Starting phenix.real_space_refine on Sun Jan 26 12:43:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5x58_6703/01_2025/5x58_6703.cif Found real_map, /net/cci-nas-00/data/ceres_data/5x58_6703/01_2025/5x58_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/cci-nas-00/data/ceres_data/5x58_6703/01_2025/5x58_6703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5x58_6703/01_2025/5x58_6703.map" model { file = "/net/cci-nas-00/data/ceres_data/5x58_6703/01_2025/5x58_6703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5x58_6703/01_2025/5x58_6703.cif" } 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. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 25265 Number of models: 1 Model: "" Number of chains: 4 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: "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 Restraints were copied for chains: C Time building chain proxies: 25.96, per 1000 atoms: 1.03 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=12, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 6.37 Conformation dependent library (CDL) restraints added in 4.0 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: 3.75 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: 10.64 Time building geometry restraints manager: 7.41 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: 0.00 - 3.62: 34611 3.62 - 7.25: 513 7.25 - 10.87: 42 10.87 - 14.50: 15 14.50 - 18.12: 9 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: 15186 21.67 - 43.34: 421 43.34 - 65.01: 100 65.01 - 86.68: 38 86.68 - 108.34: 90 Dihedral angle restraints: 15835 sinusoidal: 6613 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 15832 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: 2.01 - 2.59: 264 2.59 - 3.17: 20284 3.17 - 3.74: 38859 3.74 - 4.32: 55400 4.32 - 4.90: 88980 Nonbonded interactions: 203787 Sorted by model distance: nonbonded pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " model vdw 2.011 3.760 nonbonded pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 467 " pdb=" SG CYS C 474 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS C 128 " pdb=" SG CYS C 159 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS C 524 " pdb=" SG CYS C 576 " model vdw 2.038 3.760 ... (remaining 203782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.550 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: 0.720 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 69.190 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.170 ------------------------------------------------------------------------------- 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= 0.478 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 : 2.011 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 to be fit. rotamer outliers: 12 poor density : 692 time to evaluate : 2.764 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: 0.4054 time to fit residues: 441.4169 Evaluate side-chains 409 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 405 time to evaluate : 2.936 ------------------------------------------------------------------------------- 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: 0.8980 chunk 238 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 127 optimal weight: 40.0000 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 286 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 112 GLN A 135 ASN A 201 GLN A 409 ASN A 522 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 599 GLN A 614 GLN A 632 GLN A 733 ASN A 766 GLN A 883 GLN A 904 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN A 984 GLN A1090 ASN B 70 HIS B 135 ASN B 201 GLN B 280 GLN B 409 ASN B 522 ASN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN 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 883 GLN B 889 ASN B 904 GLN B 936 GLN B 937 ASN B 984 GLN B1053 GLN B1090 ASN C 70 HIS C 135 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 409 ASN C 492 GLN C 522 ASN C 526 ASN C 528 ASN C 614 GLN C 632 GLN C 733 ASN C 766 GLN C 835 GLN C 883 GLN C 896 ASN C 904 GLN C 936 GLN C 937 ASN C 984 GLN C1065 HIS ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144612 restraints weight = 39387.572| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.37 r_work: 0.3507 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25859 Z= 0.207 Angle : 0.737 13.556 35190 Z= 0.370 Chirality : 0.050 0.349 4088 Planarity : 0.005 0.073 4498 Dihedral : 13.035 82.702 4286 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.52 % Allowed : 10.41 % Favored : 87.08 % 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: -3.36 (0.13), residues: 3135 helix: -1.55 (0.18), residues: 609 sheet: -1.73 (0.19), residues: 619 loop : -2.77 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 340 HIS 0.003 0.001 HIS B1046 PHE 0.026 0.002 PHE A 460 TYR 0.034 0.002 TYR A 481 ARG 0.006 0.001 ARG B 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 555 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 486 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.7280 (m-80) cc_final: 0.6560 (m-80) REVERT: A 132 LEU cc_start: 0.6869 (mm) cc_final: 0.6579 (mm) REVERT: A 316 PHE cc_start: 0.6898 (t80) cc_final: 0.6385 (t80) REVERT: A 342 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7056 (ttm-80) REVERT: A 385 ASP cc_start: 0.7758 (m-30) cc_final: 0.7196 (m-30) REVERT: A 411 LYS cc_start: 0.7714 (tptm) cc_final: 0.7489 (tptp) REVERT: A 652 ILE cc_start: 0.8305 (mt) cc_final: 0.8046 (mt) REVERT: A 693 THR cc_start: 0.8073 (p) cc_final: 0.7815 (p) REVERT: A 736 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8973 (tt) REVERT: A 963 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7752 (mt) REVERT: A 972 GLU cc_start: 0.8151 (tt0) cc_final: 0.7854 (pt0) REVERT: B 130 PHE cc_start: 0.7399 (m-80) cc_final: 0.7069 (m-80) REVERT: B 260 THR cc_start: 0.8836 (m) cc_final: 0.8505 (p) REVERT: B 316 PHE cc_start: 0.7186 (t80) cc_final: 0.6853 (t80) REVERT: B 342 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7868 (ttm-80) REVERT: B 385 ASP cc_start: 0.7850 (m-30) cc_final: 0.7578 (m-30) REVERT: B 447 LYS cc_start: 0.6764 (mttt) cc_final: 0.6470 (mmtm) REVERT: B 539 THR cc_start: 0.8359 (m) cc_final: 0.7994 (p) REVERT: B 689 TYR cc_start: 0.7144 (t80) cc_final: 0.6867 (t80) REVERT: B 693 THR cc_start: 0.8351 (p) cc_final: 0.7823 (p) REVERT: B 961 ASP cc_start: 0.7513 (m-30) cc_final: 0.7244 (m-30) REVERT: B 972 GLU cc_start: 0.7922 (tt0) cc_final: 0.7574 (pt0) REVERT: B 1054 GLU cc_start: 0.8056 (pm20) cc_final: 0.7604 (pm20) REVERT: B 1071 PHE cc_start: 0.7690 (m-80) cc_final: 0.7143 (m-80) REVERT: C 78 ASN cc_start: 0.7835 (p0) cc_final: 0.7570 (p0) REVERT: C 260 THR cc_start: 0.8868 (m) cc_final: 0.8519 (p) REVERT: C 305 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6118 (m-80) REVERT: C 316 PHE cc_start: 0.7288 (t80) cc_final: 0.6969 (t80) REVERT: C 338 TYR cc_start: 0.7493 (p90) cc_final: 0.6802 (p90) REVERT: C 411 LYS cc_start: 0.7570 (tptm) cc_final: 0.7139 (tptp) REVERT: C 539 THR cc_start: 0.8245 (m) cc_final: 0.7856 (p) REVERT: C 599 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.5785 (mm-40) REVERT: C 745 LEU cc_start: 0.8347 (tm) cc_final: 0.8111 (mt) REVERT: C 961 ASP cc_start: 0.7572 (m-30) cc_final: 0.7266 (m-30) REVERT: C 963 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7349 (mt) REVERT: C 1071 PHE cc_start: 0.7464 (m-80) cc_final: 0.7017 (m-80) outliers start: 69 outliers final: 42 residues processed: 533 average time/residue: 0.3863 time to fit residues: 324.0771 Evaluate side-chains 415 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 368 time to evaluate : 2.801 ------------------------------------------------------------------------------- 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 112 GLN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 VAL 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 963 LEU 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 354 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 601 VAL 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 976 ASP 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 261 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL 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 Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 165 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 284 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 526 ASN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN B 129 ASN B 201 GLN B 526 ASN B 692 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B 987 GLN C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.176835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138080 restraints weight = 38980.230| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.69 r_work: 0.3527 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3239 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= 0.300 Angle : 0.738 15.110 35190 Z= 0.368 Chirality : 0.050 0.340 4088 Planarity : 0.005 0.068 4498 Dihedral : 10.569 69.065 4278 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.58 % Allowed : 11.72 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % 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: -2.71 (0.14), residues: 3135 helix: -0.21 (0.21), residues: 609 sheet: -1.55 (0.19), residues: 661 loop : -2.56 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 868 HIS 0.007 0.001 HIS A1040 PHE 0.020 0.002 PHE A 220 TYR 0.025 0.002 TYR B 442 ARG 0.015 0.001 ARG C 207 *********************** 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 482 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 384 time to evaluate : 2.646 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 132 LEU cc_start: 0.6737 (mm) cc_final: 0.6426 (mm) REVERT: A 316 PHE cc_start: 0.6752 (t80) cc_final: 0.6303 (t80) REVERT: A 342 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7702 (ttm-80) REVERT: A 453 ARG cc_start: 0.5567 (OUTLIER) cc_final: 0.4117 (pmt100) REVERT: A 539 THR cc_start: 0.8451 (m) cc_final: 0.7999 (p) REVERT: A 972 GLU cc_start: 0.8167 (tt0) cc_final: 0.7781 (pt0) REVERT: A 1054 GLU cc_start: 0.8180 (pm20) cc_final: 0.7860 (pm20) REVERT: A 1071 PHE cc_start: 0.7757 (m-80) cc_final: 0.7472 (m-80) REVERT: B 316 PHE cc_start: 0.7056 (t80) cc_final: 0.6638 (t80) REVERT: B 340 TRP cc_start: 0.7186 (p-90) cc_final: 0.6896 (p-90) REVERT: B 342 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7839 (ttm-80) REVERT: B 390 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6166 (tttt) REVERT: B 410 TYR cc_start: 0.7140 (t80) cc_final: 0.6838 (t80) REVERT: B 447 LYS cc_start: 0.7067 (mttt) cc_final: 0.6459 (mmtm) REVERT: B 481 TYR cc_start: 0.6436 (t80) cc_final: 0.5242 (t80) REVERT: B 527 PHE cc_start: 0.8201 (p90) cc_final: 0.7724 (p90) REVERT: B 539 THR cc_start: 0.8398 (m) cc_final: 0.7953 (p) REVERT: B 551 PHE cc_start: 0.7335 (m-80) cc_final: 0.7003 (m-80) REVERT: B 599 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5512 (mp10) REVERT: B 689 TYR cc_start: 0.7403 (t80) cc_final: 0.7199 (t80) REVERT: B 745 LEU cc_start: 0.8524 (tm) cc_final: 0.8120 (tt) REVERT: B 749 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8284 (pt) REVERT: B 961 ASP cc_start: 0.7531 (m-30) cc_final: 0.7284 (m-30) REVERT: B 972 GLU cc_start: 0.8224 (tt0) cc_final: 0.7655 (pt0) REVERT: B 1054 GLU cc_start: 0.8021 (pm20) cc_final: 0.7586 (pm20) REVERT: C 109 ASN cc_start: 0.7100 (p0) cc_final: 0.6458 (t0) REVERT: C 232 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7599 (mtp180) REVERT: C 260 THR cc_start: 0.8856 (m) cc_final: 0.8355 (p) REVERT: C 305 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.5851 (m-10) REVERT: C 316 PHE cc_start: 0.6985 (t80) cc_final: 0.6651 (t80) REVERT: C 338 TYR cc_start: 0.7558 (p90) cc_final: 0.6272 (p90) REVERT: C 340 TRP cc_start: 0.8025 (p-90) cc_final: 0.6973 (p-90) REVERT: C 390 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6618 (tttt) REVERT: C 411 LYS cc_start: 0.7541 (tptm) cc_final: 0.7224 (tptp) REVERT: C 442 TYR cc_start: 0.6496 (p90) cc_final: 0.6184 (p90) REVERT: C 453 ARG cc_start: 0.5346 (OUTLIER) cc_final: 0.4627 (pmt100) REVERT: C 599 GLN cc_start: 0.6272 (OUTLIER) cc_final: 0.5744 (mm-40) REVERT: C 745 LEU cc_start: 0.8451 (tm) cc_final: 0.7899 (mt) REVERT: C 746 ASN cc_start: 0.8159 (t0) cc_final: 0.7793 (t0) REVERT: C 749 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8312 (pt) REVERT: C 969 VAL cc_start: 0.8368 (m) cc_final: 0.7853 (p) REVERT: C 1071 PHE cc_start: 0.7746 (m-80) cc_final: 0.7426 (m-80) outliers start: 98 outliers final: 71 residues processed: 452 average time/residue: 0.3709 time to fit residues: 266.8686 Evaluate side-chains 405 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 325 time to evaluate : 2.617 ------------------------------------------------------------------------------- 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 231 PHE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 372 THR 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 453 ARG 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 729 THR Chi-restraints excluded: chain A residue 749 LEU 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 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 261 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 525 VAL 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 610 ILE Chi-restraints excluded: chain B residue 646 TYR 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 832 ILE Chi-restraints excluded: chain B residue 870 PHE 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 983 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 571 LEU 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 601 VAL 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 749 LEU Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 66 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 40.0000 chunk 293 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 614 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1090 ASN B 70 HIS B 492 GLN B 614 GLN B 835 GLN B 883 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 987 GLN B1090 ASN C 70 HIS C 280 GLN C 492 GLN C 614 GLN C 661 HIS C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.174174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135918 restraints weight = 39223.044| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.51 r_work: 0.3481 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 25859 Z= 0.372 Angle : 0.749 15.391 35190 Z= 0.374 Chirality : 0.052 0.365 4088 Planarity : 0.005 0.064 4498 Dihedral : 9.812 62.011 4278 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.18 % Allowed : 11.98 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % 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: -2.54 (0.14), residues: 3135 helix: 0.19 (0.21), residues: 617 sheet: -1.53 (0.19), residues: 667 loop : -2.52 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 423 HIS 0.009 0.001 HIS B1040 PHE 0.020 0.002 PHE B 551 TYR 0.024 0.002 TYR A 598 ARG 0.005 0.001 ARG A1021 *********************** 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 500 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 358 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6818 (mm) cc_final: 0.6406 (mm) REVERT: A 151 MET cc_start: 0.0491 (tmm) cc_final: 0.0013 (tmm) REVERT: A 262 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 294 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7925 (pt0) REVERT: A 316 PHE cc_start: 0.6856 (t80) cc_final: 0.6324 (t80) REVERT: A 442 TYR cc_start: 0.6270 (p90) cc_final: 0.6023 (p90) REVERT: A 451 PHE cc_start: 0.8314 (m-80) cc_final: 0.7959 (m-80) REVERT: A 453 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.4550 (pmt100) REVERT: A 514 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7750 (mttp) REVERT: A 539 THR cc_start: 0.8390 (m) cc_final: 0.7991 (p) REVERT: A 961 ASP cc_start: 0.7790 (m-30) cc_final: 0.7447 (m-30) REVERT: A 1054 GLU cc_start: 0.8250 (pm20) cc_final: 0.7942 (pm20) REVERT: A 1071 PHE cc_start: 0.7955 (m-80) cc_final: 0.7645 (m-80) REVERT: B 263 MET cc_start: 0.8253 (ttt) cc_final: 0.8006 (ttt) REVERT: B 305 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6946 (m-80) REVERT: B 316 PHE cc_start: 0.7185 (t80) cc_final: 0.6760 (t80) REVERT: B 340 TRP cc_start: 0.7624 (p-90) cc_final: 0.7388 (p-90) REVERT: B 410 TYR cc_start: 0.7203 (t80) cc_final: 0.6662 (t80) REVERT: B 447 LYS cc_start: 0.6826 (mttt) cc_final: 0.6399 (mmtm) REVERT: B 481 TYR cc_start: 0.6394 (t80) cc_final: 0.5204 (t80) REVERT: B 539 THR cc_start: 0.8468 (m) cc_final: 0.7989 (p) REVERT: B 745 LEU cc_start: 0.8553 (tm) cc_final: 0.8084 (mt) REVERT: B 749 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8451 (pt) REVERT: B 882 MET cc_start: 0.8334 (mtp) cc_final: 0.8112 (mtp) REVERT: B 961 ASP cc_start: 0.7413 (m-30) cc_final: 0.7143 (m-30) REVERT: B 972 GLU cc_start: 0.8175 (tt0) cc_final: 0.7923 (tm-30) REVERT: B 1054 GLU cc_start: 0.8040 (pm20) cc_final: 0.7654 (pm20) REVERT: B 1088 GLN cc_start: 0.8376 (pm20) cc_final: 0.8169 (pm20) REVERT: C 106 THR cc_start: 0.7679 (p) cc_final: 0.7472 (t) REVERT: C 262 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8506 (t80) REVERT: C 306 ARG cc_start: 0.6750 (mmm-85) cc_final: 0.6173 (mmm-85) REVERT: C 316 PHE cc_start: 0.7007 (t80) cc_final: 0.6605 (t80) REVERT: C 338 TYR cc_start: 0.7604 (p90) cc_final: 0.7237 (p90) REVERT: C 411 LYS cc_start: 0.7481 (tptm) cc_final: 0.7035 (tptp) REVERT: C 442 TYR cc_start: 0.6603 (p90) cc_final: 0.6292 (p90) REVERT: C 453 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4519 (pmt100) REVERT: C 614 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6708 (mp10) REVERT: C 745 LEU cc_start: 0.8515 (tm) cc_final: 0.8003 (mt) REVERT: C 746 ASN cc_start: 0.8181 (t0) cc_final: 0.7858 (t0) REVERT: C 1071 PHE cc_start: 0.7840 (m-80) cc_final: 0.7590 (m-80) outliers start: 142 outliers final: 102 residues processed: 461 average time/residue: 0.3692 time to fit residues: 272.7465 Evaluate side-chains 421 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 312 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 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 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 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 525 VAL Chi-restraints excluded: chain A residue 555 VAL 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 707 GLU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 963 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 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 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 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 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 390 LYS 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 497 VAL Chi-restraints excluded: chain B residue 555 VAL 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 628 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 693 THR 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 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 950 SER 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 1082 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 80 VAL 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 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 423 TRP Chi-restraints excluded: chain C residue 453 ARG Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 614 GLN 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 950 SER Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1042 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 104 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 112 GLN A 396 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN B 883 GLN B 931 GLN C 280 GLN C 835 GLN C 883 GLN C 896 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136054 restraints weight = 39114.441| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.47 r_work: 0.3488 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3989 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= 0.325 Angle : 0.718 13.793 35190 Z= 0.357 Chirality : 0.050 0.330 4088 Planarity : 0.005 0.065 4498 Dihedral : 9.346 59.579 4278 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.78 % Allowed : 13.58 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % 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: -2.33 (0.14), residues: 3135 helix: 0.43 (0.21), residues: 627 sheet: -1.40 (0.19), residues: 663 loop : -2.43 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 423 HIS 0.006 0.001 HIS A 70 PHE 0.018 0.002 PHE C 870 TYR 0.021 0.002 TYR A 163 ARG 0.008 0.001 ARG B 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 457 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 326 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6303 (mm) REVERT: A 151 MET cc_start: 0.0242 (tmm) cc_final: -0.0027 (tmm) REVERT: A 256 TYR cc_start: 0.8273 (m-80) cc_final: 0.8057 (m-80) REVERT: A 262 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8613 (t80) REVERT: A 294 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7876 (pt0) REVERT: A 316 PHE cc_start: 0.6819 (t80) cc_final: 0.6336 (t80) REVERT: A 442 TYR cc_start: 0.6077 (p90) cc_final: 0.5838 (p90) REVERT: A 451 PHE cc_start: 0.8316 (m-80) cc_final: 0.8069 (m-80) REVERT: A 453 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4479 (pmt100) REVERT: A 539 THR cc_start: 0.8394 (m) cc_final: 0.7984 (p) REVERT: A 961 ASP cc_start: 0.7768 (m-30) cc_final: 0.7489 (m-30) REVERT: A 1054 GLU cc_start: 0.8239 (pm20) cc_final: 0.7927 (pm20) REVERT: A 1071 PHE cc_start: 0.7950 (m-80) cc_final: 0.7689 (m-80) REVERT: B 263 MET cc_start: 0.8263 (ttt) cc_final: 0.7990 (ttt) REVERT: B 294 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7774 (mt-10) REVERT: B 306 ARG cc_start: 0.6533 (mmm-85) cc_final: 0.6081 (mmm160) REVERT: B 316 PHE cc_start: 0.7139 (t80) cc_final: 0.6688 (t80) REVERT: B 340 TRP cc_start: 0.7595 (p-90) cc_final: 0.7006 (p-90) REVERT: B 342 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7584 (ttm-80) REVERT: B 390 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6405 (pttt) REVERT: B 396 GLN cc_start: 0.6758 (mm-40) cc_final: 0.6555 (mm110) REVERT: B 410 TYR cc_start: 0.7195 (t80) cc_final: 0.6595 (t80) REVERT: B 447 LYS cc_start: 0.6945 (mttt) cc_final: 0.6513 (mmtm) REVERT: B 481 TYR cc_start: 0.6395 (t80) cc_final: 0.5308 (t80) REVERT: B 539 THR cc_start: 0.8382 (m) cc_final: 0.7862 (p) REVERT: B 614 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7087 (mp-120) REVERT: B 745 LEU cc_start: 0.8531 (tm) cc_final: 0.8060 (mt) REVERT: B 749 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8367 (pt) REVERT: B 961 ASP cc_start: 0.7519 (m-30) cc_final: 0.7306 (m-30) REVERT: B 972 GLU cc_start: 0.8191 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 1054 GLU cc_start: 0.8033 (pm20) cc_final: 0.7679 (pm20) REVERT: C 99 ARG cc_start: 0.6077 (ptp90) cc_final: 0.5834 (ptp-170) REVERT: C 262 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8591 (t80) REVERT: C 306 ARG cc_start: 0.6804 (mmm-85) cc_final: 0.6250 (mmm-85) REVERT: C 316 PHE cc_start: 0.6939 (t80) cc_final: 0.6542 (t80) REVERT: C 411 LYS cc_start: 0.7406 (tptm) cc_final: 0.6972 (tptp) REVERT: C 442 TYR cc_start: 0.6557 (p90) cc_final: 0.6239 (p90) REVERT: C 453 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.4301 (pmt100) REVERT: C 614 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6624 (mp10) REVERT: C 745 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8326 (tt) REVERT: C 961 ASP cc_start: 0.7446 (m-30) cc_final: 0.7120 (m-30) REVERT: C 1071 PHE cc_start: 0.7851 (m-80) cc_final: 0.7612 (m-80) outliers start: 131 outliers final: 98 residues processed: 420 average time/residue: 0.3615 time to fit residues: 244.3321 Evaluate side-chains 411 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 303 time to evaluate : 2.960 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 166 ASP 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 302 THR 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 386 SER 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 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 707 GLU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 LEU 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 963 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 181 HIS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 302 THR 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 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 453 ARG Chi-restraints excluded: chain B residue 497 VAL 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 614 GLN 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 729 THR 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 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 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 302 THR 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 571 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 601 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 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 745 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL 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 141 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 217 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 307 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 144 optimal weight: 0.0370 chunk 240 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 883 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.178290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140888 restraints weight = 39207.391| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.63 r_work: 0.3555 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4198 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: