Starting phenix.real_space_refine on Fri Jun 20 01:08:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyw_32896/06_2025/7wyw_32896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyw_32896/06_2025/7wyw_32896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wyw_32896/06_2025/7wyw_32896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyw_32896/06_2025/7wyw_32896.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyw_32896/06_2025/7wyw_32896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyw_32896/06_2025/7wyw_32896.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 26 5.49 5 Mg 6 5.21 5 S 118 5.16 5 C 14632 2.51 5 N 3514 2.21 5 O 4310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22606 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 477 Unusual residues: {' MG': 3, 'CLR': 3, 'PCW': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: C, K, N, L, G, D, M Time building chain proxies: 23.59, per 1000 atoms: 1.04 Number of scatterers: 22606 At special positions: 0 Unit cell: (216.276, 180.768, 103.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 26 15.00 Mg 6 11.99 O 4310 8.00 N 3514 7.00 C 14632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 4.2 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 20 sheets defined 49.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.831A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.530A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.676A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.378A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.928A pdb=" N VAL A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.504A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.690A pdb=" N SER A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.853A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.657A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 707 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.641A pdb=" N LYS A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.752A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.667A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.240A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 939 removed outlier: 3.512A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.553A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.761A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.519A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 29 through 62 removed outlier: 3.897A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.515A pdb=" N SER B 98 " --> pdb=" O ASN B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.576A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.003A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.563A pdb=" N ARG B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.749A pdb=" N TYR B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 40 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 89 through 97 removed outlier: 3.832A pdb=" N GLN C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 160 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.530A pdb=" N ARG C 264 " --> pdb=" O THR C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 282 through 313 Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.677A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 354 removed outlier: 4.378A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.928A pdb=" N VAL C 364 " --> pdb=" O LEU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.504A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.690A pdb=" N SER C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.854A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.657A pdb=" N ALA C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 707 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.640A pdb=" N LYS C 727 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.752A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 797 Proline residue: C 789 - end of helix Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 846 through 854 removed outlier: 3.668A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.240A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 892 Processing helix chain 'C' and resid 907 through 939 removed outlier: 3.511A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 Processing helix chain 'C' and resid 951 through 971 removed outlier: 3.552A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.761A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.518A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1022 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 29 through 62 removed outlier: 3.897A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.514A pdb=" N SER D 98 " --> pdb=" O ASN D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.577A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 4.004A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.563A pdb=" N ARG D 223 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.749A pdb=" N TYR D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 removed outlier: 11.684A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226 removed outlier: 4.102A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.713A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.852A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.599A pdb=" N ILE A 492 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 479 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 490 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.062A pdb=" N MET A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.791A pdb=" N GLU B 24 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.562A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE B 226 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AB2, first strand: chain 'C' and resid 177 through 181 removed outlier: 11.683A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.103A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.713A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.852A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.599A pdb=" N ILE C 492 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU C 479 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU C 490 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.063A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.792A pdb=" N GLU D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.563A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 88 through 91 982 hydrogen bonds defined for protein. 2862 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: 9.41 Time building geometry restraints manager: 7.81 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: 6617 1.34 - 1.46: 4989 1.46 - 1.58: 11190 1.58 - 1.71: 56 1.71 - 1.83: 172 Bond restraints: 23024 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C39 PCW G 103 " pdb=" C40 PCW G 103 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C39 PCW E 103 " pdb=" C40 PCW E 103 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C19 PCW C1114 " pdb=" C20 PCW C1114 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28593 2.46 - 4.93: 1944 4.93 - 7.39: 383 7.39 - 9.85: 116 9.85 - 12.32: 22 Bond angle restraints: 31058 Sorted by residual: angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 113.12 104.67 8.45 1.25e+00 6.40e-01 4.57e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 113.12 104.67 8.45 1.25e+00 6.40e-01 4.57e+01 angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 98.29 10.38 1.55e+00 4.16e-01 4.49e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 98.33 10.34 1.55e+00 4.16e-01 4.45e+01 angle pdb=" N LEU B 202 " pdb=" CA LEU B 202 " pdb=" C LEU B 202 " ideal model delta sigma weight residual 112.38 118.76 -6.38 1.22e+00 6.72e-01 2.74e+01 ... (remaining 31053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 14047 35.88 - 71.76: 761 71.76 - 107.64: 86 107.64 - 143.52: 40 143.52 - 179.41: 2 Dihedral angle restraints: 14936 sinusoidal: 7280 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW G 102 " pdb=" C31 PCW G 102 " pdb=" C32 PCW G 102 " pdb=" O2 PCW G 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.24 -179.41 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW E 102 " pdb=" C31 PCW E 102 " pdb=" C32 PCW E 102 " pdb=" O2 PCW E 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.23 -179.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW C1112 " pdb=" C31 PCW C1112 " pdb=" C32 PCW C1112 " pdb=" O2 PCW C1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.80 -138.37 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 14933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2807 0.075 - 0.150: 592 0.150 - 0.224: 65 0.224 - 0.299: 31 0.299 - 0.374: 17 Chirality restraints: 3512 Sorted by residual: chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.30e+01 chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.93e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.05e+01 ... (remaining 3509 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO C 125 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO A 125 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 569 " 0.059 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO C 570 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 570 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 570 " 0.049 5.00e-02 4.00e+02 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 104 2.47 - 3.08: 15040 3.08 - 3.68: 30720 3.68 - 4.29: 48098 4.29 - 4.90: 78369 Nonbonded interactions: 172331 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.861 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.861 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1204 " model vdw 1.990 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1204 " model vdw 1.995 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 1.998 2.170 ... (remaining 172326 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.800 Check model and map are aligned: 0.180 Set scattering table: 0.190 Process input model: 65.290 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.011 0.307 23068 Z= 0.561 Angle : 1.472 17.386 31184 Z= 0.749 Chirality : 0.067 0.374 3512 Planarity : 0.009 0.096 3804 Dihedral : 20.107 179.406 10006 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 10.30 % Allowed : 9.24 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.14), residues: 2636 helix: -1.87 (0.13), residues: 1194 sheet: -2.32 (0.29), residues: 260 loop : -2.69 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 33 HIS 0.012 0.002 HIS C 493 PHE 0.030 0.002 PHE B 297 TYR 0.039 0.002 TYR D 40 ARG 0.013 0.001 ARG A 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01813 ( 8) link_NAG-ASN : angle 4.01258 ( 24) link_ALPHA1-6 : bond 0.00735 ( 4) link_ALPHA1-6 : angle 1.31400 ( 12) link_BETA1-2 : bond 0.00900 ( 2) link_BETA1-2 : angle 5.43796 ( 6) link_BETA1-4 : bond 0.00989 ( 14) link_BETA1-4 : angle 6.25410 ( 42) link_ALPHA1-3 : bond 0.00834 ( 6) link_ALPHA1-3 : angle 3.18198 ( 18) hydrogen bonds : bond 0.16845 ( 982) hydrogen bonds : angle 7.44814 ( 2862) link_BETA1-6 : bond 0.00348 ( 4) link_BETA1-6 : angle 1.33886 ( 12) SS BOND : bond 0.00390 ( 6) SS BOND : angle 2.19286 ( 12) covalent geometry : bond 0.01117 (23024) covalent geometry : angle 1.44791 (31058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 312 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.5855 (tp) REVERT: A 127 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.5915 (p0) REVERT: A 158 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7646 (tmm) REVERT: A 231 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8039 (t80) REVERT: A 460 ILE cc_start: 0.8630 (mm) cc_final: 0.8306 (mt) REVERT: A 493 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: A 708 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: A 933 ASP cc_start: 0.8789 (t70) cc_final: 0.8466 (t0) REVERT: A 1002 ASP cc_start: 0.8151 (t0) cc_final: 0.7932 (t0) REVERT: A 1011 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7436 (tpt90) REVERT: A 1016 TRP cc_start: 0.8497 (t60) cc_final: 0.8236 (t60) REVERT: B 20 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7380 (m) REVERT: B 137 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7469 (mtt180) REVERT: B 266 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7927 (p) REVERT: G 13 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 52 HIS cc_start: 0.7591 (m170) cc_final: 0.7215 (m90) REVERT: C 63 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5935 (tp) REVERT: C 64 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6679 (t) REVERT: C 127 ASN cc_start: 0.6446 (OUTLIER) cc_final: 0.5983 (p0) REVERT: C 158 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7652 (tmm) REVERT: C 231 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8167 (t80) REVERT: C 267 MET cc_start: 0.8448 (ppp) cc_final: 0.8074 (ppp) REVERT: C 460 ILE cc_start: 0.8686 (mm) cc_final: 0.8342 (tp) REVERT: C 708 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 837 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7337 (ptt-90) REVERT: C 852 MET cc_start: 0.6667 (mmm) cc_final: 0.6368 (mmm) REVERT: C 933 ASP cc_start: 0.8887 (t70) cc_final: 0.8579 (t0) REVERT: D 20 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7833 (m) REVERT: D 266 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7498 (p) REVERT: E 13 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8203 (p) outliers start: 233 outliers final: 34 residues processed: 502 average time/residue: 0.4732 time to fit residues: 341.5152 Evaluate side-chains 197 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 239 optimal weight: 0.0870 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 167 GLN A 360 ASN A 474 ASN A 486 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A1019 GLN B 56 GLN B 107 HIS B 146 GLN B 203 GLN B 258 GLN B 284 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 167 GLN C 360 ASN C 474 ASN C 486 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN C1019 GLN D 56 GLN D 107 HIS D 203 GLN D 258 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.093938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069434 restraints weight = 66309.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071680 restraints weight = 37699.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072452 restraints weight = 25540.979| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23068 Z= 0.177 Angle : 0.737 11.912 31184 Z= 0.359 Chirality : 0.047 0.422 3512 Planarity : 0.006 0.057 3804 Dihedral : 17.519 175.199 5151 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.58 % Allowed : 11.94 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 2636 helix: -0.00 (0.15), residues: 1184 sheet: -1.93 (0.27), residues: 276 loop : -1.97 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 156 HIS 0.008 0.002 HIS C 493 PHE 0.022 0.002 PHE C 793 TYR 0.020 0.001 TYR C 569 ARG 0.006 0.001 ARG C 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 8) link_NAG-ASN : angle 2.58494 ( 24) link_ALPHA1-6 : bond 0.00727 ( 4) link_ALPHA1-6 : angle 1.92189 ( 12) link_BETA1-2 : bond 0.00556 ( 2) link_BETA1-2 : angle 5.14010 ( 6) link_BETA1-4 : bond 0.01092 ( 14) link_BETA1-4 : angle 4.07813 ( 42) link_ALPHA1-3 : bond 0.00864 ( 6) link_ALPHA1-3 : angle 3.73365 ( 18) hydrogen bonds : bond 0.06158 ( 982) hydrogen bonds : angle 5.33855 ( 2862) link_BETA1-6 : bond 0.00341 ( 4) link_BETA1-6 : angle 1.66736 ( 12) SS BOND : bond 0.00215 ( 6) SS BOND : angle 1.00020 ( 12) covalent geometry : bond 0.00403 (23024) covalent geometry : angle 0.70820 (31058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 141 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.8155 (m-70) cc_final: 0.7763 (m-70) REVERT: A 127 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.5784 (p0) REVERT: A 158 MET cc_start: 0.8379 (mmp) cc_final: 0.7745 (tmm) REVERT: A 231 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 351 MET cc_start: 0.8264 (mmm) cc_final: 0.7885 (mtt) REVERT: A 424 ILE cc_start: 0.7866 (mt) cc_final: 0.7643 (mt) REVERT: A 967 PHE cc_start: 0.7796 (t80) cc_final: 0.7392 (t80) REVERT: B 20 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7822 (m) REVERT: B 85 ILE cc_start: 0.7504 (mt) cc_final: 0.6117 (mm) REVERT: G 13 THR cc_start: 0.8458 (m) cc_final: 0.8032 (p) REVERT: C 127 ASN cc_start: 0.6292 (OUTLIER) cc_final: 0.5801 (p0) REVERT: C 158 MET cc_start: 0.8333 (mmp) cc_final: 0.7737 (tmm) REVERT: C 231 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8180 (t80) REVERT: C 351 MET cc_start: 0.8171 (mmm) cc_final: 0.7949 (mtt) REVERT: C 507 MET cc_start: 0.8218 (ttp) cc_final: 0.7747 (tmm) REVERT: C 837 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7218 (ptt-90) REVERT: C 967 PHE cc_start: 0.7858 (t80) cc_final: 0.7485 (t80) REVERT: D 20 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8015 (m) REVERT: D 85 ILE cc_start: 0.7467 (mt) cc_final: 0.6229 (mm) REVERT: E 13 THR cc_start: 0.8523 (m) cc_final: 0.8167 (p) outliers start: 81 outliers final: 35 residues processed: 212 average time/residue: 0.3613 time to fit residues: 121.4192 Evaluate side-chains 150 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS A 744 GLN ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS C 744 GLN ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.089669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066945 restraints weight = 66446.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066992 restraints weight = 49450.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067534 restraints weight = 40909.496| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23068 Z= 0.207 Angle : 0.715 11.941 31184 Z= 0.342 Chirality : 0.047 0.425 3512 Planarity : 0.005 0.058 3804 Dihedral : 15.940 163.958 5092 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.09 % Allowed : 13.22 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2636 helix: 0.46 (0.15), residues: 1200 sheet: -1.44 (0.28), residues: 266 loop : -1.36 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 156 HIS 0.011 0.002 HIS C 52 PHE 0.021 0.002 PHE C 793 TYR 0.022 0.002 TYR A 569 ARG 0.007 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 8) link_NAG-ASN : angle 2.08358 ( 24) link_ALPHA1-6 : bond 0.00895 ( 4) link_ALPHA1-6 : angle 2.10677 ( 12) link_BETA1-2 : bond 0.00428 ( 2) link_BETA1-2 : angle 4.69951 ( 6) link_BETA1-4 : bond 0.00855 ( 14) link_BETA1-4 : angle 3.49611 ( 42) link_ALPHA1-3 : bond 0.01133 ( 6) link_ALPHA1-3 : angle 3.39680 ( 18) hydrogen bonds : bond 0.05775 ( 982) hydrogen bonds : angle 4.79220 ( 2862) link_BETA1-6 : bond 0.00402 ( 4) link_BETA1-6 : angle 1.68267 ( 12) SS BOND : bond 0.00140 ( 6) SS BOND : angle 1.57117 ( 12) covalent geometry : bond 0.00488 (23024) covalent geometry : angle 0.69174 (31058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 117 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8262 (mmp) cc_final: 0.7721 (tmm) REVERT: A 404 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: A 413 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6328 (ptpp) REVERT: B 20 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (m) REVERT: G 10 GLU cc_start: 0.8162 (pm20) cc_final: 0.7923 (pm20) REVERT: C 127 ASN cc_start: 0.6782 (OUTLIER) cc_final: 0.5957 (p0) REVERT: C 158 MET cc_start: 0.8286 (mmp) cc_final: 0.7806 (tmm) REVERT: C 404 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: C 413 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6276 (ptpp) REVERT: C 417 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7488 (p) REVERT: D 20 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8199 (m) REVERT: E 10 GLU cc_start: 0.8144 (pm20) cc_final: 0.7847 (pm20) outliers start: 70 outliers final: 42 residues processed: 180 average time/residue: 0.4210 time to fit residues: 125.8714 Evaluate side-chains 149 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 247 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.089408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066356 restraints weight = 67430.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066095 restraints weight = 51779.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066813 restraints weight = 38379.335| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23068 Z= 0.170 Angle : 0.641 10.529 31184 Z= 0.305 Chirality : 0.046 0.435 3512 Planarity : 0.004 0.037 3804 Dihedral : 15.135 161.159 5070 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.01 % Allowed : 13.44 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2636 helix: 0.80 (0.15), residues: 1214 sheet: -1.09 (0.29), residues: 246 loop : -1.19 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 894 HIS 0.011 0.001 HIS A 557 PHE 0.024 0.001 PHE A 793 TYR 0.023 0.001 TYR A 684 ARG 0.005 0.000 ARG A 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 8) link_NAG-ASN : angle 1.99427 ( 24) link_ALPHA1-6 : bond 0.00888 ( 4) link_ALPHA1-6 : angle 2.17816 ( 12) link_BETA1-2 : bond 0.00346 ( 2) link_BETA1-2 : angle 4.63450 ( 6) link_BETA1-4 : bond 0.00654 ( 14) link_BETA1-4 : angle 3.38484 ( 42) link_ALPHA1-3 : bond 0.01108 ( 6) link_ALPHA1-3 : angle 3.62929 ( 18) hydrogen bonds : bond 0.05142 ( 982) hydrogen bonds : angle 4.54299 ( 2862) link_BETA1-6 : bond 0.00155 ( 4) link_BETA1-6 : angle 1.70954 ( 12) SS BOND : bond 0.00114 ( 6) SS BOND : angle 1.06440 ( 12) covalent geometry : bond 0.00398 (23024) covalent geometry : angle 0.61547 (31058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 110 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8218 (mmp) cc_final: 0.7768 (tmm) REVERT: A 404 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 413 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6346 (ptpp) REVERT: A 816 MET cc_start: 0.8344 (mmp) cc_final: 0.7782 (mmp) REVERT: G 10 GLU cc_start: 0.8196 (pm20) cc_final: 0.7898 (pm20) REVERT: G 13 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8550 (p) REVERT: C 158 MET cc_start: 0.8301 (mmp) cc_final: 0.7906 (tmm) REVERT: C 404 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: E 10 GLU cc_start: 0.8183 (pm20) cc_final: 0.7826 (pm20) REVERT: E 13 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (p) outliers start: 68 outliers final: 49 residues processed: 171 average time/residue: 0.3058 time to fit residues: 86.9589 Evaluate side-chains 148 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 2 optimal weight: 0.0370 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 9 optimal weight: 0.0040 chunk 32 optimal weight: 7.9990 chunk 236 optimal weight: 0.0770 chunk 211 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 overall best weight: 2.0232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A1019 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN D 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.089860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066761 restraints weight = 67136.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067022 restraints weight = 52082.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067423 restraints weight = 42500.016| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23068 Z= 0.127 Angle : 0.584 10.367 31184 Z= 0.276 Chirality : 0.044 0.462 3512 Planarity : 0.004 0.038 3804 Dihedral : 14.251 156.725 5060 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.18 % Allowed : 14.28 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.16), residues: 2636 helix: 1.12 (0.15), residues: 1228 sheet: -0.71 (0.29), residues: 266 loop : -1.03 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP C 894 HIS 0.019 0.001 HIS C 52 PHE 0.021 0.001 PHE C 793 TYR 0.027 0.001 TYR C 684 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 8) link_NAG-ASN : angle 1.72087 ( 24) link_ALPHA1-6 : bond 0.00864 ( 4) link_ALPHA1-6 : angle 1.96879 ( 12) link_BETA1-2 : bond 0.00417 ( 2) link_BETA1-2 : angle 4.57399 ( 6) link_BETA1-4 : bond 0.00664 ( 14) link_BETA1-4 : angle 3.15409 ( 42) link_ALPHA1-3 : bond 0.01137 ( 6) link_ALPHA1-3 : angle 3.63879 ( 18) hydrogen bonds : bond 0.04465 ( 982) hydrogen bonds : angle 4.32026 ( 2862) link_BETA1-6 : bond 0.00169 ( 4) link_BETA1-6 : angle 1.64706 ( 12) SS BOND : bond 0.00093 ( 6) SS BOND : angle 0.69853 ( 12) covalent geometry : bond 0.00292 (23024) covalent geometry : angle 0.55874 (31058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 110 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7851 (tmm) REVERT: A 267 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8178 (tmm) REVERT: A 404 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: B 266 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.7868 (p) REVERT: G 10 GLU cc_start: 0.8166 (pm20) cc_final: 0.7837 (pm20) REVERT: G 13 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8535 (p) REVERT: C 52 HIS cc_start: 0.8056 (m-70) cc_final: 0.7622 (m-70) REVERT: C 158 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7951 (tmm) REVERT: C 267 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8133 (tmm) REVERT: C 404 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: C 413 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6330 (ptpp) REVERT: E 10 GLU cc_start: 0.8146 (pm20) cc_final: 0.7803 (pm20) REVERT: E 13 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8590 (p) outliers start: 72 outliers final: 42 residues processed: 171 average time/residue: 0.3391 time to fit residues: 94.8927 Evaluate side-chains 151 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 72 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.088718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066075 restraints weight = 67107.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065913 restraints weight = 52227.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066565 restraints weight = 39057.963| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23068 Z= 0.144 Angle : 0.600 12.079 31184 Z= 0.281 Chirality : 0.045 0.476 3512 Planarity : 0.004 0.039 3804 Dihedral : 13.705 161.662 5056 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.27 % Allowed : 14.90 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2636 helix: 1.16 (0.15), residues: 1230 sheet: -0.45 (0.32), residues: 246 loop : -0.91 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP A 894 HIS 0.022 0.001 HIS C 52 PHE 0.023 0.001 PHE A 793 TYR 0.022 0.001 TYR A 684 ARG 0.005 0.000 ARG C 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 8) link_NAG-ASN : angle 1.64944 ( 24) link_ALPHA1-6 : bond 0.00906 ( 4) link_ALPHA1-6 : angle 1.93884 ( 12) link_BETA1-2 : bond 0.00450 ( 2) link_BETA1-2 : angle 4.59155 ( 6) link_BETA1-4 : bond 0.00650 ( 14) link_BETA1-4 : angle 3.06061 ( 42) link_ALPHA1-3 : bond 0.01108 ( 6) link_ALPHA1-3 : angle 3.70125 ( 18) hydrogen bonds : bond 0.04618 ( 982) hydrogen bonds : angle 4.30417 ( 2862) link_BETA1-6 : bond 0.00117 ( 4) link_BETA1-6 : angle 1.66615 ( 12) SS BOND : bond 0.00091 ( 6) SS BOND : angle 0.76841 ( 12) covalent geometry : bond 0.00337 (23024) covalent geometry : angle 0.57651 (31058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 104 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7879 (tmm) REVERT: A 164 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5688 (ptp) REVERT: A 267 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8138 (tmm) REVERT: A 404 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: A 413 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6359 (ptpp) REVERT: B 266 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.7964 (p) REVERT: G 10 GLU cc_start: 0.8205 (pm20) cc_final: 0.7846 (pm20) REVERT: G 13 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8635 (p) REVERT: C 158 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: C 267 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8129 (tmm) REVERT: C 404 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7200 (tt0) REVERT: C 413 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6304 (ptpp) REVERT: D 266 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7834 (p) REVERT: E 13 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8626 (p) outliers start: 74 outliers final: 45 residues processed: 167 average time/residue: 0.3125 time to fit residues: 86.0054 Evaluate side-chains 155 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 234 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 214 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065690 restraints weight = 67575.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064462 restraints weight = 55137.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064841 restraints weight = 50326.722| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23068 Z= 0.175 Angle : 0.628 12.397 31184 Z= 0.296 Chirality : 0.045 0.490 3512 Planarity : 0.004 0.038 3804 Dihedral : 13.470 165.783 5056 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.45 % Allowed : 14.94 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2636 helix: 1.13 (0.15), residues: 1232 sheet: -0.39 (0.32), residues: 246 loop : -0.83 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.003 TRP A 894 HIS 0.013 0.001 HIS C 52 PHE 0.022 0.002 PHE C 793 TYR 0.019 0.001 TYR A 684 ARG 0.005 0.000 ARG A 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 8) link_NAG-ASN : angle 1.60311 ( 24) link_ALPHA1-6 : bond 0.00899 ( 4) link_ALPHA1-6 : angle 1.97950 ( 12) link_BETA1-2 : bond 0.00434 ( 2) link_BETA1-2 : angle 4.67818 ( 6) link_BETA1-4 : bond 0.00607 ( 14) link_BETA1-4 : angle 2.91381 ( 42) link_ALPHA1-3 : bond 0.00952 ( 6) link_ALPHA1-3 : angle 3.66864 ( 18) hydrogen bonds : bond 0.04934 ( 982) hydrogen bonds : angle 4.36664 ( 2862) link_BETA1-6 : bond 0.00227 ( 4) link_BETA1-6 : angle 1.72681 ( 12) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.84890 ( 12) covalent geometry : bond 0.00417 (23024) covalent geometry : angle 0.60649 (31058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 103 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (tmm) REVERT: A 404 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: A 413 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6454 (ptpp) REVERT: A 473 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6631 (mtm180) REVERT: A 488 TYR cc_start: 0.7717 (p90) cc_final: 0.7174 (p90) REVERT: B 55 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8868 (tp) REVERT: B 266 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8014 (p) REVERT: G 10 GLU cc_start: 0.8216 (pm20) cc_final: 0.7859 (pm20) REVERT: G 13 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8744 (p) REVERT: C 158 MET cc_start: 0.8158 (mmp) cc_final: 0.7873 (tmm) REVERT: C 267 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8145 (tmm) REVERT: C 404 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: C 413 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6468 (ptpp) REVERT: D 55 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8897 (tp) REVERT: E 13 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8765 (p) outliers start: 78 outliers final: 55 residues processed: 172 average time/residue: 0.3173 time to fit residues: 89.7221 Evaluate side-chains 161 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 95 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 35 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.087286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064954 restraints weight = 67476.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065339 restraints weight = 54142.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065724 restraints weight = 41591.783| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23068 Z= 0.180 Angle : 0.636 13.340 31184 Z= 0.299 Chirality : 0.045 0.492 3512 Planarity : 0.004 0.039 3804 Dihedral : 13.258 167.902 5056 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.14 % Allowed : 15.34 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2636 helix: 1.12 (0.15), residues: 1232 sheet: -0.40 (0.32), residues: 246 loop : -0.82 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP A 894 HIS 0.005 0.001 HIS C 557 PHE 0.023 0.001 PHE A 793 TYR 0.018 0.001 TYR A 684 ARG 0.005 0.000 ARG D 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 8) link_NAG-ASN : angle 1.56595 ( 24) link_ALPHA1-6 : bond 0.00905 ( 4) link_ALPHA1-6 : angle 2.06483 ( 12) link_BETA1-2 : bond 0.00420 ( 2) link_BETA1-2 : angle 4.70375 ( 6) link_BETA1-4 : bond 0.00592 ( 14) link_BETA1-4 : angle 2.86048 ( 42) link_ALPHA1-3 : bond 0.00920 ( 6) link_ALPHA1-3 : angle 3.66791 ( 18) hydrogen bonds : bond 0.04904 ( 982) hydrogen bonds : angle 4.40218 ( 2862) link_BETA1-6 : bond 0.00145 ( 4) link_BETA1-6 : angle 1.74669 ( 12) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.89567 ( 12) covalent geometry : bond 0.00429 (23024) covalent geometry : angle 0.61521 (31058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 100 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8075 (tmm) REVERT: A 404 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: A 413 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6402 (ptpp) REVERT: A 473 ARG cc_start: 0.6705 (mtt180) cc_final: 0.6289 (mtm180) REVERT: A 488 TYR cc_start: 0.7627 (p90) cc_final: 0.7329 (p90) REVERT: A 507 MET cc_start: 0.7195 (tpp) cc_final: 0.6844 (tpp) REVERT: B 55 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8901 (tp) REVERT: B 266 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7907 (p) REVERT: G 10 GLU cc_start: 0.8199 (pm20) cc_final: 0.7850 (pm20) REVERT: G 13 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8788 (p) REVERT: C 267 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7980 (tmm) REVERT: C 404 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: C 413 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6384 (ptpp) REVERT: D 266 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7824 (p) REVERT: E 13 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8771 (p) outliers start: 71 outliers final: 53 residues processed: 165 average time/residue: 0.3064 time to fit residues: 83.4104 Evaluate side-chains 159 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 95 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 165 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 210 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.088720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066540 restraints weight = 67252.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066826 restraints weight = 50171.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067312 restraints weight = 39514.518| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23068 Z= 0.122 Angle : 0.592 13.851 31184 Z= 0.274 Chirality : 0.044 0.492 3512 Planarity : 0.003 0.038 3804 Dihedral : 12.733 167.902 5056 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.43 % Allowed : 15.83 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2636 helix: 1.33 (0.15), residues: 1232 sheet: -0.29 (0.32), residues: 246 loop : -0.72 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 894 HIS 0.005 0.001 HIS C 557 PHE 0.021 0.001 PHE C 793 TYR 0.018 0.001 TYR A 684 ARG 0.006 0.000 ARG D 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 8) link_NAG-ASN : angle 1.43163 ( 24) link_ALPHA1-6 : bond 0.00898 ( 4) link_ALPHA1-6 : angle 2.02734 ( 12) link_BETA1-2 : bond 0.00434 ( 2) link_BETA1-2 : angle 4.67541 ( 6) link_BETA1-4 : bond 0.00620 ( 14) link_BETA1-4 : angle 2.68115 ( 42) link_ALPHA1-3 : bond 0.00850 ( 6) link_ALPHA1-3 : angle 3.65890 ( 18) hydrogen bonds : bond 0.04284 ( 982) hydrogen bonds : angle 4.24155 ( 2862) link_BETA1-6 : bond 0.00099 ( 4) link_BETA1-6 : angle 1.63209 ( 12) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.60379 ( 12) covalent geometry : bond 0.00280 (23024) covalent geometry : angle 0.57134 (31058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7986 (tmm) REVERT: A 404 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: A 413 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6393 (ptpp) REVERT: A 473 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6525 (mtm180) REVERT: A 488 TYR cc_start: 0.7732 (p90) cc_final: 0.7269 (p90) REVERT: A 578 PHE cc_start: 0.7035 (m-80) cc_final: 0.6787 (m-80) REVERT: B 266 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7821 (p) REVERT: G 10 GLU cc_start: 0.8144 (pm20) cc_final: 0.7738 (pm20) REVERT: G 13 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8728 (p) REVERT: C 267 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7963 (tmm) REVERT: C 404 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: C 413 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6380 (ptpp) REVERT: D 266 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7776 (p) REVERT: E 13 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8716 (p) outliers start: 55 outliers final: 43 residues processed: 153 average time/residue: 0.3096 time to fit residues: 78.0310 Evaluate side-chains 155 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 247 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN C 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.086931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.065023 restraints weight = 67403.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063872 restraints weight = 56298.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064418 restraints weight = 43173.047| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23068 Z= 0.183 Angle : 0.647 13.447 31184 Z= 0.302 Chirality : 0.045 0.489 3512 Planarity : 0.004 0.039 3804 Dihedral : 12.637 169.274 5056 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.43 % Allowed : 15.69 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2636 helix: 1.18 (0.15), residues: 1236 sheet: -0.35 (0.32), residues: 246 loop : -0.74 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 894 HIS 0.008 0.001 HIS C 493 PHE 0.024 0.001 PHE C 793 TYR 0.016 0.001 TYR A 684 ARG 0.005 0.000 ARG D 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 8) link_NAG-ASN : angle 1.56615 ( 24) link_ALPHA1-6 : bond 0.00891 ( 4) link_ALPHA1-6 : angle 2.09174 ( 12) link_BETA1-2 : bond 0.00417 ( 2) link_BETA1-2 : angle 4.73746 ( 6) link_BETA1-4 : bond 0.00568 ( 14) link_BETA1-4 : angle 2.75005 ( 42) link_ALPHA1-3 : bond 0.00861 ( 6) link_ALPHA1-3 : angle 3.60487 ( 18) hydrogen bonds : bond 0.04904 ( 982) hydrogen bonds : angle 4.34752 ( 2862) link_BETA1-6 : bond 0.00152 ( 4) link_BETA1-6 : angle 1.78031 ( 12) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.83142 ( 12) covalent geometry : bond 0.00436 (23024) covalent geometry : angle 0.62708 (31058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8089 (tmm) REVERT: A 404 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: A 413 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6479 (ptpp) REVERT: A 578 PHE cc_start: 0.7242 (m-80) cc_final: 0.6898 (m-80) REVERT: B 266 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7896 (p) REVERT: G 10 GLU cc_start: 0.8217 (pm20) cc_final: 0.7830 (pm20) REVERT: G 13 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8769 (p) REVERT: G 39 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8551 (mp) REVERT: C 267 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8101 (tmm) REVERT: C 404 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: C 413 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6415 (ptpp) REVERT: C 470 MET cc_start: 0.7736 (tmm) cc_final: 0.7331 (tmm) REVERT: D 266 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.7872 (p) REVERT: E 13 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8755 (p) outliers start: 55 outliers final: 43 residues processed: 147 average time/residue: 0.3504 time to fit residues: 85.9952 Evaluate side-chains 149 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 179 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 157 optimal weight: 0.0980 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.087854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066328 restraints weight = 66955.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065247 restraints weight = 56488.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065913 restraints weight = 43765.458| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23068 Z= 0.141 Angle : 0.607 13.690 31184 Z= 0.282 Chirality : 0.044 0.486 3512 Planarity : 0.003 0.038 3804 Dihedral : 12.216 167.835 5056 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.65 % Allowed : 15.43 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.44 (0.16), residues: 2636 helix: 1.28 (0.15), residues: 1246 sheet: 0.27 (0.33), residues: 246 loop : -0.78 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 894 HIS 0.006 0.001 HIS C 557 PHE 0.021 0.001 PHE C 793 TYR 0.015 0.001 TYR A 684 ARG 0.006 0.000 ARG D 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 8) link_NAG-ASN : angle 1.42377 ( 24) link_ALPHA1-6 : bond 0.00870 ( 4) link_ALPHA1-6 : angle 2.03610 ( 12) link_BETA1-2 : bond 0.00414 ( 2) link_BETA1-2 : angle 4.71612 ( 6) link_BETA1-4 : bond 0.00597 ( 14) link_BETA1-4 : angle 2.59147 ( 42) link_ALPHA1-3 : bond 0.00862 ( 6) link_ALPHA1-3 : angle 3.60126 ( 18) hydrogen bonds : bond 0.04434 ( 982) hydrogen bonds : angle 4.21285 ( 2862) link_BETA1-6 : bond 0.00116 ( 4) link_BETA1-6 : angle 1.67020 ( 12) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.66474 ( 12) covalent geometry : bond 0.00332 (23024) covalent geometry : angle 0.58698 (31058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6270.92 seconds wall clock time: 112 minutes 11.01 seconds (6731.01 seconds total)