Starting phenix.real_space_refine on Sun Sep 29 18:21:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/09_2024/7wyw_32896.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/09_2024/7wyw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/09_2024/7wyw_32896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/09_2024/7wyw_32896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/09_2024/7wyw_32896.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyw_32896/09_2024/7wyw_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 22.93, per 1000 atoms: 1.01 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=3, 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 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: 5.83 Conformation dependent library (CDL) restraints added in 2.4 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: 2.92 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: 8.52 Time building geometry restraints manager: 6.68 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: 14040 35.88 - 71.76: 759 71.76 - 107.64: 86 107.64 - 143.52: 40 143.52 - 179.41: 2 Dihedral angle restraints: 14927 sinusoidal: 7271 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 14924 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: 107 2.47 - 3.08: 15044 3.08 - 3.68: 30722 3.68 - 4.29: 48098 4.29 - 4.90: 78369 Nonbonded interactions: 172340 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 172335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and resid 1 through 4) selection = (chain 'H' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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: 0.910 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: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 58.680 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.280 ------------------------------------------------------------------------------- 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 23024 Z= 0.640 Angle : 1.448 12.318 31058 Z= 0.744 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 *********************** 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 fitting. rotamer outliers: 233 poor density : 312 time to evaluate : 2.391 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: 0.4207 time to fit residues: 302.7215 Evaluate side-chains 197 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 142 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 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 243 GLN D 258 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23024 Z= 0.262 Angle : 0.703 9.386 31058 Z= 0.350 Chirality : 0.047 0.420 3512 Planarity : 0.006 0.049 3804 Dihedral : 17.397 174.719 5151 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.54 % Allowed : 11.89 % Favored : 84.57 % 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: -1.60 (0.15), residues: 2636 helix: 0.00 (0.15), residues: 1182 sheet: -1.83 (0.28), residues: 276 loop : -1.97 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 156 HIS 0.007 0.002 HIS C 493 PHE 0.021 0.002 PHE C 793 TYR 0.022 0.001 TYR C 569 ARG 0.006 0.001 ARG C 281 *********************** 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 fitting. rotamer outliers: 80 poor density : 142 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.7685 (m-70) cc_final: 0.7382 (m-70) REVERT: A 127 ASN cc_start: 0.6439 (OUTLIER) cc_final: 0.5879 (p0) REVERT: A 158 MET cc_start: 0.8276 (mmp) cc_final: 0.7794 (tmm) REVERT: A 231 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8173 (t80) REVERT: A 351 MET cc_start: 0.8139 (mmm) cc_final: 0.7786 (mtt) REVERT: A 424 ILE cc_start: 0.7887 (mt) cc_final: 0.7670 (mt) REVERT: A 967 PHE cc_start: 0.7779 (t80) cc_final: 0.7399 (t80) REVERT: B 20 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7789 (m) REVERT: B 85 ILE cc_start: 0.7582 (mt) cc_final: 0.6321 (mm) REVERT: G 13 THR cc_start: 0.8517 (m) cc_final: 0.8114 (p) REVERT: C 127 ASN cc_start: 0.6311 (OUTLIER) cc_final: 0.5841 (p0) REVERT: C 158 MET cc_start: 0.8274 (mmp) cc_final: 0.7855 (tmm) REVERT: C 351 MET cc_start: 0.8056 (mmm) cc_final: 0.7846 (mtt) REVERT: C 967 PHE cc_start: 0.7772 (t80) cc_final: 0.7423 (t80) REVERT: D 20 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7953 (m) REVERT: D 85 ILE cc_start: 0.7498 (mt) cc_final: 0.6186 (mm) REVERT: E 13 THR cc_start: 0.8567 (m) cc_final: 0.8237 (p) outliers start: 80 outliers final: 36 residues processed: 209 average time/residue: 0.3352 time to fit residues: 111.2266 Evaluate side-chains 153 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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 935 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 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 267 MET 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 583 LEU 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 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 66 optimal weight: 0.0010 chunk 240 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- 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 744 GLN ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23024 Z= 0.260 Angle : 0.634 11.523 31058 Z= 0.309 Chirality : 0.045 0.406 3512 Planarity : 0.004 0.040 3804 Dihedral : 15.759 167.108 5083 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.61 % Allowed : 13.26 % Favored : 84.13 % 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: -0.74 (0.16), residues: 2636 helix: 0.64 (0.15), residues: 1198 sheet: -1.51 (0.27), residues: 286 loop : -1.40 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 894 HIS 0.014 0.002 HIS C 683 PHE 0.020 0.002 PHE C 793 TYR 0.018 0.002 TYR A 569 ARG 0.007 0.001 ARG A1011 *********************** 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 176 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 117 time to evaluate : 2.549 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: 0.8215 (mmp) cc_final: 0.7774 (tmm) REVERT: A 231 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (t80) REVERT: A 404 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: A 413 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6197 (ptpp) REVERT: B 20 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8030 (m) REVERT: G 10 GLU cc_start: 0.8079 (pm20) cc_final: 0.7821 (pm20) REVERT: G 13 THR cc_start: 0.8648 (m) cc_final: 0.8304 (p) REVERT: C 52 HIS cc_start: 0.8086 (m90) cc_final: 0.7840 (m90) REVERT: C 158 MET cc_start: 0.8202 (mmp) cc_final: 0.7862 (tmm) REVERT: C 404 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: D 20 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8164 (m) REVERT: E 10 GLU cc_start: 0.8106 (pm20) cc_final: 0.7868 (pm20) outliers start: 59 outliers final: 37 residues processed: 169 average time/residue: 0.3224 time to fit residues: 89.4736 Evaluate side-chains 148 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 105 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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 231 PHE 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 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 303 VAL Chi-restraints excluded: chain G residue 33 ILE 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 427 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU 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 73 VAL Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 167 THR 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 237 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 114 optimal weight: 0.0070 chunk 161 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23024 Z= 0.319 Angle : 0.665 9.620 31058 Z= 0.324 Chirality : 0.047 0.429 3512 Planarity : 0.004 0.038 3804 Dihedral : 15.045 157.674 5071 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.45 % Allowed : 12.91 % Favored : 83.64 % 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: -0.48 (0.16), residues: 2636 helix: 0.74 (0.15), residues: 1204 sheet: -1.00 (0.30), residues: 246 loop : -1.26 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.003 TRP C 894 HIS 0.007 0.002 HIS A 557 PHE 0.024 0.002 PHE A 793 TYR 0.022 0.002 TYR A 569 ARG 0.009 0.001 ARG C 61 *********************** 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 192 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 114 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8424 (tp) REVERT: A 52 HIS cc_start: 0.7629 (m-70) cc_final: 0.7321 (m-70) REVERT: A 158 MET cc_start: 0.8243 (mmp) cc_final: 0.7852 (tmm) REVERT: A 404 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: A 413 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6236 (ptpp) REVERT: G 10 GLU cc_start: 0.8136 (pm20) cc_final: 0.7871 (pm20) REVERT: G 13 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8732 (p) REVERT: C 158 MET cc_start: 0.8247 (mmp) cc_final: 0.7907 (tmm) REVERT: C 404 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: C 413 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6252 (ptpp) REVERT: C 417 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7680 (p) REVERT: C 424 ILE cc_start: 0.7854 (mt) cc_final: 0.7624 (mt) REVERT: C 571 PHE cc_start: 0.5381 (OUTLIER) cc_final: 0.5171 (p90) REVERT: E 10 GLU cc_start: 0.8174 (pm20) cc_final: 0.7938 (pm20) REVERT: E 13 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8768 (p) outliers start: 78 outliers final: 51 residues processed: 184 average time/residue: 0.3185 time to fit residues: 95.3166 Evaluate side-chains 155 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 95 time to evaluate : 2.325 ------------------------------------------------------------------------------- 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 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN 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 B residue 47 LEU 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 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 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 417 THR 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 571 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 846 ASN 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 160 CYS 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 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 212 optimal weight: 0.2980 chunk 144 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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** A1019 GLN B 146 GLN C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23024 Z= 0.172 Angle : 0.560 11.287 31058 Z= 0.267 Chirality : 0.044 0.470 3512 Planarity : 0.004 0.039 3804 Dihedral : 14.235 154.375 5061 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.79 % Allowed : 14.68 % 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: 0.02 (0.16), residues: 2636 helix: 1.13 (0.15), residues: 1222 sheet: -0.63 (0.31), residues: 246 loop : -1.02 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 894 HIS 0.007 0.001 HIS A 557 PHE 0.020 0.001 PHE C 793 TYR 0.012 0.001 TYR A 684 ARG 0.004 0.000 ARG C 67 *********************** 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 177 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 114 time to evaluate : 2.642 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: 0.8154 (mmp) cc_final: 0.7872 (tmm) REVERT: A 267 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: A 351 MET cc_start: 0.8091 (mmm) cc_final: 0.7848 (mtt) REVERT: A 404 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: B 266 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7864 (p) REVERT: G 10 GLU cc_start: 0.8122 (pm20) cc_final: 0.7915 (pm20) REVERT: C 351 MET cc_start: 0.8085 (mmm) cc_final: 0.7875 (mtt) REVERT: C 404 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: C 413 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6241 (ptpp) REVERT: D 266 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7809 (p) REVERT: E 10 GLU cc_start: 0.8139 (pm20) cc_final: 0.7931 (pm20) outliers start: 63 outliers final: 37 residues processed: 168 average time/residue: 0.3049 time to fit residues: 85.0505 Evaluate side-chains 143 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU 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 583 LEU Chi-restraints excluded: chain A residue 846 ASN 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 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 33 ILE 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 164 MET 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 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 684 TYR Chi-restraints excluded: chain C residue 846 ASN 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 266 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23024 Z= 0.294 Angle : 0.624 11.545 31058 Z= 0.298 Chirality : 0.046 0.481 3512 Planarity : 0.004 0.040 3804 Dihedral : 13.939 159.440 5056 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.54 % Allowed : 14.94 % 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: -0.04 (0.16), residues: 2636 helix: 1.00 (0.15), residues: 1232 sheet: -0.63 (0.31), residues: 246 loop : -0.98 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 894 HIS 0.006 0.001 HIS A 557 PHE 0.025 0.002 PHE A 793 TYR 0.013 0.002 TYR A 994 ARG 0.004 0.000 ARG A1011 *********************** 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 179 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 99 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8123 (mmp) cc_final: 0.7881 (tmm) REVERT: A 164 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5633 (ptp) REVERT: A 404 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: A 413 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6365 (ptpp) REVERT: A 423 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8015 (ttm-80) REVERT: A 816 MET cc_start: 0.8381 (mmp) cc_final: 0.7751 (mmp) REVERT: B 55 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 266 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8042 (p) REVERT: G 10 GLU cc_start: 0.8130 (pm20) cc_final: 0.7852 (pm20) REVERT: G 13 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8784 (p) REVERT: C 267 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8251 (tmm) REVERT: C 404 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: C 413 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6382 (ptpp) REVERT: C 507 MET cc_start: 0.7443 (tmm) cc_final: 0.7068 (tmm) REVERT: D 55 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (tp) REVERT: D 266 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.7932 (p) REVERT: E 10 GLU cc_start: 0.8098 (pm20) cc_final: 0.7810 (pm20) REVERT: E 13 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8789 (p) outliers start: 80 outliers final: 55 residues processed: 170 average time/residue: 0.3171 time to fit residues: 88.3646 Evaluate side-chains 161 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 93 time to evaluate : 2.416 ------------------------------------------------------------------------------- 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 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 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 423 ARG 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 846 ASN 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 B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE 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 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 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 440 VAL 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 684 TYR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN 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 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 210 VAL Chi-restraints excluded: chain D residue 213 LEU 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 D residue 305 SER 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 246 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23024 Z= 0.188 Angle : 0.561 13.006 31058 Z= 0.265 Chirality : 0.044 0.494 3512 Planarity : 0.003 0.040 3804 Dihedral : 13.405 160.467 5056 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.27 % Allowed : 15.12 % 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: 0.22 (0.16), residues: 2636 helix: 1.22 (0.15), residues: 1230 sheet: -0.45 (0.31), residues: 246 loop : -0.87 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 894 HIS 0.007 0.001 HIS C 52 PHE 0.021 0.001 PHE C 793 TYR 0.009 0.001 TYR A 869 ARG 0.004 0.000 ARG A1006 *********************** 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 179 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 105 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8022 (tmm) REVERT: A 404 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: A 413 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6378 (ptpp) REVERT: A 423 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8081 (ttm-80) REVERT: A 473 ARG cc_start: 0.6866 (mtt180) cc_final: 0.6488 (mtm180) REVERT: B 266 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.7879 (p) REVERT: G 10 GLU cc_start: 0.8147 (pm20) cc_final: 0.7830 (pm20) REVERT: G 13 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8768 (p) REVERT: C 267 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8122 (tmm) REVERT: C 404 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: C 413 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6344 (ptpp) REVERT: C 423 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7928 (ttm-80) REVERT: D 266 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7813 (p) REVERT: E 10 GLU cc_start: 0.8116 (pm20) cc_final: 0.7844 (pm20) REVERT: E 13 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8770 (p) outliers start: 74 outliers final: 52 residues processed: 167 average time/residue: 0.3295 time to fit residues: 88.6679 Evaluate side-chains 163 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 99 time to evaluate : 2.420 ------------------------------------------------------------------------------- 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 417 THR Chi-restraints excluded: chain A residue 423 ARG 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 758 ILE Chi-restraints excluded: chain A residue 846 ASN 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 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 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 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 423 ARG Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 440 VAL 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 684 TYR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 125 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 23024 Z= 0.360 Angle : 0.663 12.696 31058 Z= 0.316 Chirality : 0.046 0.490 3512 Planarity : 0.004 0.040 3804 Dihedral : 13.472 162.874 5056 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.49 % Allowed : 15.21 % Favored : 81.30 % 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: -0.02 (0.16), residues: 2636 helix: 0.96 (0.15), residues: 1234 sheet: -0.67 (0.31), residues: 258 loop : -0.89 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 894 HIS 0.006 0.001 HIS A 557 PHE 0.025 0.002 PHE C 793 TYR 0.022 0.002 TYR A 684 ARG 0.004 0.001 ARG A 893 *********************** 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 177 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 98 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: A 413 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6424 (ptpp) REVERT: A 423 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7968 (ttm-80) REVERT: A 473 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6392 (mtm180) REVERT: B 266 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7976 (p) REVERT: G 10 GLU cc_start: 0.8176 (pm20) cc_final: 0.7875 (pm20) REVERT: G 13 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8849 (p) REVERT: C 267 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8264 (tmm) REVERT: C 404 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: C 413 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6333 (ptpp) REVERT: D 266 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7862 (p) REVERT: E 10 GLU cc_start: 0.8111 (pm20) cc_final: 0.7866 (pm20) REVERT: E 13 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8851 (p) outliers start: 79 outliers final: 59 residues processed: 170 average time/residue: 0.3364 time to fit residues: 92.8454 Evaluate side-chains 168 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 99 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 423 ARG 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 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 846 ASN 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 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 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 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 440 VAL 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 571 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN 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 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 D residue 305 SER 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 243 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** C 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23024 Z= 0.150 Angle : 0.566 14.007 31058 Z= 0.264 Chirality : 0.043 0.494 3512 Planarity : 0.003 0.041 3804 Dihedral : 12.716 161.597 5056 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.39 % Allowed : 16.09 % 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: 0.38 (0.16), residues: 2636 helix: 1.34 (0.15), residues: 1236 sheet: -0.42 (0.31), residues: 258 loop : -0.76 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 894 HIS 0.005 0.001 HIS A 557 PHE 0.019 0.001 PHE C 793 TYR 0.011 0.001 TYR A 684 ARG 0.008 0.000 ARG D 223 *********************** 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 160 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 106 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8011 (tmm) REVERT: A 404 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: A 413 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6349 (ptpp) REVERT: A 423 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7987 (ttm-80) REVERT: A 473 ARG cc_start: 0.6846 (mtt180) cc_final: 0.6584 (mtm180) REVERT: A 936 ILE cc_start: 0.8669 (pt) cc_final: 0.8398 (pt) REVERT: A 1006 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7784 (mtt180) REVERT: G 10 GLU cc_start: 0.8099 (pm20) cc_final: 0.7759 (pm20) REVERT: G 13 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8812 (p) REVERT: C 267 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8011 (tmm) REVERT: C 404 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: C 413 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6421 (ptpp) REVERT: D 266 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7801 (p) REVERT: E 13 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8809 (p) outliers start: 54 outliers final: 39 residues processed: 152 average time/residue: 0.3275 time to fit residues: 80.9883 Evaluate side-chains 149 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 100 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 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 423 ARG 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 846 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE 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 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET 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 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 719 VAL Chi-restraints excluded: chain C residue 846 ASN 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 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 D residue 305 SER 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 250 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 242 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23024 Z= 0.337 Angle : 0.657 13.799 31058 Z= 0.311 Chirality : 0.046 0.490 3512 Planarity : 0.004 0.040 3804 Dihedral : 12.810 163.096 5056 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.56 % Allowed : 15.92 % 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: 0.17 (0.16), residues: 2636 helix: 1.11 (0.15), residues: 1234 sheet: -0.51 (0.31), residues: 258 loop : -0.79 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 894 HIS 0.004 0.001 HIS A 290 PHE 0.025 0.002 PHE C 793 TYR 0.021 0.002 TYR A 488 ARG 0.007 0.001 ARG A1006 ********************** 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 154 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 96 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: A 267 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8132 (tmm) REVERT: A 404 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: A 413 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6419 (ptpp) REVERT: A 423 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8105 (ttm-80) REVERT: A 488 TYR cc_start: 0.7677 (p90) cc_final: 0.7161 (p90) REVERT: A 507 MET cc_start: 0.7872 (mmm) cc_final: 0.6811 (tpp) REVERT: G 10 GLU cc_start: 0.8106 (pm20) cc_final: 0.7817 (pm20) REVERT: G 13 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8840 (p) REVERT: G 39 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 267 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8114 (tmm) REVERT: C 404 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: C 413 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6398 (ptpp) REVERT: D 266 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7866 (p) REVERT: E 10 GLU cc_start: 0.8027 (pm20) cc_final: 0.7784 (pm20) REVERT: E 13 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8860 (p) outliers start: 58 outliers final: 44 residues processed: 148 average time/residue: 0.3311 time to fit residues: 79.5579 Evaluate side-chains 149 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 94 time to evaluate : 2.475 ------------------------------------------------------------------------------- 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 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 423 ARG 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 719 VAL Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE 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 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 164 MET Chi-restraints excluded: chain C residue 267 MET 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 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 719 VAL Chi-restraints excluded: chain C residue 846 ASN 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 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 D residue 305 SER 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 223 optimal weight: 0.3980 chunk 64 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** ** C 557 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 = 0.3694 r_free = 0.3694 target = 0.088878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066922 restraints weight = 67255.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066891 restraints weight = 58184.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067527 restraints weight = 42616.425| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23024 Z= 0.148 Angle : 0.566 13.756 31058 Z= 0.263 Chirality : 0.043 0.488 3512 Planarity : 0.003 0.040 3804 Dihedral : 12.084 160.399 5056 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.30 % Allowed : 16.27 % Favored : 81.43 % 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: 0.52 (0.16), residues: 2636 helix: 1.42 (0.15), residues: 1244 sheet: -0.04 (0.34), residues: 230 loop : -0.74 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 894 HIS 0.003 0.001 HIS A 557 PHE 0.019 0.001 PHE C 793 TYR 0.017 0.001 TYR A 488 ARG 0.006 0.000 ARG D 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.72 seconds wall clock time: 63 minutes 10.77 seconds (3790.77 seconds total)