Starting phenix.real_space_refine on Mon Feb 19 16:23:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/02_2024/5x58_6703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/02_2024/5x58_6703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/02_2024/5x58_6703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/02_2024/5x58_6703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/02_2024/5x58_6703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/02_2024/5x58_6703.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 16102 2.51 5 N 4127 2.21 5 O 4904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B ARG 977": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "C ARG 1073": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25265 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8234 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1001} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8226 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8217 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 999} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 14.25, per 1000 atoms: 0.56 Number of scatterers: 25265 At special positions: 0 Unit cell: (149.5, 139.1, 159.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4904 8.00 N 4127 7.00 C 16102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 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=3, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 691 " " NAG A1303 " - " ASN A 699 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A1056 " " NAG A1306 " - " ASN A 357 " " NAG A1307 " - " ASN A 330 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 227 " " NAG A1311 " - " ASN A 158 " " NAG A1312 " - " ASN A 119 " " NAG A1313 " - " ASN A 65 " " NAG B1301 " - " ASN B 602 " " NAG B1302 " - " ASN B 691 " " NAG B1303 " - " ASN B 699 " " NAG B1304 " - " ASN B 783 " " NAG B1305 " - " ASN B1056 " " NAG B1306 " - " ASN B 357 " " NAG B1307 " - " ASN B 330 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 227 " " NAG B1311 " - " ASN B 158 " " NAG B1312 " - " ASN B 119 " " NAG B1313 " - " ASN B 65 " " NAG C1301 " - " ASN C 602 " " NAG C1302 " - " ASN C 691 " " NAG C1303 " - " ASN C 699 " " NAG C1304 " - " ASN C 783 " " NAG C1305 " - " ASN C1056 " " NAG C1306 " - " ASN C 357 " " NAG C1307 " - " ASN C 330 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 227 " " NAG C1311 " - " ASN C 158 " " NAG C1312 " - " ASN C 119 " " NAG C1313 " - " ASN C 65 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.68 Conformation dependent library (CDL) restraints added in 4.9 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 22.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.583A pdb=" N GLY A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.694A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 4.170A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS A 929 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1014 removed outlier: 3.645A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.965A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.582A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 744 through 765 removed outlier: 4.109A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.932A pdb=" N LYS B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.584A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.811A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS C 929 " --> pdb=" O THR C 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 988 " --> pdb=" O GLN C 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 71 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 5.700A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER A 310 " --> pdb=" O ASN A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN A 321 " --> pdb=" O VAL A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.546A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 771 removed outlier: 6.097A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.524A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.743A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.598A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER B 310 " --> pdb=" O ASN B 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 652 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD5, first strand: chain 'B' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 38 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU C 216 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP C 57 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE2, first strand: chain 'C' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER C 310 " --> pdb=" O ASN C 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.962A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 652 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2244 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: 10.31 Time building geometry restraints manager: 10.56 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: 7870 1.34 - 1.46: 5722 1.46 - 1.58: 12087 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25859 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 ... (remaining 25854 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.80: 598 105.80 - 112.96: 13629 112.96 - 120.11: 9098 120.11 - 127.27: 11599 127.27 - 134.42: 266 Bond angle restraints: 35190 Sorted by residual: angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.17 -9.26 1.17e+00 7.31e-01 6.27e+01 angle pdb=" N ARG C 306 " pdb=" CA ARG C 306 " pdb=" C ARG C 306 " ideal model delta sigma weight residual 110.91 120.13 -9.22 1.17e+00 7.31e-01 6.21e+01 angle pdb=" N ARG B 306 " pdb=" CA ARG B 306 " pdb=" C ARG B 306 " ideal model delta sigma weight residual 110.91 120.12 -9.21 1.17e+00 7.31e-01 6.20e+01 angle pdb=" N VAL B 354 " pdb=" CA VAL B 354 " pdb=" C VAL B 354 " ideal model delta sigma weight residual 110.72 103.92 6.80 1.01e+00 9.80e-01 4.53e+01 angle pdb=" N VAL C 354 " pdb=" CA VAL C 354 " pdb=" C VAL C 354 " ideal model delta sigma weight residual 110.72 103.94 6.78 1.01e+00 9.80e-01 4.51e+01 ... (remaining 35185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 15197 21.67 - 43.34: 425 43.34 - 65.01: 102 65.01 - 86.68: 39 86.68 - 108.34: 90 Dihedral angle restraints: 15853 sinusoidal: 6631 harmonic: 9222 Sorted by residual: dihedral pdb=" CA THR B 616 " pdb=" C THR B 616 " pdb=" N PRO B 617 " pdb=" CA PRO B 617 " ideal model delta harmonic sigma weight residual 180.00 132.11 47.89 0 5.00e+00 4.00e-02 9.17e+01 dihedral pdb=" CA THR C 616 " pdb=" C THR C 616 " pdb=" N PRO C 617 " pdb=" CA PRO C 617 " ideal model delta harmonic sigma weight residual 180.00 132.17 47.83 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA THR A 616 " pdb=" C THR A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual 180.00 132.18 47.82 0 5.00e+00 4.00e-02 9.15e+01 ... (remaining 15850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3462 0.084 - 0.168: 551 0.168 - 0.252: 48 0.252 - 0.336: 17 0.336 - 0.420: 10 Chirality restraints: 4088 Sorted by residual: chirality pdb=" CB ILE B 787 " pdb=" CA ILE B 787 " pdb=" CG1 ILE B 787 " pdb=" CG2 ILE B 787 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB ILE C 787 " pdb=" CA ILE C 787 " pdb=" CG1 ILE C 787 " pdb=" CG2 ILE C 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO C 617 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.042 5.00e-02 4.00e+02 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6567 2.80 - 3.32: 22850 3.32 - 3.85: 42174 3.85 - 4.37: 49285 4.37 - 4.90: 82893 Nonbonded interactions: 203769 Sorted by model distance: nonbonded pdb=" O GLU A 647 " pdb=" OH TYR A 677 " model vdw 2.272 2.440 nonbonded pdb=" O GLU C 647 " pdb=" OH TYR C 677 " model vdw 2.273 2.440 nonbonded pdb=" O GLU B 647 " pdb=" OH TYR B 677 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR A 738 " pdb=" OD1 ASP A 976 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR B 738 " pdb=" OD1 ASP B 976 " model vdw 2.314 2.440 ... (remaining 203764 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' and (resid 18 through 662 or resid 673 through 809 or resid 831 throu \ gh 1104 or resid 1302 through 1301)) selection = (chain 'B' and (resid 18 through 662 or resid 673 through 1104 or resid 1301 thr \ ough 1314)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 3.290 Check model and map are aligned: 0.370 Set scattering table: 0.260 Process input model: 69.080 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.130 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: 78.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.007 0.090 25859 Z= 0.476 Angle : 1.173 18.125 35190 Z= 0.657 Chirality : 0.066 0.420 4088 Planarity : 0.006 0.075 4498 Dihedral : 14.958 108.345 9865 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.44 % Allowed : 4.82 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 5.88 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.12), residues: 3135 helix: -4.02 (0.11), residues: 609 sheet: -2.43 (0.18), residues: 614 loop : -3.11 (0.12), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 423 HIS 0.013 0.002 HIS C1030 PHE 0.024 0.003 PHE C 870 TYR 0.034 0.003 TYR B 481 ARG 0.012 0.001 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 692 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8744 (t0) cc_final: 0.8308 (m-30) REVERT: A 84 LYS cc_start: 0.8654 (mmpt) cc_final: 0.8444 (tppt) REVERT: A 109 ASN cc_start: 0.7042 (p0) cc_final: 0.6251 (t0) REVERT: A 130 PHE cc_start: 0.7489 (m-80) cc_final: 0.6445 (m-80) REVERT: A 131 GLU cc_start: 0.6027 (tt0) cc_final: 0.5675 (pt0) REVERT: A 184 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8151 (mp0) REVERT: A 189 ASN cc_start: 0.8134 (t0) cc_final: 0.7691 (t0) REVERT: A 256 TYR cc_start: 0.8241 (m-80) cc_final: 0.8004 (m-80) REVERT: A 411 LYS cc_start: 0.7307 (tptm) cc_final: 0.6861 (tppt) REVERT: A 640 GLU cc_start: 0.8080 (tt0) cc_final: 0.7866 (tp30) REVERT: A 692 ASN cc_start: 0.8774 (m-40) cc_final: 0.8518 (p0) REVERT: A 707 GLU cc_start: 0.9144 (tt0) cc_final: 0.8920 (tt0) REVERT: A 733 ASN cc_start: 0.8794 (t160) cc_final: 0.8453 (m-40) REVERT: A 745 LEU cc_start: 0.8469 (tm) cc_final: 0.8115 (tp) REVERT: A 755 GLU cc_start: 0.8039 (pp20) cc_final: 0.7588 (mm-30) REVERT: A 762 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7894 (mm-30) REVERT: A 768 LYS cc_start: 0.8727 (tttp) cc_final: 0.8518 (tppt) REVERT: A 769 GLN cc_start: 0.8809 (pm20) cc_final: 0.8571 (pm20) REVERT: A 796 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7526 (mmtm) REVERT: A 833 CYS cc_start: 0.6335 (m) cc_final: 0.5736 (p) REVERT: A 851 MET cc_start: 0.8887 (mtt) cc_final: 0.8641 (mtm) REVERT: A 918 GLU cc_start: 0.8987 (tt0) cc_final: 0.8761 (mm-30) REVERT: A 963 LEU cc_start: 0.8200 (mm) cc_final: 0.7925 (mt) REVERT: A 970 GLU cc_start: 0.8255 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 972 GLU cc_start: 0.8453 (tt0) cc_final: 0.7826 (pp20) REVERT: A 1055 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8265 (ttm-80) REVERT: A 1071 PHE cc_start: 0.8032 (m-80) cc_final: 0.7759 (m-80) REVERT: B 57 ASP cc_start: 0.8731 (t0) cc_final: 0.8173 (m-30) REVERT: B 78 ASN cc_start: 0.7872 (p0) cc_final: 0.7662 (p0) REVERT: B 109 ASN cc_start: 0.7048 (p0) cc_final: 0.6204 (t0) REVERT: B 130 PHE cc_start: 0.7360 (m-80) cc_final: 0.7065 (m-80) REVERT: B 131 GLU cc_start: 0.5948 (tt0) cc_final: 0.5677 (pt0) REVERT: B 132 LEU cc_start: 0.6054 (mm) cc_final: 0.5692 (mm) REVERT: B 184 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7916 (mp0) REVERT: B 260 THR cc_start: 0.8990 (m) cc_final: 0.8767 (p) REVERT: B 410 TYR cc_start: 0.7792 (t80) cc_final: 0.7196 (t80) REVERT: B 447 LYS cc_start: 0.6739 (mttt) cc_final: 0.6497 (mmtm) REVERT: B 689 TYR cc_start: 0.7845 (t80) cc_final: 0.7641 (t80) REVERT: B 692 ASN cc_start: 0.8514 (m-40) cc_final: 0.8290 (p0) REVERT: B 693 THR cc_start: 0.8777 (p) cc_final: 0.8318 (p) REVERT: B 733 ASN cc_start: 0.8850 (t160) cc_final: 0.8473 (m-40) REVERT: B 745 LEU cc_start: 0.8634 (tm) cc_final: 0.7995 (mt) REVERT: B 746 ASN cc_start: 0.8705 (t0) cc_final: 0.8492 (t0) REVERT: B 755 GLU cc_start: 0.8148 (pp20) cc_final: 0.7731 (mm-30) REVERT: B 762 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8185 (mm-30) REVERT: B 796 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7399 (tppt) REVERT: B 851 MET cc_start: 0.8917 (mtt) cc_final: 0.8670 (mtm) REVERT: B 884 MET cc_start: 0.8788 (mmm) cc_final: 0.8463 (tpt) REVERT: B 886 TYR cc_start: 0.9018 (t80) cc_final: 0.8761 (t80) REVERT: B 897 VAL cc_start: 0.9092 (t) cc_final: 0.8875 (m) REVERT: B 918 GLU cc_start: 0.9112 (tt0) cc_final: 0.8863 (mm-30) REVERT: B 972 GLU cc_start: 0.8579 (tt0) cc_final: 0.7986 (pt0) REVERT: B 1049 TYR cc_start: 0.8758 (t80) cc_final: 0.8486 (t80) REVERT: B 1054 GLU cc_start: 0.8820 (pm20) cc_final: 0.8282 (pm20) REVERT: B 1055 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8442 (ttm-80) REVERT: C 57 ASP cc_start: 0.8714 (t0) cc_final: 0.8253 (m-30) REVERT: C 101 TRP cc_start: 0.7736 (m-90) cc_final: 0.7500 (m-90) REVERT: C 109 ASN cc_start: 0.6946 (p0) cc_final: 0.6331 (t0) REVERT: C 131 GLU cc_start: 0.5825 (tt0) cc_final: 0.5220 (pt0) REVERT: C 132 LEU cc_start: 0.5754 (mm) cc_final: 0.5217 (mm) REVERT: C 184 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8357 (mp0) REVERT: C 207 ARG cc_start: 0.6166 (ptm160) cc_final: 0.5796 (mmt-90) REVERT: C 260 THR cc_start: 0.8946 (m) cc_final: 0.8598 (p) REVERT: C 340 TRP cc_start: 0.6175 (p-90) cc_final: 0.5553 (p-90) REVERT: C 411 LYS cc_start: 0.7242 (tptm) cc_final: 0.6839 (tppt) REVERT: C 518 ASP cc_start: 0.7451 (t70) cc_final: 0.7226 (p0) REVERT: C 560 ASP cc_start: 0.8526 (t70) cc_final: 0.8321 (t0) REVERT: C 733 ASN cc_start: 0.8678 (t160) cc_final: 0.8354 (m110) REVERT: C 745 LEU cc_start: 0.8476 (tm) cc_final: 0.8176 (mt) REVERT: C 746 ASN cc_start: 0.8739 (t0) cc_final: 0.8478 (t0) REVERT: C 755 GLU cc_start: 0.7836 (pp20) cc_final: 0.7505 (mm-30) REVERT: C 762 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8036 (mm-30) REVERT: C 768 LYS cc_start: 0.8611 (tttp) cc_final: 0.8334 (ttmm) REVERT: C 769 GLN cc_start: 0.8694 (pm20) cc_final: 0.8327 (pm20) REVERT: C 796 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7428 (mmtm) REVERT: C 900 GLU cc_start: 0.8735 (tt0) cc_final: 0.8495 (tt0) REVERT: C 918 GLU cc_start: 0.8972 (tt0) cc_final: 0.8757 (tm-30) REVERT: C 963 LEU cc_start: 0.8077 (mm) cc_final: 0.7733 (mt) REVERT: C 970 GLU cc_start: 0.8366 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 972 GLU cc_start: 0.8633 (tt0) cc_final: 0.8130 (tm-30) REVERT: C 1055 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8550 (ttm-80) REVERT: C 1071 PHE cc_start: 0.8060 (m-80) cc_final: 0.7773 (m-10) outliers start: 12 outliers final: 4 residues processed: 704 average time/residue: 0.3915 time to fit residues: 425.8634 Evaluate side-chains 409 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 405 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 920 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 246 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.0870 chunk 183 optimal weight: 0.8980 chunk 286 optimal weight: 10.0000 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 135 ASN A 409 ASN A 522 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 614 GLN A 632 GLN A 733 ASN A 766 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A 937 ASN ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN A1101 ASN B 70 HIS B 135 ASN B 280 GLN B 409 ASN B 522 ASN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 614 GLN B 632 GLN B 733 ASN B 766 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN B 904 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 937 ASN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 GLN B1090 ASN B1101 ASN C 70 HIS C 135 ASN C 201 GLN C 409 ASN C 522 ASN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 632 GLN C 733 ASN C 766 GLN ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 GLN C 896 ASN C 904 GLN C 917 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN C 937 ASN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25859 Z= 0.208 Angle : 0.721 13.620 35190 Z= 0.362 Chirality : 0.049 0.351 4088 Planarity : 0.005 0.072 4498 Dihedral : 13.529 85.781 4286 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.63 % Allowed : 10.62 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.92 % 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: -3.39 (0.13), residues: 3135 helix: -1.58 (0.18), residues: 610 sheet: -1.82 (0.18), residues: 669 loop : -2.77 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 340 HIS 0.004 0.001 HIS B1040 PHE 0.027 0.002 PHE A 460 TYR 0.033 0.002 TYR A 481 ARG 0.006 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 473 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8439 (t0) cc_final: 0.8157 (m-30) REVERT: A 78 ASN cc_start: 0.8089 (p0) cc_final: 0.7862 (p0) REVERT: A 84 LYS cc_start: 0.8452 (mmpt) cc_final: 0.8101 (ttpp) REVERT: A 130 PHE cc_start: 0.7383 (m-80) cc_final: 0.6564 (m-80) REVERT: A 132 LEU cc_start: 0.5391 (mm) cc_final: 0.5050 (mm) REVERT: A 184 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7869 (mp0) REVERT: A 411 LYS cc_start: 0.7242 (tptm) cc_final: 0.7035 (tptp) REVERT: A 497 VAL cc_start: 0.8840 (t) cc_final: 0.8640 (p) REVERT: A 640 GLU cc_start: 0.8274 (tt0) cc_final: 0.8015 (tp30) REVERT: A 693 THR cc_start: 0.8467 (p) cc_final: 0.8239 (p) REVERT: A 733 ASN cc_start: 0.8660 (t0) cc_final: 0.8259 (m110) REVERT: A 745 LEU cc_start: 0.8523 (tm) cc_final: 0.8159 (mt) REVERT: A 755 GLU cc_start: 0.8230 (pp20) cc_final: 0.7769 (tp30) REVERT: A 762 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7876 (mm-30) REVERT: A 796 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7606 (mmtm) REVERT: A 833 CYS cc_start: 0.6635 (m) cc_final: 0.6011 (p) REVERT: A 918 GLU cc_start: 0.9078 (tt0) cc_final: 0.8868 (mm-30) REVERT: A 972 GLU cc_start: 0.8383 (tt0) cc_final: 0.7715 (pt0) REVERT: A 1055 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7936 (ttm110) REVERT: B 57 ASP cc_start: 0.8416 (t0) cc_final: 0.8041 (m-30) REVERT: B 84 LYS cc_start: 0.8512 (mmpt) cc_final: 0.8250 (mmtt) REVERT: B 130 PHE cc_start: 0.7317 (m-80) cc_final: 0.6835 (m-80) REVERT: B 260 THR cc_start: 0.8905 (m) cc_final: 0.8520 (p) REVERT: B 342 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7283 (ttm-80) REVERT: B 410 TYR cc_start: 0.7375 (t80) cc_final: 0.7038 (t80) REVERT: B 447 LYS cc_start: 0.6796 (mttt) cc_final: 0.6347 (mmtm) REVERT: B 539 THR cc_start: 0.7985 (m) cc_final: 0.7485 (p) REVERT: B 689 TYR cc_start: 0.7702 (t80) cc_final: 0.7490 (t80) REVERT: B 693 THR cc_start: 0.8736 (p) cc_final: 0.8168 (p) REVERT: B 733 ASN cc_start: 0.8778 (t0) cc_final: 0.8337 (m-40) REVERT: B 755 GLU cc_start: 0.8043 (pp20) cc_final: 0.7442 (tp30) REVERT: B 762 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8086 (mm-30) REVERT: B 796 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7451 (tppt) REVERT: B 886 TYR cc_start: 0.8989 (t80) cc_final: 0.8751 (t80) REVERT: B 959 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7841 (tm) REVERT: B 961 ASP cc_start: 0.7502 (m-30) cc_final: 0.7255 (m-30) REVERT: B 972 GLU cc_start: 0.8404 (tt0) cc_final: 0.7759 (pt0) REVERT: B 1054 GLU cc_start: 0.8501 (pm20) cc_final: 0.7901 (pm20) REVERT: B 1055 ARG cc_start: 0.8297 (mmm160) cc_final: 0.8021 (ttm-80) REVERT: B 1071 PHE cc_start: 0.7711 (m-80) cc_final: 0.7223 (m-80) REVERT: C 57 ASP cc_start: 0.8514 (t0) cc_final: 0.8123 (m-30) REVERT: C 78 ASN cc_start: 0.7845 (p0) cc_final: 0.7529 (p0) REVERT: C 131 GLU cc_start: 0.5862 (tt0) cc_final: 0.5648 (pt0) REVERT: C 207 ARG cc_start: 0.6299 (ptm160) cc_final: 0.5935 (mmt-90) REVERT: C 260 THR cc_start: 0.8920 (m) cc_final: 0.8468 (p) REVERT: C 305 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: C 338 TYR cc_start: 0.7263 (p90) cc_final: 0.6766 (p90) REVERT: C 340 TRP cc_start: 0.7286 (p-90) cc_final: 0.6286 (p-90) REVERT: C 410 TYR cc_start: 0.7573 (t80) cc_final: 0.7076 (t80) REVERT: C 411 LYS cc_start: 0.7104 (tptm) cc_final: 0.6821 (tptp) REVERT: C 518 ASP cc_start: 0.7833 (t70) cc_final: 0.7457 (p0) REVERT: C 539 THR cc_start: 0.7816 (m) cc_final: 0.7305 (p) REVERT: C 599 GLN cc_start: 0.6122 (OUTLIER) cc_final: 0.5711 (mm-40) REVERT: C 733 ASN cc_start: 0.8661 (t0) cc_final: 0.8262 (m110) REVERT: C 745 LEU cc_start: 0.8717 (tm) cc_final: 0.8276 (mt) REVERT: C 746 ASN cc_start: 0.8320 (t0) cc_final: 0.8084 (t0) REVERT: C 755 GLU cc_start: 0.7930 (pp20) cc_final: 0.7421 (tp30) REVERT: C 762 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8031 (mm-30) REVERT: C 768 LYS cc_start: 0.8617 (tttp) cc_final: 0.8320 (tppp) REVERT: C 796 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7333 (mmtm) REVERT: C 918 GLU cc_start: 0.9064 (tt0) cc_final: 0.8802 (tm-30) REVERT: C 961 ASP cc_start: 0.7432 (m-30) cc_final: 0.7173 (m-30) REVERT: C 963 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7478 (mt) REVERT: C 972 GLU cc_start: 0.8381 (tt0) cc_final: 0.7814 (pt0) REVERT: C 1054 GLU cc_start: 0.8562 (pm20) cc_final: 0.8298 (pm20) REVERT: C 1055 ARG cc_start: 0.8407 (mmm160) cc_final: 0.8143 (ttm-80) outliers start: 72 outliers final: 45 residues processed: 525 average time/residue: 0.3843 time to fit residues: 317.4439 Evaluate side-chains 429 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 380 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 CYS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 286 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 526 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 987 GLN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN C 766 GLN C 917 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 25859 Z= 0.296 Angle : 0.722 15.375 35190 Z= 0.359 Chirality : 0.050 0.345 4088 Planarity : 0.005 0.067 4498 Dihedral : 10.633 69.306 4278 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.49 % Allowed : 11.68 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 3135 helix: -0.24 (0.20), residues: 626 sheet: -1.39 (0.19), residues: 640 loop : -2.61 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 340 HIS 0.008 0.001 HIS A1040 PHE 0.022 0.002 PHE A 329 TYR 0.024 0.002 TYR B 442 ARG 0.007 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 390 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8414 (t0) cc_final: 0.8110 (m-30) REVERT: A 84 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8155 (mmmt) REVERT: A 132 LEU cc_start: 0.5891 (mm) cc_final: 0.5585 (mm) REVERT: A 151 MET cc_start: 0.4161 (tpt) cc_final: 0.3852 (tmm) REVERT: A 184 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7883 (mp0) REVERT: A 294 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8142 (pt0) REVERT: A 451 PHE cc_start: 0.7865 (m-80) cc_final: 0.7503 (m-80) REVERT: A 514 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7533 (mttp) REVERT: A 640 GLU cc_start: 0.8357 (tt0) cc_final: 0.8081 (tp30) REVERT: A 733 ASN cc_start: 0.8672 (t0) cc_final: 0.8212 (m110) REVERT: A 745 LEU cc_start: 0.8609 (tm) cc_final: 0.8284 (tp) REVERT: A 755 GLU cc_start: 0.8219 (pp20) cc_final: 0.7728 (tp30) REVERT: A 762 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8143 (mm-30) REVERT: A 796 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7486 (mmtm) REVERT: A 833 CYS cc_start: 0.6740 (m) cc_final: 0.6048 (p) REVERT: A 918 GLU cc_start: 0.8985 (tt0) cc_final: 0.8759 (mm-30) REVERT: A 972 GLU cc_start: 0.8516 (tt0) cc_final: 0.7895 (pt0) REVERT: A 1055 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7919 (ttm-80) REVERT: A 1071 PHE cc_start: 0.7784 (m-80) cc_final: 0.7559 (m-80) REVERT: B 84 LYS cc_start: 0.8482 (mmpt) cc_final: 0.8221 (mmtt) REVERT: B 263 MET cc_start: 0.8777 (ttt) cc_final: 0.8557 (ttt) REVERT: B 340 TRP cc_start: 0.6972 (p-90) cc_final: 0.6614 (p-90) REVERT: B 342 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7314 (ttm-80) REVERT: B 390 LYS cc_start: 0.6318 (OUTLIER) cc_final: 0.6013 (tttt) REVERT: B 410 TYR cc_start: 0.7543 (t80) cc_final: 0.6944 (t80) REVERT: B 447 LYS cc_start: 0.6883 (mttt) cc_final: 0.6408 (mmtm) REVERT: B 481 TYR cc_start: 0.5710 (t80) cc_final: 0.4477 (t80) REVERT: B 524 CYS cc_start: 0.8551 (m) cc_final: 0.8128 (t) REVERT: B 539 THR cc_start: 0.8080 (m) cc_final: 0.7548 (p) REVERT: B 599 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5686 (mm-40) REVERT: B 733 ASN cc_start: 0.8787 (t0) cc_final: 0.8456 (m-40) REVERT: B 745 LEU cc_start: 0.8700 (tm) cc_final: 0.8231 (tt) REVERT: B 749 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7967 (pt) REVERT: B 755 GLU cc_start: 0.8305 (pp20) cc_final: 0.7682 (tp30) REVERT: B 762 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8223 (mm-30) REVERT: B 790 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6930 (p0) REVERT: B 796 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7558 (tppt) REVERT: B 833 CYS cc_start: 0.6857 (m) cc_final: 0.6289 (p) REVERT: B 886 TYR cc_start: 0.9078 (t80) cc_final: 0.8822 (t80) REVERT: B 959 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7894 (tm) REVERT: B 961 ASP cc_start: 0.7482 (m-30) cc_final: 0.7261 (m-30) REVERT: B 972 GLU cc_start: 0.8299 (tt0) cc_final: 0.7621 (pt0) REVERT: B 1054 GLU cc_start: 0.8642 (pm20) cc_final: 0.8049 (pm20) REVERT: B 1055 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7956 (ttm-80) REVERT: C 57 ASP cc_start: 0.8501 (t0) cc_final: 0.8159 (m-30) REVERT: C 207 ARG cc_start: 0.6014 (ptm160) cc_final: 0.5697 (mmt-90) REVERT: C 232 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7884 (mtp180) REVERT: C 260 THR cc_start: 0.8937 (m) cc_final: 0.8367 (p) REVERT: C 305 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.5994 (m-10) REVERT: C 338 TYR cc_start: 0.7399 (p90) cc_final: 0.6320 (p90) REVERT: C 342 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7570 (mtp85) REVERT: C 411 LYS cc_start: 0.7168 (tptm) cc_final: 0.6852 (tptp) REVERT: C 442 TYR cc_start: 0.5863 (p90) cc_final: 0.5635 (p90) REVERT: C 518 ASP cc_start: 0.7710 (t70) cc_final: 0.7333 (p0) REVERT: C 539 THR cc_start: 0.7970 (m) cc_final: 0.7423 (p) REVERT: C 599 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5841 (mm-40) REVERT: C 733 ASN cc_start: 0.8593 (t0) cc_final: 0.8171 (m110) REVERT: C 745 LEU cc_start: 0.8695 (tm) cc_final: 0.8358 (mt) REVERT: C 746 ASN cc_start: 0.8469 (t0) cc_final: 0.8218 (t0) REVERT: C 755 GLU cc_start: 0.8198 (pp20) cc_final: 0.7618 (tp30) REVERT: C 762 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8165 (mm-30) REVERT: C 768 LYS cc_start: 0.8684 (tttp) cc_final: 0.8353 (tppp) REVERT: C 796 LYS cc_start: 0.7768 (mtmm) cc_final: 0.7310 (tppt) REVERT: C 918 GLU cc_start: 0.9033 (tt0) cc_final: 0.8762 (tm-30) REVERT: C 969 VAL cc_start: 0.7996 (m) cc_final: 0.7635 (p) REVERT: C 972 GLU cc_start: 0.8400 (tt0) cc_final: 0.8004 (tm-30) REVERT: C 1054 GLU cc_start: 0.8797 (pm20) cc_final: 0.8384 (pp20) REVERT: C 1055 ARG cc_start: 0.8353 (mmm160) cc_final: 0.8061 (ttm-80) REVERT: C 1071 PHE cc_start: 0.7764 (m-80) cc_final: 0.7494 (m-80) outliers start: 123 outliers final: 93 residues processed: 477 average time/residue: 0.3607 time to fit residues: 272.6097 Evaluate side-chains 449 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 349 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 599 GLN Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 766 GLN Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 287 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 150 optimal weight: 0.2980 chunk 272 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN A1101 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B1090 ASN B1101 ASN C 492 GLN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 25859 Z= 0.358 Angle : 0.726 14.795 35190 Z= 0.363 Chirality : 0.051 0.346 4088 Planarity : 0.005 0.063 4498 Dihedral : 9.920 63.121 4278 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 5.15 % Allowed : 12.08 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3135 helix: 0.17 (0.21), residues: 626 sheet: -1.25 (0.20), residues: 633 loop : -2.57 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 423 HIS 0.008 0.001 HIS B1040 PHE 0.019 0.002 PHE C 62 TYR 0.025 0.002 TYR A 598 ARG 0.004 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 379 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8410 (t0) cc_final: 0.8090 (m-30) REVERT: A 132 LEU cc_start: 0.4985 (mm) cc_final: 0.4636 (mm) REVERT: A 151 MET cc_start: 0.4394 (tpt) cc_final: 0.4081 (tmm) REVERT: A 184 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7839 (mp0) REVERT: A 207 ARG cc_start: 0.6316 (ptm160) cc_final: 0.6069 (mmt-90) REVERT: A 262 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8327 (t80) REVERT: A 294 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8137 (pt0) REVERT: A 306 ARG cc_start: 0.7103 (mmm-85) cc_final: 0.6621 (tpp80) REVERT: A 442 TYR cc_start: 0.5926 (p90) cc_final: 0.5693 (p90) REVERT: A 451 PHE cc_start: 0.7987 (m-80) cc_final: 0.7648 (m-80) REVERT: A 514 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7449 (mttp) REVERT: A 524 CYS cc_start: 0.7975 (t) cc_final: 0.7582 (t) REVERT: A 539 THR cc_start: 0.7900 (m) cc_final: 0.7384 (p) REVERT: A 640 GLU cc_start: 0.8418 (tt0) cc_final: 0.8143 (tp30) REVERT: A 733 ASN cc_start: 0.8798 (t0) cc_final: 0.8478 (m110) REVERT: A 755 GLU cc_start: 0.8097 (pp20) cc_final: 0.7612 (tp30) REVERT: A 762 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8149 (mm-30) REVERT: A 796 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7404 (mmtm) REVERT: A 833 CYS cc_start: 0.6796 (m) cc_final: 0.6015 (p) REVERT: A 961 ASP cc_start: 0.7650 (m-30) cc_final: 0.7379 (m-30) REVERT: A 1054 GLU cc_start: 0.8671 (pm20) cc_final: 0.8245 (pm20) REVERT: A 1055 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7909 (mtm-85) REVERT: A 1071 PHE cc_start: 0.7970 (m-80) cc_final: 0.7715 (m-80) REVERT: B 84 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8235 (mmtt) REVERT: B 306 ARG cc_start: 0.6882 (mmm-85) cc_final: 0.6376 (mmm160) REVERT: B 340 TRP cc_start: 0.6884 (p-90) cc_final: 0.6621 (p-90) REVERT: B 390 LYS cc_start: 0.6285 (OUTLIER) cc_final: 0.5987 (tttt) REVERT: B 410 TYR cc_start: 0.7353 (t80) cc_final: 0.6742 (t80) REVERT: B 447 LYS cc_start: 0.6823 (mttt) cc_final: 0.6337 (mmtm) REVERT: B 481 TYR cc_start: 0.5667 (t80) cc_final: 0.4266 (t80) REVERT: B 514 LYS cc_start: 0.7600 (mtmm) cc_final: 0.7284 (mttp) REVERT: B 524 CYS cc_start: 0.8612 (m) cc_final: 0.8242 (t) REVERT: B 539 THR cc_start: 0.8127 (m) cc_final: 0.7527 (p) REVERT: B 730 GLU cc_start: 0.8403 (pm20) cc_final: 0.7755 (mm-30) REVERT: B 733 ASN cc_start: 0.8811 (t0) cc_final: 0.8478 (m-40) REVERT: B 745 LEU cc_start: 0.8725 (tm) cc_final: 0.8064 (mt) REVERT: B 749 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8076 (pt) REVERT: B 755 GLU cc_start: 0.8299 (pp20) cc_final: 0.7750 (tp30) REVERT: B 762 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8425 (mm-30) REVERT: B 790 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7089 (p0) REVERT: B 796 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7522 (tppt) REVERT: B 802 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: B 972 GLU cc_start: 0.8280 (tt0) cc_final: 0.7809 (tm-30) REVERT: B 1054 GLU cc_start: 0.8760 (pm20) cc_final: 0.8117 (pm20) REVERT: B 1055 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7921 (mtm-85) REVERT: C 232 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.7862 (mtp180) REVERT: C 262 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8381 (t80) REVERT: C 306 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6602 (mmm160) REVERT: C 313 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8277 (p) REVERT: C 411 LYS cc_start: 0.7053 (tptm) cc_final: 0.6767 (tptp) REVERT: C 442 TYR cc_start: 0.5880 (p90) cc_final: 0.5649 (p90) REVERT: C 518 ASP cc_start: 0.7688 (t70) cc_final: 0.7324 (p0) REVERT: C 539 THR cc_start: 0.8014 (m) cc_final: 0.7429 (p) REVERT: C 708 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9110 (t) REVERT: C 733 ASN cc_start: 0.8793 (t0) cc_final: 0.8449 (m110) REVERT: C 745 LEU cc_start: 0.8838 (tm) cc_final: 0.8598 (tt) REVERT: C 755 GLU cc_start: 0.8178 (pp20) cc_final: 0.7489 (tp30) REVERT: C 762 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8422 (mm-30) REVERT: C 768 LYS cc_start: 0.8711 (tttp) cc_final: 0.8418 (tppt) REVERT: C 796 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7344 (tppt) REVERT: C 918 GLU cc_start: 0.9013 (tt0) cc_final: 0.8765 (mm-30) REVERT: C 970 GLU cc_start: 0.8082 (mp0) cc_final: 0.7803 (pm20) REVERT: C 972 GLU cc_start: 0.8439 (tt0) cc_final: 0.8080 (tm-30) REVERT: C 1054 GLU cc_start: 0.8804 (pm20) cc_final: 0.8434 (pp20) REVERT: C 1055 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7950 (ttm-80) REVERT: C 1071 PHE cc_start: 0.7957 (m-80) cc_final: 0.7744 (m-80) outliers start: 141 outliers final: 104 residues processed: 477 average time/residue: 0.3610 time to fit residues: 272.0332 Evaluate side-chains 464 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 352 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 950 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 210 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 155 optimal weight: 7.9990 chunk 273 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN C 614 GLN C 835 GLN C 896 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25859 Z= 0.303 Angle : 0.688 14.076 35190 Z= 0.343 Chirality : 0.049 0.329 4088 Planarity : 0.004 0.066 4498 Dihedral : 9.293 59.662 4278 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 5.73 % Allowed : 13.07 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % 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: -2.28 (0.14), residues: 3135 helix: 0.47 (0.21), residues: 642 sheet: -1.19 (0.19), residues: 643 loop : -2.49 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 423 HIS 0.006 0.001 HIS B1040 PHE 0.018 0.002 PHE C 870 TYR 0.021 0.002 TYR A 481 ARG 0.007 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 375 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8391 (t0) cc_final: 0.8094 (m-30) REVERT: A 151 MET cc_start: 0.4365 (tpt) cc_final: 0.4072 (tmm) REVERT: A 207 ARG cc_start: 0.6193 (ptm160) cc_final: 0.5983 (mmt-90) REVERT: A 262 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8369 (t80) REVERT: A 294 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8143 (pt0) REVERT: A 306 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6557 (mmm160) REVERT: A 442 TYR cc_start: 0.5760 (p90) cc_final: 0.5540 (p90) REVERT: A 451 PHE cc_start: 0.8018 (m-80) cc_final: 0.7791 (m-80) REVERT: A 453 ARG cc_start: 0.5657 (OUTLIER) cc_final: 0.4184 (pmt100) REVERT: A 514 LYS cc_start: 0.7325 (mtmm) cc_final: 0.6825 (mttp) REVERT: A 539 THR cc_start: 0.7917 (m) cc_final: 0.7382 (p) REVERT: A 560 ASP cc_start: 0.8489 (t0) cc_final: 0.8278 (t0) REVERT: A 640 GLU cc_start: 0.8361 (tt0) cc_final: 0.8075 (tp30) REVERT: A 733 ASN cc_start: 0.8842 (t0) cc_final: 0.8496 (m110) REVERT: A 755 GLU cc_start: 0.8035 (pp20) cc_final: 0.7619 (tp30) REVERT: A 762 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8182 (mm-30) REVERT: A 796 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7263 (mmtm) REVERT: A 833 CYS cc_start: 0.6742 (m) cc_final: 0.5964 (p) REVERT: A 961 ASP cc_start: 0.7644 (m-30) cc_final: 0.7361 (m-30) REVERT: A 1054 GLU cc_start: 0.8641 (pm20) cc_final: 0.8208 (pm20) REVERT: A 1055 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7917 (mtm-85) REVERT: B 263 MET cc_start: 0.8666 (ttt) cc_final: 0.8299 (tpt) REVERT: B 306 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6706 (mmm160) REVERT: B 340 TRP cc_start: 0.6809 (p-90) cc_final: 0.6546 (p-90) REVERT: B 390 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.6194 (pttt) REVERT: B 410 TYR cc_start: 0.7350 (t80) cc_final: 0.6745 (t80) REVERT: B 447 LYS cc_start: 0.6386 (mttt) cc_final: 0.5967 (mmtm) REVERT: B 524 CYS cc_start: 0.8623 (m) cc_final: 0.8245 (t) REVERT: B 539 THR cc_start: 0.8204 (m) cc_final: 0.7523 (p) REVERT: B 730 GLU cc_start: 0.8386 (pm20) cc_final: 0.7648 (mm-30) REVERT: B 733 ASN cc_start: 0.8752 (t0) cc_final: 0.8247 (m-40) REVERT: B 745 LEU cc_start: 0.8701 (tm) cc_final: 0.8055 (mt) REVERT: B 749 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7986 (pt) REVERT: B 755 GLU cc_start: 0.8169 (pp20) cc_final: 0.7656 (tp30) REVERT: B 762 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8434 (mm-30) REVERT: B 790 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7115 (p0) REVERT: B 796 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7577 (tppt) REVERT: B 946 LYS cc_start: 0.8664 (mtpm) cc_final: 0.8447 (mtpp) REVERT: B 972 GLU cc_start: 0.8214 (tt0) cc_final: 0.7759 (tm-30) REVERT: B 1042 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 1054 GLU cc_start: 0.8675 (pm20) cc_final: 0.8002 (pm20) REVERT: B 1055 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7880 (mtm-85) REVERT: B 1071 PHE cc_start: 0.8001 (m-80) cc_final: 0.7750 (m-80) REVERT: C 232 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7770 (mtp-110) REVERT: C 262 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8537 (t80) REVERT: C 306 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6707 (mmm160) REVERT: C 313 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 411 LYS cc_start: 0.6975 (tptm) cc_final: 0.6675 (tptp) REVERT: C 442 TYR cc_start: 0.5816 (p90) cc_final: 0.5573 (p90) REVERT: C 453 ARG cc_start: 0.5578 (OUTLIER) cc_final: 0.4112 (pmt100) REVERT: C 518 ASP cc_start: 0.7569 (t70) cc_final: 0.7221 (p0) REVERT: C 539 THR cc_start: 0.8037 (m) cc_final: 0.7470 (p) REVERT: C 614 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6407 (mp-120) REVERT: C 733 ASN cc_start: 0.8769 (t0) cc_final: 0.8427 (m110) REVERT: C 755 GLU cc_start: 0.8127 (pp20) cc_final: 0.7489 (tp30) REVERT: C 762 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8385 (mm-30) REVERT: C 768 LYS cc_start: 0.8689 (tttp) cc_final: 0.8397 (tppt) REVERT: C 796 LYS cc_start: 0.7776 (mtmm) cc_final: 0.7341 (tppt) REVERT: C 918 GLU cc_start: 0.9068 (tt0) cc_final: 0.8833 (tm-30) REVERT: C 972 GLU cc_start: 0.8489 (tt0) cc_final: 0.8043 (tm-30) REVERT: C 1054 GLU cc_start: 0.8791 (pm20) cc_final: 0.8484 (pp20) REVERT: C 1055 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7954 (ttm-80) outliers start: 157 outliers final: 119 residues processed: 485 average time/residue: 0.3741 time to fit residues: 286.4539 Evaluate side-chains 480 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 351 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 TRP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 950 SER Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 253 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A 917 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 526 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25859 Z= 0.182 Angle : 0.642 13.602 35190 Z= 0.317 Chirality : 0.047 0.316 4088 Planarity : 0.004 0.065 4498 Dihedral : 8.697 59.799 4278 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.07 % Allowed : 14.35 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 3135 helix: 0.91 (0.21), residues: 653 sheet: -1.00 (0.20), residues: 622 loop : -2.35 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 423 HIS 0.003 0.000 HIS C1030 PHE 0.017 0.001 PHE C 870 TYR 0.019 0.001 TYR A 481 ARG 0.007 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 383 time to evaluate : 2.870 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: A 57 ASP cc_start: 0.8334 (t0) cc_final: 0.8068 (m-30) REVERT: A 151 MET cc_start: 0.4344 (OUTLIER) cc_final: 0.4090 (tmm) REVERT: A 184 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7852 (mp0) REVERT: A 207 ARG cc_start: 0.6179 (ptm160) cc_final: 0.5976 (mmt-90) REVERT: A 262 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8054 (t80) REVERT: A 294 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8153 (pt0) REVERT: A 306 ARG cc_start: 0.6600 (mmm-85) cc_final: 0.6017 (mmm160) REVERT: A 387 PHE cc_start: 0.7910 (p90) cc_final: 0.7607 (p90) REVERT: A 442 TYR cc_start: 0.5767 (p90) cc_final: 0.5541 (p90) REVERT: A 451 PHE cc_start: 0.7886 (m-80) cc_final: 0.7663 (m-80) REVERT: A 453 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.3678 (pmt100) REVERT: A 514 LYS cc_start: 0.7351 (mtmm) cc_final: 0.6852 (mttp) REVERT: A 539 THR cc_start: 0.7921 (m) cc_final: 0.7352 (p) REVERT: A 560 ASP cc_start: 0.8492 (t0) cc_final: 0.8274 (t0) REVERT: A 640 GLU cc_start: 0.8461 (tt0) cc_final: 0.8196 (tp30) REVERT: A 733 ASN cc_start: 0.8708 (t0) cc_final: 0.8255 (m110) REVERT: A 755 GLU cc_start: 0.7939 (pp20) cc_final: 0.7572 (tp30) REVERT: A 762 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8143 (mm-30) REVERT: A 790 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 796 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7295 (mmtm) REVERT: A 833 CYS cc_start: 0.6661 (m) cc_final: 0.5878 (p) REVERT: A 961 ASP cc_start: 0.7694 (m-30) cc_final: 0.7370 (m-30) REVERT: A 1022 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 1054 GLU cc_start: 0.8639 (pm20) cc_final: 0.8207 (pm20) REVERT: A 1055 ARG cc_start: 0.8172 (mmm160) cc_final: 0.7881 (ttm-80) REVERT: B 263 MET cc_start: 0.8579 (ttt) cc_final: 0.8219 (tpt) REVERT: B 294 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8469 (mt-10) REVERT: B 306 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6670 (mmm160) REVERT: B 410 TYR cc_start: 0.7304 (t80) cc_final: 0.6686 (t80) REVERT: B 447 LYS cc_start: 0.6400 (mttt) cc_final: 0.5959 (mmtm) REVERT: B 524 CYS cc_start: 0.8463 (m) cc_final: 0.8095 (t) REVERT: B 539 THR cc_start: 0.8180 (m) cc_final: 0.7510 (p) REVERT: B 722 MET cc_start: 0.9260 (tpt) cc_final: 0.9043 (tpt) REVERT: B 730 GLU cc_start: 0.8341 (pm20) cc_final: 0.7605 (mm-30) REVERT: B 733 ASN cc_start: 0.8743 (t0) cc_final: 0.8240 (m-40) REVERT: B 749 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7802 (pt) REVERT: B 755 GLU cc_start: 0.8090 (pp20) cc_final: 0.7704 (tp30) REVERT: B 762 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8276 (mm-30) REVERT: B 796 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7554 (tppt) REVERT: B 972 GLU cc_start: 0.8213 (tt0) cc_final: 0.7753 (tm-30) REVERT: B 1049 TYR cc_start: 0.8705 (t80) cc_final: 0.8457 (t80) REVERT: B 1054 GLU cc_start: 0.8648 (pm20) cc_final: 0.7935 (pm20) REVERT: B 1055 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7867 (mtm-85) REVERT: B 1071 PHE cc_start: 0.7619 (m-80) cc_final: 0.7332 (m-80) REVERT: C 232 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7840 (mtp-110) REVERT: C 262 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8390 (t80) REVERT: C 306 ARG cc_start: 0.7134 (mmm-85) cc_final: 0.6659 (mmm160) REVERT: C 338 TYR cc_start: 0.7335 (p90) cc_final: 0.6880 (p90) REVERT: C 411 LYS cc_start: 0.6976 (tptm) cc_final: 0.6708 (tptp) REVERT: C 442 TYR cc_start: 0.5866 (p90) cc_final: 0.5621 (p90) REVERT: C 514 LYS cc_start: 0.7412 (mtmm) cc_final: 0.7157 (mttm) REVERT: C 518 ASP cc_start: 0.7478 (t70) cc_final: 0.7115 (p0) REVERT: C 539 THR cc_start: 0.8062 (m) cc_final: 0.7498 (p) REVERT: C 614 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: C 733 ASN cc_start: 0.8768 (t0) cc_final: 0.8459 (m110) REVERT: C 755 GLU cc_start: 0.8069 (pp20) cc_final: 0.7476 (tp30) REVERT: C 762 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8342 (mm-30) REVERT: C 768 LYS cc_start: 0.8526 (tttp) cc_final: 0.8207 (tppt) REVERT: C 796 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7252 (tppt) REVERT: C 961 ASP cc_start: 0.7211 (m-30) cc_final: 0.6991 (m-30) REVERT: C 970 GLU cc_start: 0.7871 (mp0) cc_final: 0.7597 (pm20) REVERT: C 972 GLU cc_start: 0.8516 (tt0) cc_final: 0.8079 (tm-30) REVERT: C 1054 GLU cc_start: 0.8707 (pm20) cc_final: 0.8435 (pp20) REVERT: C 1055 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7828 (mtm-85) outliers start: 139 outliers final: 99 residues processed: 481 average time/residue: 0.3675 time to fit residues: 280.1305 Evaluate side-chains 464 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 357 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 TRP Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 222 optimal weight: 30.0000 chunk 172 optimal weight: 0.9980 chunk 256 optimal weight: 0.1980 chunk 170 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25859 Z= 0.225 Angle : 0.655 14.626 35190 Z= 0.323 Chirality : 0.048 0.319 4088 Planarity : 0.004 0.064 4498 Dihedral : 8.368 59.769 4278 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.86 % Allowed : 14.79 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % 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: -1.84 (0.15), residues: 3135 helix: 1.13 (0.21), residues: 647 sheet: -0.92 (0.20), residues: 622 loop : -2.32 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 340 HIS 0.004 0.001 HIS A1040 PHE 0.020 0.001 PHE A 220 TYR 0.018 0.001 TYR A 481 ARG 0.004 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 369 time to evaluate : 2.866 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: A 57 ASP cc_start: 0.8325 (t0) cc_final: 0.8064 (m-30) REVERT: A 151 MET cc_start: 0.4338 (OUTLIER) cc_final: 0.4050 (tmm) REVERT: A 184 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7851 (mp0) REVERT: A 262 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 294 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8135 (pt0) REVERT: A 306 ARG cc_start: 0.6626 (mmm-85) cc_final: 0.6081 (mmm160) REVERT: A 387 PHE cc_start: 0.7824 (p90) cc_final: 0.7462 (p90) REVERT: A 453 ARG cc_start: 0.5406 (OUTLIER) cc_final: 0.3734 (pmt100) REVERT: A 514 LYS cc_start: 0.7352 (mtmm) cc_final: 0.6831 (mttp) REVERT: A 539 THR cc_start: 0.7916 (m) cc_final: 0.7332 (p) REVERT: A 560 ASP cc_start: 0.8506 (t0) cc_final: 0.8279 (t0) REVERT: A 640 GLU cc_start: 0.8489 (tt0) cc_final: 0.8224 (tp30) REVERT: A 733 ASN cc_start: 0.8846 (t0) cc_final: 0.8531 (m110) REVERT: A 755 GLU cc_start: 0.8019 (pp20) cc_final: 0.7698 (tp30) REVERT: A 762 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8277 (mm-30) REVERT: A 790 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7032 (p0) REVERT: A 796 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7304 (mmtm) REVERT: A 833 CYS cc_start: 0.6683 (m) cc_final: 0.5906 (p) REVERT: A 907 ASN cc_start: 0.8398 (m110) cc_final: 0.8000 (m-40) REVERT: A 961 ASP cc_start: 0.7638 (m-30) cc_final: 0.7356 (m-30) REVERT: A 972 GLU cc_start: 0.8547 (tt0) cc_final: 0.8006 (pt0) REVERT: A 1022 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 1054 GLU cc_start: 0.8706 (pm20) cc_final: 0.8211 (pm20) REVERT: A 1055 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7838 (ttm-80) REVERT: B 263 MET cc_start: 0.8652 (ttt) cc_final: 0.8257 (tpt) REVERT: B 294 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8467 (mt-10) REVERT: B 306 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6394 (tpt-90) REVERT: B 410 TYR cc_start: 0.7282 (t80) cc_final: 0.6777 (t80) REVERT: B 447 LYS cc_start: 0.6534 (mttt) cc_final: 0.6104 (mmtm) REVERT: B 453 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.4939 (ptt-90) REVERT: B 524 CYS cc_start: 0.8376 (m) cc_final: 0.7935 (t) REVERT: B 539 THR cc_start: 0.8019 (m) cc_final: 0.7304 (p) REVERT: B 599 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5809 (mp-120) REVERT: B 730 GLU cc_start: 0.8338 (pm20) cc_final: 0.7611 (mm-30) REVERT: B 733 ASN cc_start: 0.8741 (t0) cc_final: 0.8236 (m-40) REVERT: B 745 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 749 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7806 (pt) REVERT: B 755 GLU cc_start: 0.8019 (pp20) cc_final: 0.7600 (tp30) REVERT: B 762 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8300 (mm-30) REVERT: B 796 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7605 (tppt) REVERT: B 972 GLU cc_start: 0.8262 (tt0) cc_final: 0.7796 (tm-30) REVERT: B 1049 TYR cc_start: 0.8731 (t80) cc_final: 0.8463 (t80) REVERT: B 1054 GLU cc_start: 0.8666 (pm20) cc_final: 0.7945 (pm20) REVERT: B 1055 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7757 (mtm-85) REVERT: B 1071 PHE cc_start: 0.7741 (m-80) cc_final: 0.7537 (m-10) REVERT: C 109 ASN cc_start: 0.6616 (OUTLIER) cc_final: 0.6271 (m-40) REVERT: C 232 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7886 (mtp-110) REVERT: C 262 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8477 (t80) REVERT: C 306 ARG cc_start: 0.7288 (mmm-85) cc_final: 0.6831 (mmm160) REVERT: C 411 LYS cc_start: 0.6957 (tptm) cc_final: 0.6652 (tptp) REVERT: C 442 TYR cc_start: 0.5848 (p90) cc_final: 0.5611 (p90) REVERT: C 481 TYR cc_start: 0.4928 (t80) cc_final: 0.3968 (t80) REVERT: C 514 LYS cc_start: 0.7613 (mtmm) cc_final: 0.7360 (mttm) REVERT: C 518 ASP cc_start: 0.7688 (t70) cc_final: 0.7294 (p0) REVERT: C 539 THR cc_start: 0.8064 (m) cc_final: 0.7484 (p) REVERT: C 733 ASN cc_start: 0.8762 (t0) cc_final: 0.8455 (m110) REVERT: C 755 GLU cc_start: 0.8144 (pp20) cc_final: 0.7571 (tp30) REVERT: C 762 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8344 (mm-30) REVERT: C 768 LYS cc_start: 0.8487 (tttp) cc_final: 0.8252 (tppt) REVERT: C 796 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7241 (tppt) REVERT: C 961 ASP cc_start: 0.7196 (m-30) cc_final: 0.6952 (m-30) REVERT: C 970 GLU cc_start: 0.7860 (mp0) cc_final: 0.7520 (pm20) REVERT: C 972 GLU cc_start: 0.8528 (tt0) cc_final: 0.8072 (tm-30) REVERT: C 1054 GLU cc_start: 0.8734 (pm20) cc_final: 0.8296 (pp20) REVERT: C 1055 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7854 (ttm-80) REVERT: C 1095 GLN cc_start: 0.8401 (mm110) cc_final: 0.8078 (mm-40) outliers start: 133 outliers final: 100 residues processed: 465 average time/residue: 0.3633 time to fit residues: 268.6649 Evaluate side-chains 465 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 354 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 TRP Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 661 HIS B 931 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25859 Z= 0.274 Angle : 0.676 14.407 35190 Z= 0.335 Chirality : 0.048 0.324 4088 Planarity : 0.004 0.062 4498 Dihedral : 8.234 59.977 4278 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 5.11 % Allowed : 15.01 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % 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: -1.87 (0.15), residues: 3135 helix: 1.05 (0.21), residues: 646 sheet: -0.91 (0.20), residues: 628 loop : -2.34 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 340 HIS 0.010 0.001 HIS A 70 PHE 0.019 0.001 PHE A 220 TYR 0.022 0.001 TYR B 367 ARG 0.003 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 366 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8417 (t0) cc_final: 0.8099 (m-30) REVERT: A 151 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.4062 (tmm) REVERT: A 184 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7851 (mp0) REVERT: A 262 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8337 (t80) REVERT: A 294 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8149 (pt0) REVERT: A 306 ARG cc_start: 0.7048 (mmm-85) cc_final: 0.6523 (mmm160) REVERT: A 387 PHE cc_start: 0.7849 (p90) cc_final: 0.7438 (p90) REVERT: A 453 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.4134 (pmt100) REVERT: A 514 LYS cc_start: 0.7238 (mtmm) cc_final: 0.6634 (mttp) REVERT: A 539 THR cc_start: 0.7920 (m) cc_final: 0.7348 (p) REVERT: A 560 ASP cc_start: 0.8500 (t0) cc_final: 0.8266 (t0) REVERT: A 640 GLU cc_start: 0.8500 (tt0) cc_final: 0.8229 (tp30) REVERT: A 733 ASN cc_start: 0.8830 (t0) cc_final: 0.8506 (m110) REVERT: A 755 GLU cc_start: 0.8019 (pp20) cc_final: 0.7658 (tp30) REVERT: A 762 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8283 (mm-30) REVERT: A 796 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7317 (mmtm) REVERT: A 833 CYS cc_start: 0.6704 (m) cc_final: 0.5913 (p) REVERT: A 907 ASN cc_start: 0.8385 (m110) cc_final: 0.7971 (m-40) REVERT: A 961 ASP cc_start: 0.7481 (m-30) cc_final: 0.7210 (m-30) REVERT: A 972 GLU cc_start: 0.8561 (tt0) cc_final: 0.8015 (pt0) REVERT: A 1054 GLU cc_start: 0.8719 (pm20) cc_final: 0.8454 (pm20) REVERT: A 1055 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7720 (ttm-80) REVERT: B 294 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8461 (mt-10) REVERT: B 306 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6782 (mmm160) REVERT: B 410 TYR cc_start: 0.7252 (t80) cc_final: 0.6696 (t80) REVERT: B 447 LYS cc_start: 0.6539 (mttt) cc_final: 0.6110 (mmtm) REVERT: B 524 CYS cc_start: 0.8439 (m) cc_final: 0.8082 (t) REVERT: B 599 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6291 (mm-40) REVERT: B 730 GLU cc_start: 0.8372 (pm20) cc_final: 0.7647 (mm-30) REVERT: B 733 ASN cc_start: 0.8740 (t0) cc_final: 0.8225 (m-40) REVERT: B 745 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8059 (mt) REVERT: B 749 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7872 (pt) REVERT: B 755 GLU cc_start: 0.7948 (pp20) cc_final: 0.7507 (tp30) REVERT: B 762 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8441 (mm-30) REVERT: B 796 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7615 (tppt) REVERT: B 946 LYS cc_start: 0.8661 (mtpm) cc_final: 0.8444 (mtpp) REVERT: B 972 GLU cc_start: 0.8312 (tt0) cc_final: 0.7819 (tm-30) REVERT: B 1049 TYR cc_start: 0.8757 (t80) cc_final: 0.8466 (t80) REVERT: B 1054 GLU cc_start: 0.8639 (pm20) cc_final: 0.7893 (pm20) REVERT: B 1055 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7666 (mtm-85) REVERT: C 131 GLU cc_start: 0.5937 (tt0) cc_final: 0.5704 (pt0) REVERT: C 232 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7872 (mtp-110) REVERT: C 262 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8607 (t80) REVERT: C 306 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.6702 (mmm160) REVERT: C 411 LYS cc_start: 0.6807 (tptm) cc_final: 0.6552 (tptp) REVERT: C 442 TYR cc_start: 0.5735 (p90) cc_final: 0.5464 (p90) REVERT: C 453 ARG cc_start: 0.5457 (OUTLIER) cc_final: 0.4153 (pmt100) REVERT: C 481 TYR cc_start: 0.5178 (t80) cc_final: 0.4199 (t80) REVERT: C 514 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7396 (mttm) REVERT: C 518 ASP cc_start: 0.7592 (t70) cc_final: 0.7177 (p0) REVERT: C 539 THR cc_start: 0.8072 (m) cc_final: 0.7482 (p) REVERT: C 733 ASN cc_start: 0.8785 (t0) cc_final: 0.8479 (m110) REVERT: C 755 GLU cc_start: 0.8104 (pp20) cc_final: 0.7512 (tp30) REVERT: C 762 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8355 (mm-30) REVERT: C 768 LYS cc_start: 0.8466 (tttp) cc_final: 0.8211 (tppt) REVERT: C 796 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7261 (tppt) REVERT: C 961 ASP cc_start: 0.7332 (m-30) cc_final: 0.7091 (m-30) REVERT: C 970 GLU cc_start: 0.7923 (mp0) cc_final: 0.7549 (pm20) REVERT: C 972 GLU cc_start: 0.8477 (tt0) cc_final: 0.8018 (tm-30) REVERT: C 1054 GLU cc_start: 0.8749 (pm20) cc_final: 0.8334 (pp20) REVERT: C 1055 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7832 (mtm-85) outliers start: 140 outliers final: 112 residues processed: 466 average time/residue: 0.3595 time to fit residues: 266.1996 Evaluate side-chains 475 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 355 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 0.3980 chunk 222 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 255 optimal weight: 0.3980 chunk 267 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25859 Z= 0.174 Angle : 0.643 14.581 35190 Z= 0.317 Chirality : 0.047 0.308 4088 Planarity : 0.004 0.063 4498 Dihedral : 7.882 59.607 4278 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.09 % Allowed : 16.21 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.65 (0.15), residues: 3135 helix: 1.45 (0.21), residues: 651 sheet: -0.84 (0.20), residues: 617 loop : -2.26 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 340 HIS 0.002 0.000 HIS A 661 PHE 0.019 0.001 PHE A 316 TYR 0.020 0.001 TYR B 367 ARG 0.007 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 386 time to evaluate : 2.713 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: A 57 ASP cc_start: 0.8422 (t0) cc_final: 0.8123 (m-30) REVERT: A 151 MET cc_start: 0.4417 (OUTLIER) cc_final: 0.4142 (tmm) REVERT: A 184 GLU cc_start: 0.8685 (mt-10) cc_final: 0.7918 (mp0) REVERT: A 262 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8157 (t80) REVERT: A 294 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8183 (pt0) REVERT: A 306 ARG cc_start: 0.6607 (mmm-85) cc_final: 0.6103 (mmm160) REVERT: A 387 PHE cc_start: 0.7827 (p90) cc_final: 0.7456 (p90) REVERT: A 442 TYR cc_start: 0.5888 (p90) cc_final: 0.5639 (p90) REVERT: A 514 LYS cc_start: 0.7214 (mtmm) cc_final: 0.6637 (mttp) REVERT: A 539 THR cc_start: 0.7931 (m) cc_final: 0.7382 (p) REVERT: A 560 ASP cc_start: 0.8535 (t0) cc_final: 0.8285 (t0) REVERT: A 640 GLU cc_start: 0.8526 (tt0) cc_final: 0.8271 (tp30) REVERT: A 708 VAL cc_start: 0.9370 (OUTLIER) cc_final: 0.9137 (t) REVERT: A 730 GLU cc_start: 0.8132 (pm20) cc_final: 0.7306 (mm-30) REVERT: A 733 ASN cc_start: 0.8730 (t0) cc_final: 0.8235 (m110) REVERT: A 755 GLU cc_start: 0.7983 (pp20) cc_final: 0.7417 (tp30) REVERT: A 762 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8259 (mm-30) REVERT: A 796 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7354 (mmtm) REVERT: A 833 CYS cc_start: 0.6699 (m) cc_final: 0.5940 (p) REVERT: A 907 ASN cc_start: 0.8374 (m110) cc_final: 0.7981 (m-40) REVERT: A 961 ASP cc_start: 0.7472 (m-30) cc_final: 0.7125 (m-30) REVERT: A 972 GLU cc_start: 0.8572 (tt0) cc_final: 0.8019 (pt0) REVERT: A 1022 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 1054 GLU cc_start: 0.8704 (pm20) cc_final: 0.8425 (pm20) REVERT: A 1055 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7725 (ttm-80) REVERT: A 1095 GLN cc_start: 0.8396 (mm110) cc_final: 0.8024 (mm110) REVERT: B 294 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8439 (mt-10) REVERT: B 306 ARG cc_start: 0.7052 (mmm-85) cc_final: 0.6456 (tpt-90) REVERT: B 385 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 410 TYR cc_start: 0.7238 (t80) cc_final: 0.6758 (t80) REVERT: B 447 LYS cc_start: 0.6534 (mttt) cc_final: 0.6116 (mmtm) REVERT: B 524 CYS cc_start: 0.8154 (m) cc_final: 0.7784 (t) REVERT: B 730 GLU cc_start: 0.8396 (pm20) cc_final: 0.7580 (mm-30) REVERT: B 733 ASN cc_start: 0.8758 (t0) cc_final: 0.8288 (m-40) REVERT: B 745 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 749 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7761 (pt) REVERT: B 755 GLU cc_start: 0.7889 (pp20) cc_final: 0.7522 (tp30) REVERT: B 762 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8288 (mm-30) REVERT: B 796 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7699 (tppt) REVERT: B 972 GLU cc_start: 0.8291 (tt0) cc_final: 0.7780 (tm-30) REVERT: B 1049 TYR cc_start: 0.8666 (t80) cc_final: 0.8409 (t80) REVERT: B 1054 GLU cc_start: 0.8587 (pm20) cc_final: 0.7796 (pm20) REVERT: B 1055 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7682 (ttm-80) REVERT: C 109 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6313 (m-40) REVERT: C 131 GLU cc_start: 0.5947 (tt0) cc_final: 0.4967 (pt0) REVERT: C 232 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7899 (mtp-110) REVERT: C 262 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8439 (t80) REVERT: C 306 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6832 (mmm160) REVERT: C 411 LYS cc_start: 0.6847 (tptm) cc_final: 0.6590 (tptp) REVERT: C 442 TYR cc_start: 0.5808 (p90) cc_final: 0.5547 (p90) REVERT: C 518 ASP cc_start: 0.7582 (t70) cc_final: 0.7159 (p0) REVERT: C 733 ASN cc_start: 0.8781 (t0) cc_final: 0.8472 (m110) REVERT: C 755 GLU cc_start: 0.7985 (pp20) cc_final: 0.7493 (tp30) REVERT: C 762 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8318 (mm-30) REVERT: C 768 LYS cc_start: 0.8295 (tttp) cc_final: 0.8064 (tppt) REVERT: C 796 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7297 (tppt) REVERT: C 961 ASP cc_start: 0.7309 (m-30) cc_final: 0.7047 (m-30) REVERT: C 970 GLU cc_start: 0.7894 (mp0) cc_final: 0.7612 (pm20) REVERT: C 972 GLU cc_start: 0.8520 (tt0) cc_final: 0.8050 (tm-30) REVERT: C 974 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8028 (mt0) REVERT: C 1054 GLU cc_start: 0.8709 (pm20) cc_final: 0.8308 (pp20) REVERT: C 1055 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7846 (ttm-80) REVERT: C 1095 GLN cc_start: 0.8313 (mm110) cc_final: 0.7969 (mm-40) outliers start: 112 outliers final: 88 residues processed: 467 average time/residue: 0.3588 time to fit residues: 266.2254 Evaluate side-chains 458 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 361 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 646 TYR Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 646 TYR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 313 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 915 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN C 641 HIS ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 25859 Z= 0.323 Angle : 0.703 15.143 35190 Z= 0.348 Chirality : 0.050 0.385 4088 Planarity : 0.004 0.059 4498 Dihedral : 7.924 58.518 4278 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.94 % Allowed : 16.76 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.89 (0.15), residues: 3135 helix: 1.07 (0.21), residues: 634 sheet: -0.98 (0.20), residues: 635 loop : -2.32 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 340 HIS 0.006 0.001 HIS A1040 PHE 0.019 0.002 PHE A 62 TYR 0.027 0.002 TYR B 598 ARG 0.006 0.001 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 359 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8543 (t0) cc_final: 0.8220 (m-30) REVERT: A 85 ASP cc_start: 0.8518 (m-30) cc_final: 0.7804 (t0) REVERT: A 151 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.4308 (tmm) REVERT: A 184 GLU cc_start: 0.8708 (mt-10) cc_final: 0.7919 (mp0) REVERT: A 262 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8618 (t80) REVERT: A 294 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8143 (pt0) REVERT: A 306 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6666 (mmm160) REVERT: A 313 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 387 PHE cc_start: 0.7923 (p90) cc_final: 0.7410 (p90) REVERT: A 410 TYR cc_start: 0.6735 (t80) cc_final: 0.5646 (t80) REVERT: A 442 TYR cc_start: 0.5874 (p90) cc_final: 0.5673 (p90) REVERT: A 453 ARG cc_start: 0.5666 (OUTLIER) cc_final: 0.4044 (pmt100) REVERT: A 514 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6575 (mttp) REVERT: A 539 THR cc_start: 0.7970 (m) cc_final: 0.7364 (p) REVERT: A 560 ASP cc_start: 0.8473 (t0) cc_final: 0.8228 (t0) REVERT: A 640 GLU cc_start: 0.8499 (tt0) cc_final: 0.8236 (tp30) REVERT: A 733 ASN cc_start: 0.8845 (t0) cc_final: 0.8502 (m110) REVERT: A 755 GLU cc_start: 0.8159 (pp20) cc_final: 0.7745 (tp30) REVERT: A 762 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8350 (mm-30) REVERT: A 796 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7319 (mmtm) REVERT: A 833 CYS cc_start: 0.6774 (m) cc_final: 0.6023 (p) REVERT: A 907 ASN cc_start: 0.8401 (m110) cc_final: 0.7980 (m-40) REVERT: A 972 GLU cc_start: 0.8606 (tt0) cc_final: 0.8027 (pt0) REVERT: A 1054 GLU cc_start: 0.8742 (pm20) cc_final: 0.8488 (pm20) REVERT: A 1055 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7722 (mtm-85) REVERT: B 32 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: B 232 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7543 (ttp80) REVERT: B 263 MET cc_start: 0.8762 (ttt) cc_final: 0.8519 (ttt) REVERT: B 294 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8443 (mt-10) REVERT: B 306 ARG cc_start: 0.7195 (mmm-85) cc_final: 0.6831 (mmm160) REVERT: B 340 TRP cc_start: 0.6961 (p-90) cc_final: 0.6639 (p-90) REVERT: B 410 TYR cc_start: 0.7221 (t80) cc_final: 0.6577 (t80) REVERT: B 447 LYS cc_start: 0.6684 (mttt) cc_final: 0.6271 (mmtm) REVERT: B 524 CYS cc_start: 0.8481 (m) cc_final: 0.8091 (t) REVERT: B 730 GLU cc_start: 0.8435 (pm20) cc_final: 0.7746 (mm-30) REVERT: B 733 ASN cc_start: 0.8726 (t0) cc_final: 0.8197 (m-40) REVERT: B 745 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8020 (mt) REVERT: B 749 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7974 (pt) REVERT: B 755 GLU cc_start: 0.7996 (pp20) cc_final: 0.7551 (tp30) REVERT: B 762 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8407 (mm-30) REVERT: B 796 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7556 (tppt) REVERT: B 946 LYS cc_start: 0.8627 (mtpm) cc_final: 0.8418 (mtpp) REVERT: B 972 GLU cc_start: 0.8363 (tt0) cc_final: 0.7845 (tm-30) REVERT: B 1049 TYR cc_start: 0.8682 (t80) cc_final: 0.8405 (t80) REVERT: B 1054 GLU cc_start: 0.8675 (pm20) cc_final: 0.7931 (pm20) REVERT: B 1055 ARG cc_start: 0.7893 (mmm160) cc_final: 0.7550 (mtm-85) REVERT: C 131 GLU cc_start: 0.5945 (tt0) cc_final: 0.5712 (pt0) REVERT: C 232 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7615 (ttp80) REVERT: C 262 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8645 (t80) REVERT: C 306 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.6824 (mmm160) REVERT: C 411 LYS cc_start: 0.6806 (tptm) cc_final: 0.6550 (tptp) REVERT: C 442 TYR cc_start: 0.5700 (p90) cc_final: 0.5454 (p90) REVERT: C 453 ARG cc_start: 0.5615 (OUTLIER) cc_final: 0.4400 (pmt100) REVERT: C 518 ASP cc_start: 0.7615 (t70) cc_final: 0.7308 (p0) REVERT: C 733 ASN cc_start: 0.8742 (t0) cc_final: 0.8430 (m110) REVERT: C 755 GLU cc_start: 0.8219 (pp20) cc_final: 0.7597 (tp30) REVERT: C 762 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8368 (mm-30) REVERT: C 768 LYS cc_start: 0.8497 (tttp) cc_final: 0.8267 (tppt) REVERT: C 796 LYS cc_start: 0.7778 (mtmm) cc_final: 0.7333 (tppt) REVERT: C 961 ASP cc_start: 0.7308 (m-30) cc_final: 0.7056 (m-30) REVERT: C 970 GLU cc_start: 0.8130 (mp0) cc_final: 0.7753 (pm20) REVERT: C 972 GLU cc_start: 0.8473 (tt0) cc_final: 0.7998 (tm-30) REVERT: C 1054 GLU cc_start: 0.8771 (pm20) cc_final: 0.8357 (pp20) REVERT: C 1055 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7814 (mtm-85) outliers start: 108 outliers final: 93 residues processed: 438 average time/residue: 0.3656 time to fit residues: 254.0424 Evaluate side-chains 457 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 355 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 646 TYR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 707 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.6980 chunk 266 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 HIS ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.179594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137576 restraints weight = 38748.613| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.49 r_work: 0.3643 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25859 Z= 0.274 Angle : 0.683 14.447 35190 Z= 0.338 Chirality : 0.049 0.323 4088 Planarity : 0.004 0.062 4498 Dihedral : 7.871 57.889 4278 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.80 % Allowed : 16.94 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -1.83 (0.15), residues: 3135 helix: 1.17 (0.21), residues: 634 sheet: -0.91 (0.20), residues: 624 loop : -2.30 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 340 HIS 0.009 0.001 HIS C 641 PHE 0.023 0.002 PHE B1071 TYR 0.042 0.001 TYR B 598 ARG 0.006 0.000 ARG A 207 =============================================================================== Job complete usr+sys time: 6574.75 seconds wall clock time: 119 minutes 46.54 seconds (7186.54 seconds total)