT: B 990 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 993 ILE cc_start: 0.8234 (tp) cc_final: 0.7921 (tp) REVERT: B 994 ASP cc_start: 0.7563 (m-30) cc_final: 0.7080 (m-30) REVERT: B 1002 GLN cc_start: 0.7771 (tp40) cc_final: 0.7408 (tm-30) REVERT: B 1003 SER cc_start: 0.8747 (m) cc_final: 0.7957 (t) REVERT: B 1005 GLN cc_start: 0.8267 (tp40) cc_final: 0.7629 (tp40) REVERT: B 1041 ASP cc_start: 0.7230 (t70) cc_final: 0.6642 (t0) REVERT: B 1050 MET cc_start: 0.7207 (mtp) cc_final: 0.6961 (mtp) REVERT: B 1061 VAL cc_start: 0.8755 (t) cc_final: 0.8382 (p) REVERT: B 1086 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8040 (ptpp) REVERT: B 1097 SER cc_start: 0.8625 (t) cc_final: 0.8070 (p) REVERT: C 40 ASP cc_start: 0.7920 (t70) cc_final: 0.7662 (t70) REVERT: C 41 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7408 (mttt) REVERT: C 65 PHE cc_start: 0.7078 (m-80) cc_final: 0.6688 (m-80) REVERT: C 188 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6874 (mtp85) REVERT: C 192 PHE cc_start: 0.8492 (m-80) cc_final: 0.8264 (m-80) REVERT: C 199 PHE cc_start: 0.7831 (t80) cc_final: 0.7383 (t80) REVERT: C 201 ILE cc_start: 0.8782 (mt) cc_final: 0.8520 (mp) REVERT: C 297 SER cc_start: 0.7859 (m) cc_final: 0.7247 (p) REVERT: C 298 GLU cc_start: 0.7402 (tt0) cc_final: 0.7150 (tt0) REVERT: C 301 CYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5661 (m) REVERT: C 324 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 332 ILE cc_start: 0.6624 (OUTLIER) cc_final: 0.6323 (pp) REVERT: C 436 TRP cc_start: 0.7271 (p-90) cc_final: 0.6736 (p-90) REVERT: C 531 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8212 (p) REVERT: C 542 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7311 (t0) REVERT: C 563 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7037 (mm-40) REVERT: C 588 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7861 (p) REVERT: C 619 GLU cc_start: 0.6865 (mp0) cc_final: 0.6280 (mp0) REVERT: C 642 VAL cc_start: 0.8609 (t) cc_final: 0.8363 (m) REVERT: C 644 GLN cc_start: 0.7545 (tp-100) cc_final: 0.6806 (tp40) REVERT: C 705 VAL cc_start: 0.8180 (t) cc_final: 0.7914 (m) REVERT: C 740 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7133 (tpp) REVERT: C 764 LYS cc_start: 0.8324 (tttm) cc_final: 0.7836 (ttpp) REVERT: C 765 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7486 (ttm-80) REVERT: C 776 LYS cc_start: 0.8424 (tptp) cc_final: 0.8043 (tptp) REVERT: C 854 LYS cc_start: 0.8182 (tmmt) cc_final: 0.7817 (tptp) REVERT: C 858 LEU cc_start: 0.8067 (mt) cc_final: 0.7841 (mm) REVERT: C 917 TYR cc_start: 0.7844 (m-10) cc_final: 0.7583 (m-10) REVERT: C 918 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6911 (tt0) REVERT: C 964 LYS cc_start: 0.8617 (tppt) cc_final: 0.8189 (ttmm) REVERT: C 990 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7284 (mm-30) REVERT: C 998 THR cc_start: 0.8356 (t) cc_final: 0.8078 (p) REVERT: C 1014 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7436 (ttm110) REVERT: C 1029 MET cc_start: 0.8375 (tpp) cc_final: 0.8022 (tpp) REVERT: C 1050 MET cc_start: 0.7362 (mtm) cc_final: 0.6578 (mtm) REVERT: C 1072 GLU cc_start: 0.8388 (pm20) cc_final: 0.8085 (pm20) REVERT: D 4 LEU cc_start: 0.8252 (mt) cc_final: 0.7279 (tt) REVERT: D 110 TRP cc_start: 0.5636 (m100) cc_final: 0.5415 (m100) REVERT: E 39 GLN cc_start: 0.4164 (mm110) cc_final: 0.3517 (mm110) REVERT: G 49 MET cc_start: 0.3042 (ppp) cc_final: 0.2392 (tpt) REVERT: H 60 ARG cc_start: 0.5469 (mmm160) cc_final: 0.5154 (mmt90) REVERT: H 78 ASN cc_start: 0.5361 (m110) cc_final: 0.5158 (t0) outliers start: 161 outliers final: 99 residues processed: 805 average time/residue: 0.4163 time to fit residues: 528.5743 Evaluate side-chains 795 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 677 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 306 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 321 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 183 ASN A 205 HIS A 417 ASN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 280 ASN B 388 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 506 GLN B 540 ASN B 949 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29860 Z= 0.289 Angle : 0.617 13.505 40678 Z= 0.311 Chirality : 0.045 0.255 4657 Planarity : 0.005 0.142 5239 Dihedral : 5.502 61.564 4125 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 5.15 % Allowed : 16.71 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.56 (0.13), residues: 3713 helix: 0.87 (0.21), residues: 650 sheet: -1.63 (0.17), residues: 805 loop : -2.67 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 37 HIS 0.014 0.001 HIS C1048 PHE 0.029 0.002 PHE C 106 TYR 0.023 0.002 TYR C1067 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 729 time to evaluate : 3.334 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6541 (m) cc_final: 0.6096 (p) REVERT: A 111 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5760 (p0) REVERT: A 183 ASN cc_start: 0.6650 (OUTLIER) cc_final: 0.6020 (p0) REVERT: A 190 PHE cc_start: 0.7639 (m-80) cc_final: 0.7344 (m-10) REVERT: A 198 TYR cc_start: 0.6365 (m-80) cc_final: 0.6002 (m-80) REVERT: A 226 LEU cc_start: 0.7924 (mt) cc_final: 0.7671 (mt) REVERT: A 228 ASP cc_start: 0.7664 (t0) cc_final: 0.7090 (t0) REVERT: A 281 GLU cc_start: 0.7396 (pp20) cc_final: 0.7109 (pp20) REVERT: A 290 ASP cc_start: 0.7963 (t0) cc_final: 0.7762 (t0) REVERT: A 297 SER cc_start: 0.8470 (m) cc_final: 0.8080 (p) REVERT: A 326 ILE cc_start: 0.8038 (mp) cc_final: 0.7735 (mt) REVERT: A 436 TRP cc_start: 0.6854 (p-90) cc_final: 0.6486 (p90) REVERT: A 478 LYS cc_start: -0.0413 (OUTLIER) cc_final: -0.2221 (ptmm) REVERT: A 534 VAL cc_start: 0.8637 (t) cc_final: 0.8426 (t) REVERT: A 535 LYS cc_start: 0.8540 (mttp) cc_final: 0.8333 (mttp) REVERT: A 542 ASN cc_start: 0.8247 (t0) cc_final: 0.7551 (t0) REVERT: A 547 LYS cc_start: 0.8487 (pttm) cc_final: 0.8281 (mttp) REVERT: A 592 PHE cc_start: 0.7708 (p90) cc_final: 0.6859 (p90) REVERT: A 663 ASP cc_start: 0.7328 (m-30) cc_final: 0.7065 (p0) REVERT: A 666 ILE cc_start: 0.8577 (mm) cc_final: 0.8318 (mt) REVERT: A 674 TYR cc_start: 0.8268 (t80) cc_final: 0.7829 (t80) REVERT: A 698 SER cc_start: 0.8628 (t) cc_final: 0.7991 (p) REVERT: A 710 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 759 PHE cc_start: 0.6859 (m-80) cc_final: 0.6357 (m-80) REVERT: A 762 GLN cc_start: 0.7386 (pt0) cc_final: 0.7184 (pm20) REVERT: A 763 LEU cc_start: 0.8477 (mt) cc_final: 0.8193 (mt) REVERT: A 773 GLU cc_start: 0.6589 (tm-30) cc_final: 0.5518 (tm-30) REVERT: A 803 SER cc_start: 0.8885 (m) cc_final: 0.8400 (p) REVERT: A 816 SER cc_start: 0.8081 (p) cc_final: 0.7622 (m) REVERT: A 868 GLU cc_start: 0.7410 (tp30) cc_final: 0.7102 (tp30) REVERT: A 869 MET cc_start: 0.8205 (mtt) cc_final: 0.7972 (mtm) REVERT: A 878 LEU cc_start: 0.8366 (mt) cc_final: 0.8003 (mp) REVERT: A 914 ASN cc_start: 0.7828 (p0) cc_final: 0.7594 (p0) REVERT: A 921 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8212 (mmmm) REVERT: A 922 LEU cc_start: 0.8509 (tp) cc_final: 0.8280 (tp) REVERT: A 925 ASN cc_start: 0.8512 (m-40) cc_final: 0.8140 (m-40) REVERT: A 949 GLN cc_start: 0.8346 (mm110) cc_final: 0.7936 (mm-40) REVERT: A 953 ASN cc_start: 0.8480 (m-40) cc_final: 0.8133 (m110) REVERT: A 979 ASP cc_start: 0.7483 (t70) cc_final: 0.7262 (t0) REVERT: A 983 ARG cc_start: 0.8395 (mtm180) cc_final: 0.8188 (mtp85) REVERT: A 988 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 1019 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7326 (ttp80) REVERT: A 1029 MET cc_start: 0.8432 (tpp) cc_final: 0.7606 (ttm) REVERT: A 1038 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8132 (mtpp) REVERT: A 1050 MET cc_start: 0.7304 (ttm) cc_final: 0.6862 (mtp) REVERT: A 1117 THR cc_start: 0.8559 (p) cc_final: 0.8299 (t) REVERT: A 1125 ASN cc_start: 0.7802 (p0) cc_final: 0.7478 (p0) REVERT: A 1141 LEU cc_start: 0.8358 (tp) cc_final: 0.8058 (tt) REVERT: B 104 TRP cc_start: 0.7662 (m-90) cc_final: 0.6762 (m-90) REVERT: B 105 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7764 (mm) REVERT: B 106 PHE cc_start: 0.7443 (m-80) cc_final: 0.7007 (m-80) REVERT: B 190 PHE cc_start: 0.8138 (m-80) cc_final: 0.7850 (m-10) REVERT: B 193 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7592 (mttp) REVERT: B 200 LYS cc_start: 0.8032 (mmtm) cc_final: 0.7756 (mmmm) REVERT: B 224 GLU cc_start: 0.8047 (pm20) cc_final: 0.7635 (pm20) REVERT: B 340 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7262 (mm-30) REVERT: B 343 ASN cc_start: 0.6665 (t0) cc_final: 0.6098 (t0) REVERT: B 353 TRP cc_start: 0.8414 (p-90) cc_final: 0.8114 (p-90) REVERT: B 356 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8383 (tppp) REVERT: B 357 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7463 (mtp85) REVERT: B 380 TYR cc_start: 0.6824 (m-80) cc_final: 0.6467 (m-80) REVERT: B 392 PHE cc_start: 0.6938 (m-80) cc_final: 0.6504 (m-80) REVERT: B 433 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8132 (m) REVERT: B 439 ASN cc_start: 0.7631 (t0) cc_final: 0.7227 (t0) REVERT: B 515 PHE cc_start: 0.7609 (m-80) cc_final: 0.7228 (m-80) REVERT: B 659 SER cc_start: 0.8611 (m) cc_final: 0.8047 (p) REVERT: B 663 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: B 698 SER cc_start: 0.8654 (t) cc_final: 0.8426 (p) REVERT: B 708 SER cc_start: 0.8320 (t) cc_final: 0.7917 (p) REVERT: B 759 PHE cc_start: 0.7409 (t80) cc_final: 0.7195 (t80) REVERT: B 776 LYS cc_start: 0.8279 (tmmt) cc_final: 0.7876 (ttpp) REVERT: B 854 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8154 (tttp) REVERT: B 856 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8509 (mmmm) REVERT: B 911 VAL cc_start: 0.8444 (t) cc_final: 0.8202 (m) REVERT: B 921 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8448 (mmmm) REVERT: B 933 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8002 (mtmm) REVERT: B 935 GLN cc_start: 0.7972 (tt0) cc_final: 0.7565 (tt0) REVERT: B 969 LYS cc_start: 0.8034 (pttm) cc_final: 0.7744 (pttm) REVERT: B 976 VAL cc_start: 0.8610 (t) cc_final: 0.8238 (t) REVERT: B 990 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 994 ASP cc_start: 0.7621 (m-30) cc_final: 0.7200 (m-30) REVERT: B 1002 GLN cc_start: 0.7934 (tp40) cc_final: 0.7361 (tm-30) REVERT: B 1003 SER cc_start: 0.8874 (m) cc_final: 0.8016 (t) REVERT: B 1050 MET cc_start: 0.7536 (mtp) cc_final: 0.7283 (mtp) REVERT: B 1061 VAL cc_start: 0.8764 (t) cc_final: 0.8342 (p) REVERT: B 1086 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (ptpp) REVERT: B 1097 SER cc_start: 0.8626 (t) cc_final: 0.8185 (p) REVERT: C 30 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7804 (p0) REVERT: C 40 ASP cc_start: 0.8028 (t70) cc_final: 0.7750 (t70) REVERT: C 41 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7391 (mtpp) REVERT: C 65 PHE cc_start: 0.7282 (m-80) cc_final: 0.6809 (m-80) REVERT: C 188 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6911 (mtp85) REVERT: C 199 PHE cc_start: 0.7896 (t80) cc_final: 0.7343 (t80) REVERT: C 201 ILE cc_start: 0.8814 (mt) cc_final: 0.8473 (mp) REVERT: C 297 SER cc_start: 0.8000 (m) cc_final: 0.7586 (p) REVERT: C 324 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7227 (tm-30) REVERT: C 326 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6453 (pt) REVERT: C 332 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6378 (pp) REVERT: C 436 TRP cc_start: 0.7297 (p-90) cc_final: 0.6647 (p-90) REVERT: C 531 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 542 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7498 (t0) REVERT: C 556 ASN cc_start: 0.8615 (p0) cc_final: 0.8401 (p0) REVERT: C 576 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.6999 (m) REVERT: C 615 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8334 (t) REVERT: C 619 GLU cc_start: 0.6947 (mp0) cc_final: 0.6386 (mp0) REVERT: C 644 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7010 (tp40) REVERT: C 705 VAL cc_start: 0.8336 (t) cc_final: 0.8083 (m) REVERT: C 725 GLU cc_start: 0.7290 (tt0) cc_final: 0.7058 (tt0) REVERT: C 739 THR cc_start: 0.8128 (m) cc_final: 0.7410 (m) REVERT: C 764 LYS cc_start: 0.8408 (tttm) cc_final: 0.7996 (ttpp) REVERT: C 776 LYS cc_start: 0.8510 (tptp) cc_final: 0.8098 (tptp) REVERT: C 854 LYS cc_start: 0.8285 (tmmt) cc_final: 0.7964 (tptp) REVERT: C 918 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7175 (tt0) REVERT: C 964 LYS cc_start: 0.8619 (tppt) cc_final: 0.8211 (ttmm) REVERT: C 990 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7293 (mm-30) REVERT: C 998 THR cc_start: 0.8351 (t) cc_final: 0.8066 (p) REVERT: C 1014 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7551 (ttm110) REVERT: C 1072 GLU cc_start: 0.8457 (pm20) cc_final: 0.8149 (pm20) REVERT: C 1101 HIS cc_start: 0.8620 (m-70) cc_final: 0.8298 (m90) REVERT: D 4 LEU cc_start: 0.8305 (mt) cc_final: 0.7356 (tt) REVERT: D 110 TRP cc_start: 0.5309 (m100) cc_final: 0.5056 (m100) REVERT: H 78 ASN cc_start: 0.5658 (m110) cc_final: 0.5458 (t0) REVERT: I 4 LEU cc_start: 0.5991 (mt) cc_final: 0.5665 (mt) outliers start: 167 outliers final: 118 residues processed: 841 average time/residue: 0.4131 time to fit residues: 547.0147 Evaluate side-chains 830 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 696 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 358 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 613 GLN A 710 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 949 GLN B 955 ASN C 30 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29860 Z= 0.297 Angle : 0.623 12.858 40678 Z= 0.314 Chirality : 0.045 0.226 4657 Planarity : 0.005 0.117 5239 Dihedral : 5.520 61.437 4119 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.40 % Allowed : 18.29 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.50 (0.13), residues: 3713 helix: 0.89 (0.21), residues: 647 sheet: -1.59 (0.17), residues: 826 loop : -2.62 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.017 0.001 HIS C1048 PHE 0.038 0.002 PHE C 106 TYR 0.026 0.002 TYR C 674 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 717 time to evaluate : 3.248 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: symmetry clash REVERT: A 33 THR cc_start: 0.6636 (m) cc_final: 0.6196 (p) REVERT: A 188 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6445 (mmt-90) REVERT: A 190 PHE cc_start: 0.7700 (m-80) cc_final: 0.7485 (m-10) REVERT: A 226 LEU cc_start: 0.7988 (mt) cc_final: 0.7699 (mt) REVERT: A 281 GLU cc_start: 0.7415 (pp20) cc_final: 0.7156 (pp20) REVERT: A 297 SER cc_start: 0.8464 (m) cc_final: 0.8026 (p) REVERT: A 326 ILE cc_start: 0.8060 (mp) cc_final: 0.7797 (mt) REVERT: A 436 TRP cc_start: 0.6768 (p-90) cc_final: 0.6425 (p90) REVERT: A 478 LYS cc_start: -0.0334 (OUTLIER) cc_final: -0.2091 (ptmm) REVERT: A 534 VAL cc_start: 0.8636 (t) cc_final: 0.8415 (t) REVERT: A 535 LYS cc_start: 0.8538 (mttp) cc_final: 0.8266 (mttm) REVERT: A 542 ASN cc_start: 0.8182 (t0) cc_final: 0.7481 (t0) REVERT: A 592 PHE cc_start: 0.7704 (p90) cc_final: 0.7196 (p90) REVERT: A 666 ILE cc_start: 0.8594 (mm) cc_final: 0.8354 (mt) REVERT: A 698 SER cc_start: 0.8567 (t) cc_final: 0.7988 (p) REVERT: A 710 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 737 ASP cc_start: 0.7120 (t70) cc_final: 0.6785 (t70) REVERT: A 759 PHE cc_start: 0.6851 (m-80) cc_final: 0.6368 (m-80) REVERT: A 762 GLN cc_start: 0.7399 (pt0) cc_final: 0.7179 (pm20) REVERT: A 763 LEU cc_start: 0.8486 (mt) cc_final: 0.8231 (mt) REVERT: A 773 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6033 (tm-30) REVERT: A 803 SER cc_start: 0.8897 (m) cc_final: 0.8367 (p) REVERT: A 816 SER cc_start: 0.8053 (p) cc_final: 0.7663 (t) REVERT: A 868 GLU cc_start: 0.7399 (tp30) cc_final: 0.7107 (tp30) REVERT: A 869 MET cc_start: 0.8217 (mtt) cc_final: 0.7980 (mtm) REVERT: A 878 LEU cc_start: 0.8364 (mt) cc_final: 0.8030 (mp) REVERT: A 902 MET cc_start: 0.8271 (tpp) cc_final: 0.7912 (tpp) REVERT: A 921 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8213 (mmmm) REVERT: A 922 LEU cc_start: 0.8516 (tp) cc_final: 0.8268 (tp) REVERT: A 925 ASN cc_start: 0.8480 (m-40) cc_final: 0.8123 (m-40) REVERT: A 949 GLN cc_start: 0.8372 (mm110) cc_final: 0.7956 (mm-40) REVERT: A 953 ASN cc_start: 0.8455 (m-40) cc_final: 0.8156 (m110) REVERT: A 979 ASP cc_start: 0.7496 (t70) cc_final: 0.7261 (t0) REVERT: A 988 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7220 (tm-30) REVERT: A 994 ASP cc_start: 0.7450 (m-30) cc_final: 0.7073 (t0) REVERT: A 1029 MET cc_start: 0.8403 (tpp) cc_final: 0.7589 (ttm) REVERT: A 1038 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8127 (mtpp) REVERT: A 1114 ILE cc_start: 0.8578 (mm) cc_final: 0.8287 (mt) REVERT: A 1117 THR cc_start: 0.8628 (p) cc_final: 0.8377 (t) REVERT: A 1141 LEU cc_start: 0.8390 (tp) cc_final: 0.8101 (tt) REVERT: B 60 SER cc_start: 0.8658 (t) cc_final: 0.8425 (t) REVERT: B 81 ASN cc_start: 0.8240 (t0) cc_final: 0.7920 (t0) REVERT: B 104 TRP cc_start: 0.7758 (m-90) cc_final: 0.6754 (m-90) REVERT: B 135 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6338 (p90) REVERT: B 190 PHE cc_start: 0.8190 (m-80) cc_final: 0.7879 (m-10) REVERT: B 193 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7766 (mttm) REVERT: B 200 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7784 (mmmm) REVERT: B 224 GLU cc_start: 0.8031 (pm20) cc_final: 0.7651 (pm20) REVERT: B 329 PHE cc_start: 0.8069 (m-10) cc_final: 0.7695 (m-80) REVERT: B 340 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7252 (mm-30) REVERT: B 343 ASN cc_start: 0.6674 (t0) cc_final: 0.6065 (t0) REVERT: B 353 TRP cc_start: 0.8472 (p-90) cc_final: 0.8172 (p-90) REVERT: B 356 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8433 (tppp) REVERT: B 357 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7315 (mtm110) REVERT: B 380 TYR cc_start: 0.6823 (m-80) cc_final: 0.6423 (m-80) REVERT: B 392 PHE cc_start: 0.7052 (m-80) cc_final: 0.6560 (m-80) REVERT: B 394 ASN cc_start: 0.7989 (p0) cc_final: 0.7371 (p0) REVERT: B 433 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 439 ASN cc_start: 0.7617 (t0) cc_final: 0.7365 (t0) REVERT: B 517 LEU cc_start: 0.7678 (tt) cc_final: 0.7370 (tt) REVERT: B 659 SER cc_start: 0.8587 (m) cc_final: 0.8048 (p) REVERT: B 663 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: B 698 SER cc_start: 0.8646 (t) cc_final: 0.8381 (p) REVERT: B 759 PHE cc_start: 0.7527 (t80) cc_final: 0.7151 (t80) REVERT: B 776 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7923 (ttpt) REVERT: B 854 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8157 (tttp) REVERT: B 856 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8544 (mmmm) REVERT: B 911 VAL cc_start: 0.8525 (t) cc_final: 0.8296 (m) REVERT: B 921 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8433 (mmmm) REVERT: B 933 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8000 (mtmm) REVERT: B 935 GLN cc_start: 0.7988 (tt0) cc_final: 0.7510 (tt0) REVERT: B 969 LYS cc_start: 0.8078 (pttm) cc_final: 0.7764 (pttm) REVERT: B 976 VAL cc_start: 0.8601 (t) cc_final: 0.8326 (t) REVERT: B 990 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 994 ASP cc_start: 0.7645 (m-30) cc_final: 0.7199 (m-30) REVERT: B 1002 GLN cc_start: 0.7960 (tp40) cc_final: 0.7307 (tm-30) REVERT: B 1003 SER cc_start: 0.8858 (m) cc_final: 0.7924 (t) REVERT: B 1050 MET cc_start: 0.7475 (mtp) cc_final: 0.7259 (mtp) REVERT: B 1061 VAL cc_start: 0.8770 (t) cc_final: 0.8327 (p) REVERT: B 1086 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8115 (ptpp) REVERT: B 1097 SER cc_start: 0.8625 (t) cc_final: 0.8127 (p) REVERT: C 41 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7528 (mtpp) REVERT: C 43 PHE cc_start: 0.8289 (t80) cc_final: 0.7995 (t80) REVERT: C 188 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6739 (mtp85) REVERT: C 199 PHE cc_start: 0.7890 (t80) cc_final: 0.7244 (t80) REVERT: C 201 ILE cc_start: 0.8852 (mt) cc_final: 0.8503 (mp) REVERT: C 293 LEU cc_start: 0.8470 (tp) cc_final: 0.8232 (tp) REVERT: C 297 SER cc_start: 0.8103 (m) cc_final: 0.7507 (p) REVERT: C 308 VAL cc_start: 0.8600 (t) cc_final: 0.8316 (m) REVERT: C 324 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 326 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6441 (pt) REVERT: C 332 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6379 (pp) REVERT: C 436 TRP cc_start: 0.7362 (p-90) cc_final: 0.6846 (p-90) REVERT: C 531 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8563 (p) REVERT: C 542 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7532 (t0) REVERT: C 556 ASN cc_start: 0.8564 (p0) cc_final: 0.8311 (p0) REVERT: C 576 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7134 (m) REVERT: C 615 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8304 (t) REVERT: C 619 GLU cc_start: 0.7014 (mp0) cc_final: 0.6474 (mp0) REVERT: C 644 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7039 (tp40) REVERT: C 663 ASP cc_start: 0.7601 (t70) cc_final: 0.7265 (t0) REVERT: C 705 VAL cc_start: 0.8367 (t) cc_final: 0.8124 (m) REVERT: C 725 GLU cc_start: 0.7287 (tt0) cc_final: 0.7051 (tt0) REVERT: C 764 LYS cc_start: 0.8391 (tttm) cc_final: 0.8007 (ttpp) REVERT: C 776 LYS cc_start: 0.8505 (tptp) cc_final: 0.8180 (tptp) REVERT: C 780 GLU cc_start: 0.7483 (pt0) cc_final: 0.7224 (pt0) REVERT: C 854 LYS cc_start: 0.8309 (tmmt) cc_final: 0.7998 (tptp) REVERT: C 918 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7223 (tt0) REVERT: C 964 LYS cc_start: 0.8565 (tppt) cc_final: 0.8175 (ttmm) REVERT: C 990 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7309 (mm-30) REVERT: C 998 THR cc_start: 0.8405 (t) cc_final: 0.8123 (p) REVERT: C 1014 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7563 (ttm110) REVERT: C 1048 HIS cc_start: 0.7813 (t70) cc_final: 0.7492 (t-170) REVERT: C 1050 MET cc_start: 0.7261 (mtm) cc_final: 0.6948 (mtp) REVERT: C 1072 GLU cc_start: 0.8440 (pm20) cc_final: 0.8121 (pm20) REVERT: D 4 LEU cc_start: 0.8286 (mt) cc_final: 0.7262 (tt) REVERT: G 49 MET cc_start: 0.3000 (ppp) cc_final: 0.2174 (tpt) REVERT: H 60 ARG cc_start: 0.5463 (mmt90) cc_final: 0.5105 (mmt90) REVERT: I 4 LEU cc_start: 0.6185 (mt) cc_final: 0.5968 (mt) outliers start: 175 outliers final: 135 residues processed: 833 average time/residue: 0.4277 time to fit residues: 558.1563 Evaluate side-chains 837 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 688 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 262 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 302 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 357 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 613 GLN A 710 ASN A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29860 Z= 0.208 Angle : 0.605 12.627 40678 Z= 0.302 Chirality : 0.044 0.231 4657 Planarity : 0.005 0.118 5239 Dihedral : 5.440 61.123 4117 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.09 % Allowed : 19.55 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.34 (0.13), residues: 3713 helix: 1.09 (0.21), residues: 641 sheet: -1.51 (0.17), residues: 802 loop : -2.51 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.015 0.001 HIS C1048 PHE 0.034 0.001 PHE C 106 TYR 0.024 0.001 TYR C 655 ARG 0.009 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 691 time to evaluate : 3.521 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: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6608 (m) cc_final: 0.6150 (p) REVERT: A 188 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6584 (mmt180) REVERT: A 190 PHE cc_start: 0.7598 (m-80) cc_final: 0.7272 (m-10) REVERT: A 214 GLU cc_start: 0.8122 (mp0) cc_final: 0.7887 (mp0) REVERT: A 226 LEU cc_start: 0.7911 (mt) cc_final: 0.7642 (mt) REVERT: A 281 GLU cc_start: 0.7456 (pp20) cc_final: 0.7098 (pp20) REVERT: A 297 SER cc_start: 0.8401 (m) cc_final: 0.8047 (p) REVERT: A 326 ILE cc_start: 0.8050 (mp) cc_final: 0.7811 (mt) REVERT: A 436 TRP cc_start: 0.6726 (p-90) cc_final: 0.6413 (p90) REVERT: A 478 LYS cc_start: -0.0487 (OUTLIER) cc_final: -0.2233 (ptmm) REVERT: A 495 TYR cc_start: 0.5519 (m-80) cc_final: 0.5236 (m-80) REVERT: A 534 VAL cc_start: 0.8604 (t) cc_final: 0.8392 (t) REVERT: A 535 LYS cc_start: 0.8524 (mttp) cc_final: 0.8239 (mttm) REVERT: A 592 PHE cc_start: 0.7701 (p90) cc_final: 0.7312 (p90) REVERT: A 663 ASP cc_start: 0.7236 (m-30) cc_final: 0.7019 (p0) REVERT: A 666 ILE cc_start: 0.8587 (mm) cc_final: 0.8333 (mt) REVERT: A 674 TYR cc_start: 0.8376 (t80) cc_final: 0.8170 (t80) REVERT: A 697 MET cc_start: 0.7296 (ttm) cc_final: 0.6925 (mtp) REVERT: A 698 SER cc_start: 0.8509 (t) cc_final: 0.7864 (p) REVERT: A 737 ASP cc_start: 0.7161 (t70) cc_final: 0.6812 (t70) REVERT: A 759 PHE cc_start: 0.6815 (m-80) cc_final: 0.6312 (m-80) REVERT: A 762 GLN cc_start: 0.7341 (pt0) cc_final: 0.7136 (pm20) REVERT: A 763 LEU cc_start: 0.8440 (mt) cc_final: 0.8190 (mt) REVERT: A 773 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6015 (tm-30) REVERT: A 803 SER cc_start: 0.8859 (m) cc_final: 0.8341 (p) REVERT: A 816 SER cc_start: 0.8057 (p) cc_final: 0.7616 (m) REVERT: A 825 LYS cc_start: 0.8404 (mmtm) cc_final: 0.8149 (mtpt) REVERT: A 868 GLU cc_start: 0.7375 (tp30) cc_final: 0.7075 (tp30) REVERT: A 869 MET cc_start: 0.8200 (mtt) cc_final: 0.7991 (mtm) REVERT: A 878 LEU cc_start: 0.8341 (mt) cc_final: 0.8030 (mp) REVERT: A 902 MET cc_start: 0.8192 (tpp) cc_final: 0.7877 (tpp) REVERT: A 921 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8202 (mmmm) REVERT: A 922 LEU cc_start: 0.8492 (tp) cc_final: 0.8240 (tp) REVERT: A 925 ASN cc_start: 0.8461 (m-40) cc_final: 0.8104 (m-40) REVERT: A 949 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7860 (mm-40) REVERT: A 953 ASN cc_start: 0.8450 (m-40) cc_final: 0.8163 (m110) REVERT: A 979 ASP cc_start: 0.7367 (t70) cc_final: 0.7089 (t0) REVERT: A 980 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 988 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7184 (tm-30) REVERT: A 994 ASP cc_start: 0.7431 (m-30) cc_final: 0.7088 (t0) REVERT: A 1029 MET cc_start: 0.8391 (tpp) cc_final: 0.7615 (ttm) REVERT: A 1030 SER cc_start: 0.8272 (m) cc_final: 0.7980 (t) REVERT: A 1038 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8113 (mtpp) REVERT: A 1114 ILE cc_start: 0.8600 (mm) cc_final: 0.8317 (mt) REVERT: A 1117 THR cc_start: 0.8575 (p) cc_final: 0.8322 (t) REVERT: A 1125 ASN cc_start: 0.7753 (p0) cc_final: 0.7540 (p0) REVERT: A 1141 LEU cc_start: 0.8378 (tp) cc_final: 0.8100 (tt) REVERT: B 81 ASN cc_start: 0.8305 (t0) cc_final: 0.8046 (t0) REVERT: B 104 TRP cc_start: 0.7766 (m-90) cc_final: 0.6651 (m-90) REVERT: B 170 TYR cc_start: 0.8019 (t80) cc_final: 0.7614 (t80) REVERT: B 190 PHE cc_start: 0.8197 (m-80) cc_final: 0.7889 (m-10) REVERT: B 200 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7970 (mmmm) REVERT: B 329 PHE cc_start: 0.8021 (m-10) cc_final: 0.7617 (m-80) REVERT: B 340 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 343 ASN cc_start: 0.6669 (t0) cc_final: 0.6079 (t0) REVERT: B 353 TRP cc_start: 0.8374 (p-90) cc_final: 0.7998 (p-90) REVERT: B 356 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8428 (tppp) REVERT: B 357 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7686 (mtp85) REVERT: B 380 TYR cc_start: 0.6820 (m-80) cc_final: 0.6347 (m-80) REVERT: B 392 PHE cc_start: 0.7097 (m-80) cc_final: 0.6656 (m-80) REVERT: B 394 ASN cc_start: 0.7991 (p0) cc_final: 0.7335 (p0) REVERT: B 433 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 439 ASN cc_start: 0.7561 (t0) cc_final: 0.7293 (t0) REVERT: B 528 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7652 (tmmt) REVERT: B 580 GLN cc_start: 0.7504 (mm110) cc_final: 0.7192 (mm110) REVERT: B 659 SER cc_start: 0.8584 (m) cc_final: 0.8039 (p) REVERT: B 663 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 698 SER cc_start: 0.8637 (t) cc_final: 0.8372 (p) REVERT: B 759 PHE cc_start: 0.7468 (t80) cc_final: 0.7088 (t80) REVERT: B 776 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7880 (ttpp) REVERT: B 854 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8120 (tttp) REVERT: B 856 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8518 (mmmm) REVERT: B 911 VAL cc_start: 0.8533 (t) cc_final: 0.8267 (m) REVERT: B 921 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8409 (mmmm) REVERT: B 933 LYS cc_start: 0.8259 (mtpt) cc_final: 0.8008 (ttmm) REVERT: B 935 GLN cc_start: 0.7948 (tt0) cc_final: 0.7533 (tt0) REVERT: B 969 LYS cc_start: 0.8116 (pttm) cc_final: 0.7846 (pttm) REVERT: B 976 VAL cc_start: 0.8453 (t) cc_final: 0.8176 (t) REVERT: B 990 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 994 ASP cc_start: 0.7655 (m-30) cc_final: 0.7149 (m-30) REVERT: B 1002 GLN cc_start: 0.7906 (tp40) cc_final: 0.7336 (tm-30) REVERT: B 1003 SER cc_start: 0.8911 (m) cc_final: 0.7962 (t) REVERT: B 1061 VAL cc_start: 0.8762 (t) cc_final: 0.8298 (p) REVERT: B 1086 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8053 (ptpp) REVERT: B 1097 SER cc_start: 0.8638 (t) cc_final: 0.8120 (p) REVERT: C 30 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7712 (p0) REVERT: C 41 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7565 (mttt) REVERT: C 43 PHE cc_start: 0.8275 (t80) cc_final: 0.8037 (t80) REVERT: C 53 ASP cc_start: 0.7367 (t0) cc_final: 0.6965 (m-30) REVERT: C 188 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6751 (mtp85) REVERT: C 192 PHE cc_start: 0.8711 (m-80) cc_final: 0.8496 (m-10) REVERT: C 199 PHE cc_start: 0.7869 (t80) cc_final: 0.7203 (t80) REVERT: C 201 ILE cc_start: 0.8865 (mt) cc_final: 0.8520 (mp) REVERT: C 297 SER cc_start: 0.8030 (m) cc_final: 0.7417 (p) REVERT: C 308 VAL cc_start: 0.8590 (t) cc_final: 0.8327 (m) REVERT: C 324 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 326 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6464 (pt) REVERT: C 332 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6365 (pp) REVERT: C 436 TRP cc_start: 0.7359 (p-90) cc_final: 0.6850 (p-90) REVERT: C 531 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 542 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7502 (t0) REVERT: C 556 ASN cc_start: 0.8558 (p0) cc_final: 0.8267 (p0) REVERT: C 619 GLU cc_start: 0.6997 (mp0) cc_final: 0.6478 (mp0) REVERT: C 644 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7258 (tp40) REVERT: C 663 ASP cc_start: 0.7258 (t70) cc_final: 0.6871 (t0) REVERT: C 705 VAL cc_start: 0.8356 (t) cc_final: 0.8108 (m) REVERT: C 725 GLU cc_start: 0.7277 (tt0) cc_final: 0.7016 (tt0) REVERT: C 764 LYS cc_start: 0.8340 (tttm) cc_final: 0.7952 (ttpp) REVERT: C 776 LYS cc_start: 0.8488 (tptp) cc_final: 0.8145 (tptp) REVERT: C 780 GLU cc_start: 0.7492 (pt0) cc_final: 0.7265 (pt0) REVERT: C 811 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8098 (ttpp) REVERT: C 854 LYS cc_start: 0.8311 (tmmt) cc_final: 0.7943 (tptp) REVERT: C 950 ASP cc_start: 0.7669 (t70) cc_final: 0.6978 (t0) REVERT: C 964 LYS cc_start: 0.8516 (tppt) cc_final: 0.8148 (ttmm) REVERT: C 980 ILE cc_start: 0.8419 (mt) cc_final: 0.8147 (mt) REVERT: C 990 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7331 (mm-30) REVERT: C 998 THR cc_start: 0.8420 (t) cc_final: 0.8133 (p) REVERT: C 1014 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7534 (ttm110) REVERT: C 1029 MET cc_start: 0.8384 (tpp) cc_final: 0.7958 (tpp) REVERT: C 1048 HIS cc_start: 0.7799 (t70) cc_final: 0.7488 (t-170) REVERT: C 1050 MET cc_start: 0.7184 (mtm) cc_final: 0.6908 (mtp) REVERT: C 1072 GLU cc_start: 0.8401 (pm20) cc_final: 0.8088 (pm20) REVERT: D 4 LEU cc_start: 0.8228 (mt) cc_final: 0.6926 (tt) REVERT: G 49 MET cc_start: 0.3374 (ppp) cc_final: 0.2374 (tpt) REVERT: H 60 ARG cc_start: 0.5384 (mmt90) cc_final: 0.5120 (mmt90) outliers start: 165 outliers final: 122 residues processed: 803 average time/residue: 0.4298 time to fit residues: 539.2329 Evaluate side-chains 817 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 681 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 0.3980 chunk 142 optimal weight: 0.0010 chunk 213 optimal weight: 10.0000 chunk 107 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 176 optimal weight: 0.0070 chunk 33 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 710 ASN A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 417 ASN B 506 GLN B 954 HIS B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29860 Z= 0.153 Angle : 0.580 13.806 40678 Z= 0.288 Chirality : 0.043 0.201 4657 Planarity : 0.005 0.115 5239 Dihedral : 5.249 60.233 4117 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.19 % Allowed : 20.51 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.20 (0.13), residues: 3713 helix: 1.20 (0.21), residues: 644 sheet: -1.49 (0.17), residues: 835 loop : -2.39 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 110 HIS 0.015 0.001 HIS C1048 PHE 0.041 0.001 PHE A 192 TYR 0.022 0.001 TYR C 707 ARG 0.009 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 675 time to evaluate : 3.161 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: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6504 (m) cc_final: 0.6057 (p) REVERT: A 41 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7948 (mtpt) REVERT: A 188 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6501 (mmt180) REVERT: A 190 PHE cc_start: 0.7616 (m-80) cc_final: 0.7389 (m-10) REVERT: A 214 GLU cc_start: 0.8107 (mp0) cc_final: 0.7862 (mp0) REVERT: A 226 LEU cc_start: 0.7710 (mt) cc_final: 0.7500 (mt) REVERT: A 297 SER cc_start: 0.8385 (m) cc_final: 0.8005 (p) REVERT: A 326 ILE cc_start: 0.8032 (mp) cc_final: 0.7788 (mt) REVERT: A 436 TRP cc_start: 0.6795 (p-90) cc_final: 0.6552 (p90) REVERT: A 478 LYS cc_start: -0.0535 (OUTLIER) cc_final: -0.2372 (ptmm) REVERT: A 495 TYR cc_start: 0.5506 (m-80) cc_final: 0.5237 (m-80) REVERT: A 535 LYS cc_start: 0.8483 (mttp) cc_final: 0.8233 (mttm) REVERT: A 660 TYR cc_start: 0.7874 (m-10) cc_final: 0.7576 (m-10) REVERT: A 666 ILE cc_start: 0.8566 (mm) cc_final: 0.8303 (mt) REVERT: A 697 MET cc_start: 0.7324 (ttm) cc_final: 0.7030 (mtp) REVERT: A 698 SER cc_start: 0.8475 (t) cc_final: 0.7792 (p) REVERT: A 737 ASP cc_start: 0.7208 (t70) cc_final: 0.6794 (t70) REVERT: A 759 PHE cc_start: 0.6774 (m-80) cc_final: 0.6245 (m-80) REVERT: A 762 GLN cc_start: 0.7221 (pt0) cc_final: 0.6949 (pm20) REVERT: A 763 LEU cc_start: 0.8361 (mt) cc_final: 0.8081 (mt) REVERT: A 773 GLU cc_start: 0.6369 (tm-30) cc_final: 0.5997 (tm-30) REVERT: A 774 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6453 (mm-40) REVERT: A 803 SER cc_start: 0.8795 (m) cc_final: 0.8274 (p) REVERT: A 816 SER cc_start: 0.8029 (p) cc_final: 0.7649 (m) REVERT: A 868 GLU cc_start: 0.7351 (tp30) cc_final: 0.7064 (tp30) REVERT: A 869 MET cc_start: 0.8198 (mtt) cc_final: 0.7987 (mtm) REVERT: A 902 MET cc_start: 0.8120 (tpp) cc_final: 0.7840 (tpp) REVERT: A 921 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8170 (mmmm) REVERT: A 922 LEU cc_start: 0.8459 (tp) cc_final: 0.8204 (tp) REVERT: A 925 ASN cc_start: 0.8455 (m-40) cc_final: 0.8078 (m-40) REVERT: A 945 LEU cc_start: 0.8637 (mm) cc_final: 0.8332 (mp) REVERT: A 949 GLN cc_start: 0.8325 (mm110) cc_final: 0.7840 (mm-40) REVERT: A 953 ASN cc_start: 0.8416 (m-40) cc_final: 0.8151 (m110) REVERT: A 979 ASP cc_start: 0.7288 (t70) cc_final: 0.6994 (t0) REVERT: A 988 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7164 (tm-30) REVERT: A 994 ASP cc_start: 0.7276 (m-30) cc_final: 0.6797 (t0) REVERT: A 1029 MET cc_start: 0.8330 (tpp) cc_final: 0.7617 (ttm) REVERT: A 1038 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8182 (mttm) REVERT: A 1050 MET cc_start: 0.6944 (ttm) cc_final: 0.6740 (ttp) REVERT: A 1114 ILE cc_start: 0.8573 (mm) cc_final: 0.8260 (mt) REVERT: A 1117 THR cc_start: 0.8535 (p) cc_final: 0.8239 (t) REVERT: A 1141 LEU cc_start: 0.8349 (tp) cc_final: 0.8092 (tt) REVERT: B 104 TRP cc_start: 0.7766 (m-90) cc_final: 0.6596 (m-90) REVERT: B 170 TYR cc_start: 0.7958 (t80) cc_final: 0.7531 (t80) REVERT: B 190 PHE cc_start: 0.8184 (m-80) cc_final: 0.7828 (m-10) REVERT: B 278 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8308 (ttmt) REVERT: B 340 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7030 (mm-30) REVERT: B 341 VAL cc_start: 0.8989 (m) cc_final: 0.8720 (p) REVERT: B 353 TRP cc_start: 0.8352 (p-90) cc_final: 0.8081 (p-90) REVERT: B 356 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8428 (tppp) REVERT: B 380 TYR cc_start: 0.6802 (m-80) cc_final: 0.6294 (m-80) REVERT: B 392 PHE cc_start: 0.7022 (m-80) cc_final: 0.6752 (m-80) REVERT: B 394 ASN cc_start: 0.7945 (p0) cc_final: 0.7310 (p0) REVERT: B 433 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8225 (m) REVERT: B 436 TRP cc_start: 0.8006 (p90) cc_final: 0.7698 (p90) REVERT: B 439 ASN cc_start: 0.7389 (t0) cc_final: 0.7142 (t0) REVERT: B 580 GLN cc_start: 0.7498 (mm110) cc_final: 0.7206 (mm110) REVERT: B 645 THR cc_start: 0.8270 (p) cc_final: 0.6718 (m) REVERT: B 658 ASN cc_start: 0.7267 (t0) cc_final: 0.6946 (t0) REVERT: B 659 SER cc_start: 0.8561 (m) cc_final: 0.7672 (p) REVERT: B 698 SER cc_start: 0.8641 (t) cc_final: 0.8363 (p) REVERT: B 759 PHE cc_start: 0.7514 (t80) cc_final: 0.6668 (t80) REVERT: B 765 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6718 (mtm180) REVERT: B 776 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7866 (ttpp) REVERT: B 803 SER cc_start: 0.8606 (p) cc_final: 0.8387 (t) REVERT: B 854 LYS cc_start: 0.8249 (ttpp) cc_final: 0.8025 (tttp) REVERT: B 856 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8322 (mmmm) REVERT: B 911 VAL cc_start: 0.8471 (t) cc_final: 0.8173 (m) REVERT: B 921 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8387 (mmmm) REVERT: B 933 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7962 (ttmm) REVERT: B 935 GLN cc_start: 0.7960 (tt0) cc_final: 0.7735 (tt0) REVERT: B 954 HIS cc_start: 0.7620 (m90) cc_final: 0.7260 (m-70) REVERT: B 969 LYS cc_start: 0.8083 (pttm) cc_final: 0.7846 (pttm) REVERT: B 976 VAL cc_start: 0.8254 (t) cc_final: 0.7986 (t) REVERT: B 990 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7060 (mm-30) REVERT: B 994 ASP cc_start: 0.7625 (m-30) cc_final: 0.7102 (m-30) REVERT: B 1002 GLN cc_start: 0.7830 (tp40) cc_final: 0.7574 (tm-30) REVERT: B 1003 SER cc_start: 0.8814 (m) cc_final: 0.8435 (t) REVERT: B 1061 VAL cc_start: 0.8749 (t) cc_final: 0.8345 (p) REVERT: B 1072 GLU cc_start: 0.7856 (pm20) cc_final: 0.7621 (pm20) REVERT: B 1086 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7962 (ptpp) REVERT: B 1097 SER cc_start: 0.8662 (t) cc_final: 0.8108 (p) REVERT: C 41 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7533 (mttt) REVERT: C 43 PHE cc_start: 0.8240 (t80) cc_final: 0.7957 (t80) REVERT: C 53 ASP cc_start: 0.7376 (t0) cc_final: 0.7007 (m-30) REVERT: C 120 VAL cc_start: 0.8824 (t) cc_final: 0.8621 (p) REVERT: C 188 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6753 (mtp85) REVERT: C 192 PHE cc_start: 0.8718 (m-80) cc_final: 0.8503 (m-10) REVERT: C 199 PHE cc_start: 0.7860 (t80) cc_final: 0.7149 (t80) REVERT: C 201 ILE cc_start: 0.8855 (mt) cc_final: 0.8542 (mp) REVERT: C 297 SER cc_start: 0.7926 (m) cc_final: 0.7190 (p) REVERT: C 301 CYS cc_start: 0.5992 (m) cc_final: 0.5712 (m) REVERT: C 308 VAL cc_start: 0.8653 (t) cc_final: 0.8354 (m) REVERT: C 324 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7238 (tm-30) REVERT: C 326 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6463 (pt) REVERT: C 332 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6369 (pp) REVERT: C 436 TRP cc_start: 0.7308 (p-90) cc_final: 0.6801 (p-90) REVERT: C 531 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8531 (p) REVERT: C 542 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7289 (t0) REVERT: C 619 GLU cc_start: 0.6972 (mp0) cc_final: 0.6478 (mp0) REVERT: C 644 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7124 (tp40) REVERT: C 663 ASP cc_start: 0.7277 (t70) cc_final: 0.6875 (t0) REVERT: C 705 VAL cc_start: 0.8292 (t) cc_final: 0.8080 (m) REVERT: C 725 GLU cc_start: 0.7235 (tt0) cc_final: 0.6974 (tt0) REVERT: C 764 LYS cc_start: 0.8322 (tttm) cc_final: 0.7912 (ttpp) REVERT: C 776 LYS cc_start: 0.8431 (tptp) cc_final: 0.8020 (tptp) REVERT: C 811 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8102 (ttpp) REVERT: C 825 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8177 (ttmm) REVERT: C 950 ASP cc_start: 0.7577 (t70) cc_final: 0.6911 (t0) REVERT: C 964 LYS cc_start: 0.8556 (tppt) cc_final: 0.8192 (ttmm) REVERT: C 980 ILE cc_start: 0.8465 (mt) cc_final: 0.8223 (mt) REVERT: C 990 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 998 THR cc_start: 0.8394 (t) cc_final: 0.8114 (p) REVERT: C 1014 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7457 (ttm110) REVERT: C 1029 MET cc_start: 0.8396 (tpp) cc_final: 0.7970 (tpp) REVERT: C 1048 HIS cc_start: 0.7763 (t70) cc_final: 0.7249 (t-170) REVERT: C 1050 MET cc_start: 0.7205 (mtm) cc_final: 0.6876 (mtp) REVERT: C 1051 SER cc_start: 0.8161 (m) cc_final: 0.7854 (m) REVERT: C 1072 GLU cc_start: 0.8391 (pm20) cc_final: 0.8111 (pm20) REVERT: G 49 MET cc_start: 0.3292 (ppp) cc_final: 0.2337 (tpt) REVERT: H 60 ARG cc_start: 0.5305 (mmt90) cc_final: 0.5055 (mmt90) outliers start: 136 outliers final: 105 residues processed: 771 average time/residue: 0.4551 time to fit residues: 556.7826 Evaluate side-chains 770 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 654 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 8.9990 chunk 342 optimal weight: 30.0000 chunk 312 optimal weight: 0.0970 chunk 333 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 145 optimal weight: 0.0000 chunk 261 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 710 ASN A 774 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 955 ASN A 957 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 955 ASN C 122 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29860 Z= 0.167 Angle : 0.583 12.093 40678 Z= 0.289 Chirality : 0.043 0.195 4657 Planarity : 0.005 0.119 5239 Dihedral : 5.193 59.680 4115 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.95 % Allowed : 20.60 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.10 (0.13), residues: 3713 helix: 1.30 (0.21), residues: 645 sheet: -1.41 (0.17), residues: 819 loop : -2.33 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 110 HIS 0.014 0.001 HIS C1048 PHE 0.034 0.001 PHE A 592 TYR 0.021 0.001 TYR C 707 ARG 0.010 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 662 time to evaluate : 3.247 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: A 33 THR cc_start: 0.6551 (m) cc_final: 0.6101 (p) REVERT: A 41 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7923 (mtpt) REVERT: A 92 PHE cc_start: 0.7269 (t80) cc_final: 0.6929 (t80) REVERT: A 94 SER cc_start: 0.7324 (OUTLIER) cc_final: 0.7035 (m) REVERT: A 188 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6555 (mmt180) REVERT: A 190 PHE cc_start: 0.7627 (m-80) cc_final: 0.7379 (m-10) REVERT: A 273 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7624 (mtp85) REVERT: A 297 SER cc_start: 0.8396 (m) cc_final: 0.8004 (p) REVERT: A 436 TRP cc_start: 0.6775 (p-90) cc_final: 0.6537 (p90) REVERT: A 478 LYS cc_start: -0.0431 (OUTLIER) cc_final: -0.2200 (ptmm) REVERT: A 534 VAL cc_start: 0.8543 (t) cc_final: 0.8220 (m) REVERT: A 535 LYS cc_start: 0.8467 (mttp) cc_final: 0.8232 (mttm) REVERT: A 587 ILE cc_start: 0.8129 (mt) cc_final: 0.7566 (tt) REVERT: A 660 TYR cc_start: 0.7893 (m-10) cc_final: 0.7631 (m-10) REVERT: A 666 ILE cc_start: 0.8548 (mm) cc_final: 0.8324 (mt) REVERT: A 697 MET cc_start: 0.7330 (ttm) cc_final: 0.7051 (mtp) REVERT: A 698 SER cc_start: 0.8469 (t) cc_final: 0.7773 (p) REVERT: A 710 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7427 (p0) REVERT: A 737 ASP cc_start: 0.7191 (t70) cc_final: 0.6856 (t0) REVERT: A 759 PHE cc_start: 0.6792 (m-80) cc_final: 0.6256 (m-80) REVERT: A 762 GLN cc_start: 0.7269 (pt0) cc_final: 0.6940 (pm20) REVERT: A 763 LEU cc_start: 0.8389 (mt) cc_final: 0.8126 (mt) REVERT: A 773 GLU cc_start: 0.6504 (tm-30) cc_final: 0.5143 (tm-30) REVERT: A 777 ASN cc_start: 0.8032 (m-40) cc_final: 0.7216 (m-40) REVERT: A 803 SER cc_start: 0.8798 (m) cc_final: 0.8263 (p) REVERT: A 816 SER cc_start: 0.8044 (p) cc_final: 0.7700 (t) REVERT: A 868 GLU cc_start: 0.7380 (tp30) cc_final: 0.7081 (tp30) REVERT: A 869 MET cc_start: 0.8188 (mtt) cc_final: 0.7985 (mtm) REVERT: A 902 MET cc_start: 0.8138 (tpp) cc_final: 0.7870 (tpp) REVERT: A 921 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8181 (mmmm) REVERT: A 922 LEU cc_start: 0.8465 (tp) cc_final: 0.8216 (tp) REVERT: A 925 ASN cc_start: 0.8459 (m-40) cc_final: 0.8087 (m-40) REVERT: A 945 LEU cc_start: 0.8632 (mm) cc_final: 0.8336 (mp) REVERT: A 953 ASN cc_start: 0.8409 (m-40) cc_final: 0.8107 (m110) REVERT: A 979 ASP cc_start: 0.7300 (t70) cc_final: 0.7001 (t0) REVERT: A 988 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7175 (tm-30) REVERT: A 994 ASP cc_start: 0.7173 (m-30) cc_final: 0.6824 (t0) REVERT: A 1029 MET cc_start: 0.8312 (tpp) cc_final: 0.7672 (ttm) REVERT: A 1038 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8181 (mttm) REVERT: A 1050 MET cc_start: 0.6985 (ttm) cc_final: 0.6767 (ttp) REVERT: A 1114 ILE cc_start: 0.8563 (mm) cc_final: 0.8250 (mt) REVERT: A 1117 THR cc_start: 0.8530 (p) cc_final: 0.8236 (t) REVERT: A 1141 LEU cc_start: 0.8357 (tp) cc_final: 0.8099 (tt) REVERT: B 104 TRP cc_start: 0.7787 (m-90) cc_final: 0.6759 (m-90) REVERT: B 170 TYR cc_start: 0.7983 (t80) cc_final: 0.7539 (t80) REVERT: B 190 PHE cc_start: 0.8195 (m-80) cc_final: 0.7799 (m-10) REVERT: B 278 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8304 (ttmt) REVERT: B 340 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6998 (mm-30) REVERT: B 341 VAL cc_start: 0.8980 (m) cc_final: 0.8737 (p) REVERT: B 353 TRP cc_start: 0.8400 (p-90) cc_final: 0.8076 (p-90) REVERT: B 380 TYR cc_start: 0.6795 (m-80) cc_final: 0.6309 (m-80) REVERT: B 392 PHE cc_start: 0.7078 (m-80) cc_final: 0.6798 (m-80) REVERT: B 394 ASN cc_start: 0.7978 (p0) cc_final: 0.7331 (p0) REVERT: B 408 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7558 (ppp-140) REVERT: B 409 GLN cc_start: 0.8849 (mp10) cc_final: 0.8581 (mp10) REVERT: B 433 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8218 (m) REVERT: B 436 TRP cc_start: 0.8025 (p90) cc_final: 0.7747 (p90) REVERT: B 439 ASN cc_start: 0.7223 (t0) cc_final: 0.6993 (t0) REVERT: B 528 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7465 (tmmt) REVERT: B 580 GLN cc_start: 0.7500 (mm110) cc_final: 0.7215 (mm110) REVERT: B 645 THR cc_start: 0.8294 (p) cc_final: 0.6818 (m) REVERT: B 658 ASN cc_start: 0.7243 (t0) cc_final: 0.6897 (t0) REVERT: B 659 SER cc_start: 0.8562 (m) cc_final: 0.7670 (p) REVERT: B 698 SER cc_start: 0.8643 (t) cc_final: 0.8362 (p) REVERT: B 759 PHE cc_start: 0.7331 (t80) cc_final: 0.6873 (t80) REVERT: B 765 ARG cc_start: 0.7218 (ttm110) cc_final: 0.6757 (mtm180) REVERT: B 776 LYS cc_start: 0.8237 (tmmt) cc_final: 0.7905 (ttpt) REVERT: B 801 ASN cc_start: 0.6574 (t0) cc_final: 0.6327 (t0) REVERT: B 803 SER cc_start: 0.8630 (p) cc_final: 0.8397 (t) REVERT: B 854 LYS cc_start: 0.8259 (ttpp) cc_final: 0.8035 (tttp) REVERT: B 856 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8341 (mmmm) REVERT: B 895 GLN cc_start: 0.7001 (mt0) cc_final: 0.6580 (mt0) REVERT: B 900 MET cc_start: 0.7624 (mtp) cc_final: 0.7387 (mtt) REVERT: B 911 VAL cc_start: 0.8501 (t) cc_final: 0.8181 (m) REVERT: B 921 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8398 (mmmm) REVERT: B 933 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7941 (ttmm) REVERT: B 954 HIS cc_start: 0.7411 (m90) cc_final: 0.7121 (m-70) REVERT: B 969 LYS cc_start: 0.8109 (pttm) cc_final: 0.7873 (pttm) REVERT: B 990 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7067 (mm-30) REVERT: B 994 ASP cc_start: 0.7649 (m-30) cc_final: 0.7124 (m-30) REVERT: B 1002 GLN cc_start: 0.7870 (tp40) cc_final: 0.7578 (tm-30) REVERT: B 1003 SER cc_start: 0.8820 (m) cc_final: 0.8436 (t) REVERT: B 1029 MET cc_start: 0.8396 (tpp) cc_final: 0.8168 (ttm) REVERT: B 1050 MET cc_start: 0.7805 (mtp) cc_final: 0.7597 (ptp) REVERT: B 1061 VAL cc_start: 0.8745 (t) cc_final: 0.8364 (p) REVERT: B 1072 GLU cc_start: 0.7863 (pm20) cc_final: 0.7626 (pm20) REVERT: B 1086 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8025 (ptpp) REVERT: B 1097 SER cc_start: 0.8648 (t) cc_final: 0.8121 (p) REVERT: C 41 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7436 (mtpp) REVERT: C 43 PHE cc_start: 0.8262 (t80) cc_final: 0.7971 (t80) REVERT: C 53 ASP cc_start: 0.7378 (t0) cc_final: 0.7000 (m-30) REVERT: C 188 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6735 (mtp85) REVERT: C 199 PHE cc_start: 0.7914 (t80) cc_final: 0.7191 (t80) REVERT: C 201 ILE cc_start: 0.8865 (mt) cc_final: 0.8560 (mp) REVERT: C 297 SER cc_start: 0.7965 (m) cc_final: 0.7250 (p) REVERT: C 308 VAL cc_start: 0.8673 (t) cc_final: 0.8377 (m) REVERT: C 326 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6693 (pt) REVERT: C 332 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6375 (pp) REVERT: C 436 TRP cc_start: 0.7302 (p-90) cc_final: 0.6792 (p-90) REVERT: C 531 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 542 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7532 (t0) REVERT: C 619 GLU cc_start: 0.6986 (mp0) cc_final: 0.6465 (mp0) REVERT: C 644 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7027 (tp40) REVERT: C 663 ASP cc_start: 0.7275 (t70) cc_final: 0.6874 (t0) REVERT: C 705 VAL cc_start: 0.8142 (t) cc_final: 0.7863 (m) REVERT: C 725 GLU cc_start: 0.7243 (tt0) cc_final: 0.6977 (tt0) REVERT: C 764 LYS cc_start: 0.8313 (tttm) cc_final: 0.7904 (ttpp) REVERT: C 776 LYS cc_start: 0.8432 (tptp) cc_final: 0.7944 (tptp) REVERT: C 777 ASN cc_start: 0.7577 (m-40) cc_final: 0.7107 (m-40) REVERT: C 811 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8101 (ttpp) REVERT: C 825 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8135 (ttmm) REVERT: C 859 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.7889 (p) REVERT: C 950 ASP cc_start: 0.7648 (t70) cc_final: 0.6917 (t0) REVERT: C 964 LYS cc_start: 0.8613 (tppt) cc_final: 0.8181 (ttmm) REVERT: C 980 ILE cc_start: 0.8468 (mt) cc_final: 0.8220 (mt) REVERT: C 990 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7252 (mm-30) REVERT: C 998 THR cc_start: 0.8408 (t) cc_final: 0.8133 (p) REVERT: C 1014 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7459 (ttm110) REVERT: C 1029 MET cc_start: 0.8418 (tpp) cc_final: 0.7928 (tpp) REVERT: C 1048 HIS cc_start: 0.7775 (t70) cc_final: 0.7231 (t-170) REVERT: C 1051 SER cc_start: 0.8177 (m) cc_final: 0.7891 (m) REVERT: C 1072 GLU cc_start: 0.8408 (pm20) cc_final: 0.8128 (pm20) REVERT: G 49 MET cc_start: 0.3256 (ppp) cc_final: 0.2254 (tpt) REVERT: H 60 ARG cc_start: 0.5291 (mmt90) cc_final: 0.5052 (mmt90) outliers start: 128 outliers final: 100 residues processed: 750 average time/residue: 0.4170 time to fit residues: 492.6860 Evaluate side-chains 773 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 658 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 244 optimal weight: 50.0000 chunk 369 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 294 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 227 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 710 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.254 29860 Z= 0.253 Angle : 0.750 59.195 40678 Z= 0.414 Chirality : 0.050 1.442 4657 Planarity : 0.006 0.158 5239 Dihedral : 5.215 59.666 4115 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.76 % Allowed : 20.78 % Favored : 75.45 % Cbeta Deviations : 0.06 % 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: -2.08 (0.13), residues: 3713 helix: 1.31 (0.21), residues: 645 sheet: -1.38 (0.17), residues: 817 loop : -2.33 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 110 HIS 0.018 0.001 HIS A 505 PHE 0.035 0.001 PHE A 565 TYR 0.020 0.001 TYR C 707 ARG 0.008 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 660 time to evaluate : 3.648 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: A 33 THR cc_start: 0.6542 (m) cc_final: 0.6102 (p) REVERT: A 41 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7924 (mtpt) REVERT: A 92 PHE cc_start: 0.7282 (t80) cc_final: 0.6935 (t80) REVERT: A 94 SER cc_start: 0.7338 (OUTLIER) cc_final: 0.7036 (m) REVERT: A 188 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6554 (mmt180) REVERT: A 190 PHE cc_start: 0.7602 (m-80) cc_final: 0.7376 (m-10) REVERT: A 273 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7618 (mtp85) REVERT: A 297 SER cc_start: 0.8395 (m) cc_final: 0.8011 (p) REVERT: A 436 TRP cc_start: 0.6777 (p-90) cc_final: 0.6537 (p90) REVERT: A 478 LYS cc_start: -0.0432 (OUTLIER) cc_final: -0.0812 (ptmt) REVERT: A 534 VAL cc_start: 0.8491 (t) cc_final: 0.8268 (m) REVERT: A 535 LYS cc_start: 0.8479 (mttp) cc_final: 0.8239 (mttm) REVERT: A 587 ILE cc_start: 0.8128 (mt) cc_final: 0.7566 (tt) REVERT: A 660 TYR cc_start: 0.7890 (m-10) cc_final: 0.7633 (m-10) REVERT: A 666 ILE cc_start: 0.8583 (mm) cc_final: 0.8305 (mt) REVERT: A 697 MET cc_start: 0.7336 (ttm) cc_final: 0.7000 (mtp) REVERT: A 698 SER cc_start: 0.8467 (t) cc_final: 0.7783 (p) REVERT: A 710 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6717 (p0) REVERT: A 737 ASP cc_start: 0.7198 (t70) cc_final: 0.6807 (t70) REVERT: A 759 PHE cc_start: 0.6795 (m-80) cc_final: 0.6260 (m-80) REVERT: A 762 GLN cc_start: 0.7266 (pt0) cc_final: 0.7008 (pm20) REVERT: A 763 LEU cc_start: 0.8389 (mt) cc_final: 0.8129 (mt) REVERT: A 773 GLU cc_start: 0.6674 (tm-30) cc_final: 0.5275 (tm-30) REVERT: A 777 ASN cc_start: 0.8074 (m-40) cc_final: 0.7327 (m-40) REVERT: A 803 SER cc_start: 0.8795 (m) cc_final: 0.8263 (p) REVERT: A 816 SER cc_start: 0.8045 (p) cc_final: 0.7704 (t) REVERT: A 868 GLU cc_start: 0.7376 (tp30) cc_final: 0.7072 (tp30) REVERT: A 869 MET cc_start: 0.8189 (mtt) cc_final: 0.7989 (mtm) REVERT: A 902 MET cc_start: 0.8133 (tpp) cc_final: 0.7874 (tpp) REVERT: A 921 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8182 (mmmm) REVERT: A 922 LEU cc_start: 0.8468 (tp) cc_final: 0.8219 (tp) REVERT: A 925 ASN cc_start: 0.8464 (m-40) cc_final: 0.8089 (m-40) REVERT: A 945 LEU cc_start: 0.8630 (mm) cc_final: 0.8338 (mp) REVERT: A 953 ASN cc_start: 0.8390 (m-40) cc_final: 0.8108 (m110) REVERT: A 979 ASP cc_start: 0.7297 (t70) cc_final: 0.7013 (t0) REVERT: A 988 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7178 (tm-30) REVERT: A 994 ASP cc_start: 0.7181 (m-30) cc_final: 0.6828 (t0) REVERT: A 1029 MET cc_start: 0.8314 (tpp) cc_final: 0.7676 (ttm) REVERT: A 1038 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8181 (mttm) REVERT: A 1050 MET cc_start: 0.6981 (ttm) cc_final: 0.6765 (ttp) REVERT: A 1114 ILE cc_start: 0.8561 (mm) cc_final: 0.8252 (mt) REVERT: A 1117 THR cc_start: 0.8531 (p) cc_final: 0.8238 (t) REVERT: A 1141 LEU cc_start: 0.8359 (tp) cc_final: 0.8103 (tt) REVERT: B 104 TRP cc_start: 0.7822 (m-90) cc_final: 0.6795 (m-90) REVERT: B 170 TYR cc_start: 0.7980 (t80) cc_final: 0.7526 (t80) REVERT: B 190 PHE cc_start: 0.8189 (m-80) cc_final: 0.7803 (m-10) REVERT: B 278 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8304 (ttmt) REVERT: B 340 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6999 (mm-30) REVERT: B 341 VAL cc_start: 0.8966 (m) cc_final: 0.8739 (p) REVERT: B 353 TRP cc_start: 0.8406 (p-90) cc_final: 0.8074 (p-90) REVERT: B 380 TYR cc_start: 0.6808 (m-80) cc_final: 0.6310 (m-80) REVERT: B 392 PHE cc_start: 0.7086 (m-80) cc_final: 0.6803 (m-80) REVERT: B 394 ASN cc_start: 0.7986 (p0) cc_final: 0.7334 (p0) REVERT: B 408 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7578 (ppp-140) REVERT: B 433 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8219 (m) REVERT: B 436 TRP cc_start: 0.8026 (p90) cc_final: 0.7755 (p90) REVERT: B 528 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7468 (tmmt) REVERT: B 580 GLN cc_start: 0.7505 (mm110) cc_final: 0.7219 (mm110) REVERT: B 645 THR cc_start: 0.8297 (p) cc_final: 0.6826 (m) REVERT: B 658 ASN cc_start: 0.7221 (t0) cc_final: 0.6902 (t0) REVERT: B 659 SER cc_start: 0.8561 (m) cc_final: 0.7669 (p) REVERT: B 698 SER cc_start: 0.8649 (t) cc_final: 0.8363 (p) REVERT: B 759 PHE cc_start: 0.7310 (t80) cc_final: 0.6880 (t80) REVERT: B 765 ARG cc_start: 0.7227 (ttm110) cc_final: 0.6753 (mtm180) REVERT: B 776 LYS cc_start: 0.8242 (tmmt) cc_final: 0.7901 (ttpt) REVERT: B 801 ASN cc_start: 0.6576 (t0) cc_final: 0.6333 (t0) REVERT: B 803 SER cc_start: 0.8633 (p) cc_final: 0.8399 (t) REVERT: B 854 LYS cc_start: 0.8260 (ttpp) cc_final: 0.8041 (tttp) REVERT: B 856 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8353 (mmmm) REVERT: B 895 GLN cc_start: 0.6998 (mt0) cc_final: 0.6574 (mt0) REVERT: B 900 MET cc_start: 0.7625 (mtp) cc_final: 0.7391 (mtt) REVERT: B 911 VAL cc_start: 0.8501 (t) cc_final: 0.8191 (m) REVERT: B 921 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8399 (mmmm) REVERT: B 933 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7956 (ttmm) REVERT: B 954 HIS cc_start: 0.7437 (m90) cc_final: 0.7223 (m-70) REVERT: B 969 LYS cc_start: 0.8109 (pttm) cc_final: 0.7871 (pttm) REVERT: B 990 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 994 ASP cc_start: 0.7654 (m-30) cc_final: 0.7126 (m-30) REVERT: B 1002 GLN cc_start: 0.7872 (tp40) cc_final: 0.7585 (tm-30) REVERT: B 1003 SER cc_start: 0.8818 (m) cc_final: 0.8444 (t) REVERT: B 1029 MET cc_start: 0.8397 (tpp) cc_final: 0.8167 (ttm) REVERT: B 1061 VAL cc_start: 0.8746 (t) cc_final: 0.8368 (p) REVERT: B 1072 GLU cc_start: 0.7861 (pm20) cc_final: 0.7628 (pm20) REVERT: B 1086 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8026 (ptpp) REVERT: B 1097 SER cc_start: 0.8648 (t) cc_final: 0.8125 (p) REVERT: C 41 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7438 (mtpp) REVERT: C 43 PHE cc_start: 0.8270 (t80) cc_final: 0.7989 (t80) REVERT: C 53 ASP cc_start: 0.7388 (t0) cc_final: 0.7003 (m-30) REVERT: C 122 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7556 (p0) REVERT: C 188 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6740 (mtp85) REVERT: C 199 PHE cc_start: 0.7908 (t80) cc_final: 0.7194 (t80) REVERT: C 201 ILE cc_start: 0.8859 (mt) cc_final: 0.8563 (mp) REVERT: C 297 SER cc_start: 0.7999 (m) cc_final: 0.7381 (p) REVERT: C 308 VAL cc_start: 0.8673 (t) cc_final: 0.8378 (m) REVERT: C 332 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6377 (pp) REVERT: C 436 TRP cc_start: 0.7303 (p-90) cc_final: 0.6792 (p-90) REVERT: C 531 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8427 (p) REVERT: C 542 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7526 (t0) REVERT: C 619 GLU cc_start: 0.6989 (mp0) cc_final: 0.6465 (mp0) REVERT: C 644 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7024 (tp40) REVERT: C 663 ASP cc_start: 0.7305 (t70) cc_final: 0.6891 (t0) REVERT: C 705 VAL cc_start: 0.8146 (t) cc_final: 0.7869 (m) REVERT: C 725 GLU cc_start: 0.7248 (tt0) cc_final: 0.6979 (tt0) REVERT: C 764 LYS cc_start: 0.8338 (tttm) cc_final: 0.7897 (ttpp) REVERT: C 776 LYS cc_start: 0.8431 (tptp) cc_final: 0.8030 (tptp) REVERT: C 811 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8098 (ttpp) REVERT: C 825 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8135 (ttmm) REVERT: C 859 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.7891 (p) REVERT: C 950 ASP cc_start: 0.7652 (t70) cc_final: 0.6930 (t0) REVERT: C 964 LYS cc_start: 0.8612 (tppt) cc_final: 0.8187 (ttmm) REVERT: C 980 ILE cc_start: 0.8479 (mt) cc_final: 0.8220 (mt) REVERT: C 990 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7248 (mm-30) REVERT: C 998 THR cc_start: 0.8407 (t) cc_final: 0.8132 (p) REVERT: C 1011 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7731 (tp40) REVERT: C 1014 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7431 (ttm110) REVERT: C 1029 MET cc_start: 0.8420 (tpp) cc_final: 0.7930 (tpp) REVERT: C 1048 HIS cc_start: 0.7775 (t70) cc_final: 0.7229 (t-170) REVERT: C 1050 MET cc_start: 0.7075 (mtm) cc_final: 0.6812 (mtm) REVERT: C 1051 SER cc_start: 0.8190 (m) cc_final: 0.7897 (m) REVERT: C 1072 GLU cc_start: 0.8406 (pm20) cc_final: 0.8122 (pm20) REVERT: G 49 MET cc_start: 0.3149 (ppp) cc_final: 0.2221 (tpt) REVERT: H 60 ARG cc_start: 0.5292 (mmt90) cc_final: 0.5055 (mmt90) outliers start: 122 outliers final: 101 residues processed: 746 average time/residue: 0.4406 time to fit residues: 521.2003 Evaluate side-chains 769 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 653 time to evaluate : 3.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 38 TYR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain H residue 15 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 302 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126230 restraints weight = 55562.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130215 restraints weight = 24808.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132645 restraints weight = 14012.167| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.253 29860 Z= 0.264 Angle : 0.689 31.019 40678 Z= 0.381 Chirality : 0.050 1.442 4657 Planarity : 0.006 0.158 5239 Dihedral : 5.215 59.666 4115 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.61 % Allowed : 20.94 % Favored : 75.45 % Cbeta Deviations : 0.06 % 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: -2.08 (0.13), residues: 3713 helix: 1.31 (0.21), residues: 645 sheet: -1.38 (0.17), residues: 817 loop : -2.33 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 110 HIS 0.018 0.001 HIS A 505 PHE 0.035 0.001 PHE A 565 TYR 0.020 0.001 TYR C 707 ARG 0.008 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9043.24 seconds wall clock time: 163 minutes 15.60 seconds (9795.60 seconds total)