Starting phenix.real_space_refine on Sun Aug 24 22:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyu_32894/08_2025/7wyu_32894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyu_32894/08_2025/7wyu_32894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wyu_32894/08_2025/7wyu_32894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyu_32894/08_2025/7wyu_32894.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyu_32894/08_2025/7wyu_32894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyu_32894/08_2025/7wyu_32894.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 Mg 2 5.21 5 S 118 5.16 5 Na 4 4.78 5 C 14652 2.51 5 N 3524 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22662 Number of models: 1 Model: "" Number of chains: 22 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: "G" 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: "C" 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: "D" 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: "K" 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: "L" 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: "M" 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: "N" 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 562 Unusual residues: {' MG': 1, ' NA': 2, 'ATP': 1, 'CLR': 3, 'PCW': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 562 Unusual residues: {' MG': 1, ' NA': 2, 'ATP': 1, 'CLR': 3, 'PCW': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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: "D" 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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.59, per 1000 atoms: 0.25 Number of scatterers: 22662 At special positions: 0 Unit cell: (216.276, 178.616, 103.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 118 16.00 P 32 15.00 Mg 2 11.99 Na 4 11.00 O 4330 8.00 N 3524 7.00 C 14652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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 49.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 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 87 through 97 removed outlier: 3.611A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 128 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 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: 3.551A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.714A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.975A 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 Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.656A 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: 3.802A 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: 3.686A 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: 3.644A 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: 3.705A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.067A 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: 3.637A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.658A 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: 4.214A 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: 4.028A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.385A 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: 3.550A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.773A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.565A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.406A 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 29 through 62 removed outlier: 3.759A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.500A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.807A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.296A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.760A 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 'B' and resid 248 through 253 removed outlier: 4.240A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) 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 87 through 97 removed outlier: 3.611A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 128 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 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: 3.550A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.714A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.975A 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 Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.655A 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: 3.802A 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: 3.685A 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: 3.643A 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: 3.705A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.068A 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: 3.637A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.657A 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: 4.214A 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: 4.029A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.384A 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: 3.551A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.774A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.565A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.406A 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 29 through 62 removed outlier: 3.759A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 111 Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.808A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.297A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.759A 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 'D' and resid 248 through 253 removed outlier: 4.240A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) 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 176 through 181 removed outlier: 11.764A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.730A 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: 4.160A 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: 6.690A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.238A 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: 3.876A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 448 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.538A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.115A 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 78 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.764A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.730A 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: 4.159A 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: 6.690A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.237A 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: 3.877A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 448 " --> pdb=" O VAL C 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.537A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.115A 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 78 through 80 Processing sheet with id=AC1, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'D' and resid 124 through 125 1005 hydrogen bonds defined for protein. 2913 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: 5.08 Time building geometry restraints manager: 2.96 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: 6876 1.34 - 1.46: 5156 1.46 - 1.58: 10794 1.58 - 1.70: 92 1.70 - 1.82: 172 Bond restraints: 23090 Sorted by residual: bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.505 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.506 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C19 PCW A1110 " pdb=" C20 PCW A1110 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C39 PCW A1114 " pdb=" C40 PCW A1114 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C19 PCW C1110 " pdb=" C20 PCW C1110 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 29437 2.56 - 5.13: 1371 5.13 - 7.69: 249 7.69 - 10.26: 79 10.26 - 12.82: 26 Bond angle restraints: 31162 Sorted by residual: angle pdb=" C SER B 122 " pdb=" N PRO B 123 " pdb=" CA PRO B 123 " ideal model delta sigma weight residual 127.00 114.18 12.82 2.40e+00 1.74e-01 2.85e+01 angle pdb=" C SER D 122 " pdb=" N PRO D 123 " pdb=" CA PRO D 123 " ideal model delta sigma weight residual 127.00 114.20 12.80 2.40e+00 1.74e-01 2.84e+01 angle pdb=" N GLY C 855 " pdb=" CA GLY C 855 " pdb=" C GLY C 855 " ideal model delta sigma weight residual 113.18 124.66 -11.48 2.37e+00 1.78e-01 2.35e+01 angle pdb=" N GLY A 314 " pdb=" CA GLY A 314 " pdb=" C GLY A 314 " ideal model delta sigma weight residual 114.37 120.46 -6.09 1.26e+00 6.30e-01 2.33e+01 angle pdb=" N GLY A 855 " pdb=" CA GLY A 855 " pdb=" C GLY A 855 " ideal model delta sigma weight residual 113.18 124.61 -11.43 2.37e+00 1.78e-01 2.32e+01 ... (remaining 31157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 14105 35.98 - 71.95: 773 71.95 - 107.93: 84 107.93 - 143.91: 40 143.91 - 179.88: 2 Dihedral angle restraints: 15004 sinusoidal: 7348 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 191.83 11.95 179.88 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 191.83 11.97 179.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1113 " pdb=" C31 PCW A1113 " pdb=" C32 PCW A1113 " pdb=" O2 PCW A1113 " ideal model delta sinusoidal sigma weight residual -168.17 -29.38 -138.79 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2887 0.070 - 0.141: 512 0.141 - 0.211: 67 0.211 - 0.281: 29 0.281 - 0.352: 25 Chirality restraints: 3520 Sorted by residual: 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 -2.27 -0.13 2.00e-02 2.50e+03 4.47e+01 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 -2.27 -0.13 2.00e-02 2.50e+03 4.45e+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 -2.31 -0.09 2.00e-02 2.50e+03 1.85e+01 ... (remaining 3517 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.085 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO B 123 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.084 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO D 123 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " 0.064 5.00e-02 4.00e+02 9.86e-02 1.55e+01 pdb=" N PRO C 333 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.053 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 16193 3.11 - 3.70: 31429 3.70 - 4.30: 47344 4.30 - 4.90: 77673 Nonbonded interactions: 172739 Sorted by model distance: nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.911 2.170 nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.911 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C2001 " model vdw 1.947 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A2001 " model vdw 1.957 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 2.023 2.170 ... (remaining 172734 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.311 23134 Z= 0.544 Angle : 1.317 16.788 31288 Z= 0.605 Chirality : 0.063 0.352 3520 Planarity : 0.008 0.131 3806 Dihedral : 20.272 179.885 10074 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.55 % Favored : 92.15 % Rotamer: Outliers : 10.48 % Allowed : 8.36 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.15), residues: 2636 helix: -1.25 (0.14), residues: 1188 sheet: -2.35 (0.28), residues: 268 loop : -2.68 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 596 TYR 0.033 0.002 TYR A 131 PHE 0.025 0.002 PHE B 297 TRP 0.024 0.002 TRP A 894 HIS 0.009 0.002 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.01094 (23090) covalent geometry : angle 1.29726 (31162) SS BOND : bond 0.00120 ( 6) SS BOND : angle 1.76746 ( 12) hydrogen bonds : bond 0.16048 ( 1005) hydrogen bonds : angle 6.82334 ( 2913) link_ALPHA1-3 : bond 0.00671 ( 6) link_ALPHA1-3 : angle 2.89573 ( 18) link_ALPHA1-6 : bond 0.00566 ( 4) link_ALPHA1-6 : angle 1.36313 ( 12) link_BETA1-2 : bond 0.00610 ( 2) link_BETA1-2 : angle 5.27313 ( 6) link_BETA1-4 : bond 0.00770 ( 14) link_BETA1-4 : angle 5.53524 ( 42) link_BETA1-6 : bond 0.00203 ( 4) link_BETA1-6 : angle 0.88966 ( 12) link_NAG-ASN : bond 0.01042 ( 8) link_NAG-ASN : angle 2.67792 ( 24) *********************** 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 668 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 431 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8080 (tp) cc_final: 0.7627 (tt) REVERT: A 223 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6971 (pt0) REVERT: A 231 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6365 (t80) REVERT: A 493 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7032 (m-70) REVERT: A 523 LEU cc_start: 0.8533 (tp) cc_final: 0.8316 (tp) REVERT: A 680 ASP cc_start: 0.7318 (m-30) cc_final: 0.6849 (m-30) REVERT: A 729 ASP cc_start: 0.7881 (m-30) cc_final: 0.7651 (m-30) REVERT: A 837 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: A 846 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8072 (p0) REVERT: A 923 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.9128 (t80) REVERT: B 73 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7562 (p) REVERT: B 106 MET cc_start: 0.8734 (mmm) cc_final: 0.8502 (mmm) REVERT: B 142 ASP cc_start: 0.7796 (t0) cc_final: 0.7460 (t70) REVERT: B 219 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6764 (mtp180) REVERT: C 223 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: C 231 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6328 (t80) REVERT: C 493 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7030 (m-70) REVERT: C 658 ARG cc_start: 0.6928 (mmt-90) cc_final: 0.6503 (mmp80) REVERT: C 680 ASP cc_start: 0.7434 (m-30) cc_final: 0.6901 (m-30) REVERT: C 846 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8063 (p0) REVERT: C 967 PHE cc_start: 0.7487 (t80) cc_final: 0.7277 (t80) REVERT: D 106 MET cc_start: 0.8249 (mmm) cc_final: 0.7984 (mmm) REVERT: D 142 ASP cc_start: 0.7661 (t0) cc_final: 0.7429 (t70) outliers start: 237 outliers final: 33 residues processed: 600 average time/residue: 0.2105 time to fit residues: 182.7863 Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 160 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 129 ASN A 168 GLN A 524 ASN A 904 GLN B 56 GLN B 258 GLN B 284 ASN C 52 HIS C 129 ASN C 524 ASN C 904 GLN D 56 GLN D 258 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087122 restraints weight = 39450.473| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.49 r_work: 0.3000 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23134 Z= 0.163 Angle : 0.685 11.283 31288 Z= 0.333 Chirality : 0.046 0.438 3520 Planarity : 0.005 0.069 3806 Dihedral : 17.491 176.990 5206 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.71 % Allowed : 13.35 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.16), residues: 2636 helix: 0.46 (0.15), residues: 1216 sheet: -1.71 (0.29), residues: 262 loop : -1.80 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1006 TYR 0.024 0.002 TYR A 684 PHE 0.027 0.002 PHE C 793 TRP 0.020 0.002 TRP C 392 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00373 (23090) covalent geometry : angle 0.65755 (31162) SS BOND : bond 0.00065 ( 6) SS BOND : angle 1.12509 ( 12) hydrogen bonds : bond 0.06145 ( 1005) hydrogen bonds : angle 5.07318 ( 2913) link_ALPHA1-3 : bond 0.00886 ( 6) link_ALPHA1-3 : angle 3.82804 ( 18) link_ALPHA1-6 : bond 0.00653 ( 4) link_ALPHA1-6 : angle 2.15740 ( 12) link_BETA1-2 : bond 0.00551 ( 2) link_BETA1-2 : angle 4.91064 ( 6) link_BETA1-4 : bond 0.00983 ( 14) link_BETA1-4 : angle 3.72156 ( 42) link_BETA1-6 : bond 0.00625 ( 4) link_BETA1-6 : angle 1.54316 ( 12) link_NAG-ASN : bond 0.00626 ( 8) link_NAG-ASN : angle 2.10990 ( 24) *********************** 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 292 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 208 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: A 231 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6492 (t80) REVERT: A 461 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: A 493 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6771 (m-70) REVERT: A 822 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8878 (mt) REVERT: B 106 MET cc_start: 0.9064 (mmm) cc_final: 0.8528 (mmt) REVERT: B 142 ASP cc_start: 0.8436 (t0) cc_final: 0.8114 (t70) REVERT: B 160 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7744 (m) REVERT: B 180 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8626 (ttpt) REVERT: G 11 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8811 (ttt180) REVERT: C 100 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: C 231 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6566 (t80) REVERT: C 493 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6715 (m-70) REVERT: C 561 PRO cc_start: 0.5648 (Cg_endo) cc_final: 0.5367 (Cg_exo) REVERT: C 589 MET cc_start: 0.8741 (tpp) cc_final: 0.8184 (tpp) REVERT: C 658 ARG cc_start: 0.7273 (mmt-90) cc_final: 0.6986 (mmp80) REVERT: C 822 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9129 (mt) REVERT: C 949 MET cc_start: 0.9055 (mmm) cc_final: 0.8714 (mmm) REVERT: D 142 ASP cc_start: 0.8392 (t0) cc_final: 0.8108 (t70) outliers start: 84 outliers final: 33 residues processed: 276 average time/residue: 0.1481 time to fit residues: 64.1033 Evaluate side-chains 212 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 10.0000 chunk 242 optimal weight: 0.0170 chunk 171 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 90 optimal weight: 0.0770 chunk 84 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 557 HIS B 146 GLN B 243 GLN B 284 ASN C 118 GLN C 383 GLN C 557 HIS D 70 GLN D 243 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079881 restraints weight = 39663.983| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.51 r_work: 0.2850 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23134 Z= 0.197 Angle : 0.670 11.067 31288 Z= 0.328 Chirality : 0.046 0.418 3520 Planarity : 0.005 0.052 3806 Dihedral : 15.765 166.717 5154 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.36 % Allowed : 13.84 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2636 helix: 0.92 (0.15), residues: 1222 sheet: -1.16 (0.30), residues: 262 loop : -1.22 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.022 0.002 TYR A 869 PHE 0.025 0.002 PHE A 793 TRP 0.021 0.002 TRP D 156 HIS 0.004 0.001 HIS C 919 Details of bonding type rmsd covalent geometry : bond 0.00469 (23090) covalent geometry : angle 0.64740 (31162) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.70495 ( 12) hydrogen bonds : bond 0.06257 ( 1005) hydrogen bonds : angle 4.68376 ( 2913) link_ALPHA1-3 : bond 0.01238 ( 6) link_ALPHA1-3 : angle 3.24594 ( 18) link_ALPHA1-6 : bond 0.00768 ( 4) link_ALPHA1-6 : angle 1.72630 ( 12) link_BETA1-2 : bond 0.00337 ( 2) link_BETA1-2 : angle 4.52113 ( 6) link_BETA1-4 : bond 0.00677 ( 14) link_BETA1-4 : angle 3.34616 ( 42) link_BETA1-6 : bond 0.00301 ( 4) link_BETA1-6 : angle 1.61123 ( 12) link_NAG-ASN : bond 0.00496 ( 8) link_NAG-ASN : angle 2.11614 ( 24) *********************** 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 255 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 179 time to evaluate : 0.622 Fit side-chains REVERT: A 100 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 488 TYR cc_start: 0.8241 (p90) cc_final: 0.7946 (p90) REVERT: A 493 HIS cc_start: 0.7082 (OUTLIER) cc_final: 0.6626 (m-70) REVERT: A 589 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8143 (mtt) REVERT: B 106 MET cc_start: 0.9133 (mmm) cc_final: 0.8909 (mmm) REVERT: B 142 ASP cc_start: 0.8680 (t0) cc_final: 0.8452 (t70) REVERT: B 180 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8770 (ttpt) REVERT: C 100 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: C 267 MET cc_start: 0.8622 (tmm) cc_final: 0.8228 (ttt) REVERT: C 460 ILE cc_start: 0.8282 (tp) cc_final: 0.7692 (tt) REVERT: C 488 TYR cc_start: 0.8160 (p90) cc_final: 0.7942 (p90) REVERT: C 493 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6716 (m-70) REVERT: C 558 PHE cc_start: 0.7869 (t80) cc_final: 0.7632 (t80) REVERT: C 589 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: C 658 ARG cc_start: 0.7472 (mmt-90) cc_final: 0.7223 (mmp80) REVERT: D 18 TRP cc_start: 0.7622 (t-100) cc_final: 0.7352 (t60) REVERT: D 97 LYS cc_start: 0.8522 (tppt) cc_final: 0.8211 (tppt) REVERT: E 11 ARG cc_start: 0.8981 (ttt90) cc_final: 0.8765 (ttt180) outliers start: 76 outliers final: 45 residues processed: 237 average time/residue: 0.1401 time to fit residues: 53.0973 Evaluate side-chains 203 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 140 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 486 ASN C 654 GLN ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084266 restraints weight = 39264.050| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.48 r_work: 0.2912 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23134 Z= 0.115 Angle : 0.567 9.923 31288 Z= 0.270 Chirality : 0.043 0.436 3520 Planarity : 0.004 0.045 3806 Dihedral : 14.501 157.050 5143 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 15.87 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.16), residues: 2636 helix: 1.37 (0.15), residues: 1226 sheet: -0.76 (0.31), residues: 262 loop : -1.05 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 445 TYR 0.014 0.001 TYR C 488 PHE 0.023 0.001 PHE C 793 TRP 0.020 0.001 TRP C 392 HIS 0.002 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00254 (23090) covalent geometry : angle 0.54135 (31162) SS BOND : bond 0.00084 ( 6) SS BOND : angle 1.13085 ( 12) hydrogen bonds : bond 0.04744 ( 1005) hydrogen bonds : angle 4.36029 ( 2913) link_ALPHA1-3 : bond 0.01087 ( 6) link_ALPHA1-3 : angle 3.68993 ( 18) link_ALPHA1-6 : bond 0.00754 ( 4) link_ALPHA1-6 : angle 1.73616 ( 12) link_BETA1-2 : bond 0.00345 ( 2) link_BETA1-2 : angle 4.62593 ( 6) link_BETA1-4 : bond 0.00643 ( 14) link_BETA1-4 : angle 3.12958 ( 42) link_BETA1-6 : bond 0.00159 ( 4) link_BETA1-6 : angle 1.57577 ( 12) link_NAG-ASN : bond 0.00714 ( 8) link_NAG-ASN : angle 1.49672 ( 24) *********************** 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 234 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 TYR cc_start: 0.8276 (p90) cc_final: 0.7838 (p90) REVERT: A 493 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6509 (m-70) REVERT: A 577 ASN cc_start: 0.6693 (m-40) cc_final: 0.6416 (p0) REVERT: A 589 MET cc_start: 0.8512 (tpp) cc_final: 0.8258 (mtt) REVERT: A 676 GLU cc_start: 0.7742 (mp0) cc_final: 0.7519 (tp30) REVERT: B 97 LYS cc_start: 0.8631 (tppt) cc_final: 0.8317 (tppt) REVERT: B 106 MET cc_start: 0.9104 (mmm) cc_final: 0.8864 (mmm) REVERT: B 142 ASP cc_start: 0.8727 (t0) cc_final: 0.8477 (t70) REVERT: B 180 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8669 (ttpt) REVERT: C 460 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7990 (tp) REVERT: C 488 TYR cc_start: 0.8123 (p90) cc_final: 0.7744 (p90) REVERT: C 493 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6506 (m-70) REVERT: C 558 PHE cc_start: 0.7751 (t80) cc_final: 0.7449 (t80) REVERT: C 577 ASN cc_start: 0.6734 (m-40) cc_final: 0.6467 (p0) REVERT: C 589 MET cc_start: 0.8470 (tpp) cc_final: 0.8210 (mtt) REVERT: C 658 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.6880 (mmp80) REVERT: D 97 LYS cc_start: 0.8594 (tppt) cc_final: 0.8308 (tppt) outliers start: 56 outliers final: 30 residues processed: 219 average time/residue: 0.1538 time to fit residues: 53.5874 Evaluate side-chains 189 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 152 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 250 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 173 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 331 ASN A 384 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 GLN C 384 ASN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN D 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080249 restraints weight = 39424.285| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.57 r_work: 0.2830 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23134 Z= 0.190 Angle : 0.628 9.036 31288 Z= 0.303 Chirality : 0.045 0.443 3520 Planarity : 0.004 0.048 3806 Dihedral : 14.030 140.128 5141 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.09 % Allowed : 15.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2636 helix: 1.36 (0.15), residues: 1224 sheet: -0.60 (0.29), residues: 294 loop : -1.10 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1010 TYR 0.022 0.002 TYR A 869 PHE 0.030 0.002 PHE C 793 TRP 0.017 0.001 TRP C 392 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00460 (23090) covalent geometry : angle 0.60576 (31162) SS BOND : bond 0.00169 ( 6) SS BOND : angle 1.14911 ( 12) hydrogen bonds : bond 0.05940 ( 1005) hydrogen bonds : angle 4.44351 ( 2913) link_ALPHA1-3 : bond 0.01185 ( 6) link_ALPHA1-3 : angle 3.56117 ( 18) link_ALPHA1-6 : bond 0.00855 ( 4) link_ALPHA1-6 : angle 1.61973 ( 12) link_BETA1-2 : bond 0.00379 ( 2) link_BETA1-2 : angle 4.70430 ( 6) link_BETA1-4 : bond 0.00576 ( 14) link_BETA1-4 : angle 3.01152 ( 42) link_BETA1-6 : bond 0.00252 ( 4) link_BETA1-6 : angle 1.70118 ( 12) link_NAG-ASN : bond 0.00507 ( 8) link_NAG-ASN : angle 1.68738 ( 24) *********************** 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 228 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 HIS cc_start: 0.7010 (OUTLIER) cc_final: 0.6435 (m-70) REVERT: A 572 ASP cc_start: 0.7059 (p0) cc_final: 0.6707 (p0) REVERT: A 577 ASN cc_start: 0.6739 (m-40) cc_final: 0.5300 (t0) REVERT: A 589 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: A 676 GLU cc_start: 0.7771 (mp0) cc_final: 0.7569 (tp30) REVERT: B 97 LYS cc_start: 0.8735 (tppt) cc_final: 0.8510 (tppt) REVERT: B 106 MET cc_start: 0.9129 (mmm) cc_final: 0.8895 (mmm) REVERT: B 142 ASP cc_start: 0.8858 (t0) cc_final: 0.8548 (t70) REVERT: C 460 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8137 (tp) REVERT: C 488 TYR cc_start: 0.7847 (p90) cc_final: 0.7631 (p90) REVERT: C 493 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6599 (m-70) REVERT: C 589 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8164 (mtt) REVERT: C 658 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7128 (mmp80) REVERT: C 1002 ASP cc_start: 0.8477 (t0) cc_final: 0.8262 (m-30) REVERT: D 18 TRP cc_start: 0.8100 (t-100) cc_final: 0.7593 (t60) REVERT: D 97 LYS cc_start: 0.8740 (tppt) cc_final: 0.8434 (tppt) outliers start: 70 outliers final: 49 residues processed: 211 average time/residue: 0.1334 time to fit residues: 46.5020 Evaluate side-chains 201 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 285 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 217 optimal weight: 0.0010 chunk 19 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 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 = 0.3686 r_free = 0.3686 target = 0.119025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082390 restraints weight = 39417.242| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.28 r_work: 0.2877 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23134 Z= 0.113 Angle : 0.549 8.812 31288 Z= 0.263 Chirality : 0.043 0.459 3520 Planarity : 0.004 0.040 3806 Dihedral : 13.398 132.648 5141 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.21 % Allowed : 16.71 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2636 helix: 1.61 (0.15), residues: 1238 sheet: -0.39 (0.28), residues: 308 loop : -1.03 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1010 TYR 0.015 0.001 TYR C 488 PHE 0.022 0.001 PHE C 793 TRP 0.010 0.001 TRP C 317 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00250 (23090) covalent geometry : angle 0.52588 (31162) SS BOND : bond 0.00056 ( 6) SS BOND : angle 0.72822 ( 12) hydrogen bonds : bond 0.04699 ( 1005) hydrogen bonds : angle 4.23217 ( 2913) link_ALPHA1-3 : bond 0.01122 ( 6) link_ALPHA1-3 : angle 3.65226 ( 18) link_ALPHA1-6 : bond 0.00808 ( 4) link_ALPHA1-6 : angle 1.59984 ( 12) link_BETA1-2 : bond 0.00367 ( 2) link_BETA1-2 : angle 4.65404 ( 6) link_BETA1-4 : bond 0.00580 ( 14) link_BETA1-4 : angle 2.81871 ( 42) link_BETA1-6 : bond 0.00070 ( 4) link_BETA1-6 : angle 1.61072 ( 12) link_NAG-ASN : bond 0.00454 ( 8) link_NAG-ASN : angle 1.42177 ( 24) *********************** 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 210 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6407 (m-70) REVERT: A 572 ASP cc_start: 0.7082 (p0) cc_final: 0.6753 (p0) REVERT: A 577 ASN cc_start: 0.7013 (m-40) cc_final: 0.5650 (t0) REVERT: A 589 MET cc_start: 0.8462 (tpp) cc_final: 0.8104 (mtt) REVERT: A 676 GLU cc_start: 0.7675 (mp0) cc_final: 0.7393 (tp30) REVERT: B 97 LYS cc_start: 0.8757 (tppt) cc_final: 0.8482 (tppt) REVERT: B 106 MET cc_start: 0.9108 (mmm) cc_final: 0.8871 (mmm) REVERT: C 493 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6482 (m-70) REVERT: C 555 PHE cc_start: 0.8381 (m-10) cc_final: 0.8181 (m-10) REVERT: C 558 PHE cc_start: 0.7628 (t80) cc_final: 0.7252 (t80) REVERT: C 589 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8061 (mtt) REVERT: C 658 ARG cc_start: 0.7574 (mmt-90) cc_final: 0.7076 (mmp80) REVERT: C 822 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9387 (mt) REVERT: C 1002 ASP cc_start: 0.8379 (t0) cc_final: 0.8158 (m-30) REVERT: D 18 TRP cc_start: 0.8167 (t-100) cc_final: 0.7624 (t60) REVERT: D 97 LYS cc_start: 0.8667 (tppt) cc_final: 0.8376 (tppt) outliers start: 50 outliers final: 35 residues processed: 192 average time/residue: 0.1396 time to fit residues: 43.0368 Evaluate side-chains 192 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 209 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080427 restraints weight = 39595.918| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.37 r_work: 0.2835 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23134 Z= 0.167 Angle : 0.593 8.477 31288 Z= 0.285 Chirality : 0.044 0.460 3520 Planarity : 0.004 0.045 3806 Dihedral : 13.117 119.545 5136 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.39 % Allowed : 16.45 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.16), residues: 2636 helix: 1.55 (0.15), residues: 1226 sheet: -0.39 (0.29), residues: 308 loop : -0.94 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1010 TYR 0.019 0.002 TYR C 869 PHE 0.029 0.002 PHE A 793 TRP 0.025 0.001 TRP A 392 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00404 (23090) covalent geometry : angle 0.57117 (31162) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.93198 ( 12) hydrogen bonds : bond 0.05548 ( 1005) hydrogen bonds : angle 4.32546 ( 2913) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 3.52956 ( 18) link_ALPHA1-6 : bond 0.00864 ( 4) link_ALPHA1-6 : angle 1.59789 ( 12) link_BETA1-2 : bond 0.00333 ( 2) link_BETA1-2 : angle 4.72654 ( 6) link_BETA1-4 : bond 0.00555 ( 14) link_BETA1-4 : angle 2.79726 ( 42) link_BETA1-6 : bond 0.00095 ( 4) link_BETA1-6 : angle 1.71476 ( 12) link_NAG-ASN : bond 0.00432 ( 8) link_NAG-ASN : angle 1.58631 ( 24) *********************** 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 211 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.6251 (m-70) REVERT: A 572 ASP cc_start: 0.6998 (p0) cc_final: 0.6727 (p0) REVERT: A 577 ASN cc_start: 0.7008 (m-40) cc_final: 0.5599 (t0) REVERT: A 589 MET cc_start: 0.8447 (tpp) cc_final: 0.8051 (mtt) REVERT: A 676 GLU cc_start: 0.7807 (mp0) cc_final: 0.7449 (tp30) REVERT: B 97 LYS cc_start: 0.8860 (tppt) cc_final: 0.8539 (tppt) REVERT: B 106 MET cc_start: 0.9154 (mmm) cc_final: 0.8911 (mmm) REVERT: C 493 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6484 (m-70) REVERT: C 589 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7934 (mtt) REVERT: C 658 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.7197 (mmp80) REVERT: D 18 TRP cc_start: 0.8434 (t-100) cc_final: 0.7692 (t60) REVERT: D 23 LYS cc_start: 0.8516 (mttt) cc_final: 0.8158 (ptmt) REVERT: D 97 LYS cc_start: 0.8790 (tppt) cc_final: 0.8433 (tppt) outliers start: 54 outliers final: 41 residues processed: 195 average time/residue: 0.1407 time to fit residues: 45.1721 Evaluate side-chains 193 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080354 restraints weight = 39637.100| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.50 r_work: 0.2817 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 23134 Z= 0.170 Angle : 0.586 8.446 31288 Z= 0.283 Chirality : 0.044 0.459 3520 Planarity : 0.004 0.045 3806 Dihedral : 12.802 115.639 5132 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.52 % Allowed : 16.62 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2636 helix: 1.55 (0.15), residues: 1224 sheet: -0.36 (0.28), residues: 312 loop : -0.93 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.022 0.001 TYR C 488 PHE 0.029 0.002 PHE A 793 TRP 0.015 0.001 TRP C 317 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00411 (23090) covalent geometry : angle 0.56504 (31162) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.98787 ( 12) hydrogen bonds : bond 0.05515 ( 1005) hydrogen bonds : angle 4.31839 ( 2913) link_ALPHA1-3 : bond 0.00953 ( 6) link_ALPHA1-3 : angle 3.46104 ( 18) link_ALPHA1-6 : bond 0.00843 ( 4) link_ALPHA1-6 : angle 1.63612 ( 12) link_BETA1-2 : bond 0.00299 ( 2) link_BETA1-2 : angle 4.81724 ( 6) link_BETA1-4 : bond 0.00550 ( 14) link_BETA1-4 : angle 2.68897 ( 42) link_BETA1-6 : bond 0.00074 ( 4) link_BETA1-6 : angle 1.72274 ( 12) link_NAG-ASN : bond 0.00477 ( 8) link_NAG-ASN : angle 1.53243 ( 24) *********************** 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 217 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8172 (t70) cc_final: 0.7771 (p0) REVERT: A 493 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6303 (m-70) REVERT: A 555 PHE cc_start: 0.8495 (m-10) cc_final: 0.8286 (m-10) REVERT: A 589 MET cc_start: 0.8434 (tpp) cc_final: 0.7999 (mtt) REVERT: A 676 GLU cc_start: 0.7827 (mp0) cc_final: 0.7476 (tp30) REVERT: A 889 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8167 (mmp80) REVERT: B 23 LYS cc_start: 0.8401 (mttt) cc_final: 0.8090 (ptpt) REVERT: B 97 LYS cc_start: 0.8914 (tppt) cc_final: 0.8605 (tppt) REVERT: B 106 MET cc_start: 0.9130 (mmm) cc_final: 0.8871 (mmm) REVERT: C 493 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6406 (m-70) REVERT: C 589 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7871 (mtt) REVERT: D 18 TRP cc_start: 0.8672 (t-100) cc_final: 0.7907 (t60) REVERT: D 23 LYS cc_start: 0.8605 (mttt) cc_final: 0.8162 (ptmt) REVERT: D 97 LYS cc_start: 0.8840 (tppt) cc_final: 0.8457 (tppt) REVERT: D 140 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8427 (mt) outliers start: 57 outliers final: 41 residues processed: 201 average time/residue: 0.1331 time to fit residues: 43.8899 Evaluate side-chains 195 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 207 optimal weight: 0.0570 chunk 261 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 685 HIS C 331 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS C 946 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082316 restraints weight = 39547.917| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.37 r_work: 0.2850 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23134 Z= 0.117 Angle : 0.555 8.458 31288 Z= 0.266 Chirality : 0.043 0.469 3520 Planarity : 0.004 0.044 3806 Dihedral : 12.304 112.326 5128 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.86 % Allowed : 17.90 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2636 helix: 1.70 (0.15), residues: 1236 sheet: -0.22 (0.29), residues: 308 loop : -0.86 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 517 TYR 0.037 0.001 TYR C 488 PHE 0.024 0.001 PHE C 793 TRP 0.039 0.001 TRP C 392 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00267 (23090) covalent geometry : angle 0.53334 (31162) SS BOND : bond 0.00079 ( 6) SS BOND : angle 0.71722 ( 12) hydrogen bonds : bond 0.04751 ( 1005) hydrogen bonds : angle 4.18356 ( 2913) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 3.46595 ( 18) link_ALPHA1-6 : bond 0.00808 ( 4) link_ALPHA1-6 : angle 1.64085 ( 12) link_BETA1-2 : bond 0.00320 ( 2) link_BETA1-2 : angle 4.74191 ( 6) link_BETA1-4 : bond 0.00530 ( 14) link_BETA1-4 : angle 2.60188 ( 42) link_BETA1-6 : bond 0.00039 ( 4) link_BETA1-6 : angle 1.64956 ( 12) link_NAG-ASN : bond 0.00411 ( 8) link_NAG-ASN : angle 1.53801 ( 24) *********************** 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 202 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8139 (t70) cc_final: 0.7760 (p0) REVERT: A 493 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6264 (m-70) REVERT: A 589 MET cc_start: 0.8420 (tpp) cc_final: 0.7928 (mtt) REVERT: A 676 GLU cc_start: 0.7837 (mp0) cc_final: 0.7483 (tp30) REVERT: A 852 MET cc_start: 0.8416 (tpp) cc_final: 0.8216 (mmm) REVERT: B 23 LYS cc_start: 0.8462 (mttt) cc_final: 0.8106 (ptpt) REVERT: B 97 LYS cc_start: 0.8858 (tppt) cc_final: 0.8451 (tppt) REVERT: B 106 MET cc_start: 0.9132 (mmm) cc_final: 0.8843 (mmm) REVERT: C 391 MET cc_start: 0.8468 (mtm) cc_final: 0.8120 (mtm) REVERT: C 493 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.6435 (m-70) REVERT: C 555 PHE cc_start: 0.8374 (m-10) cc_final: 0.8166 (m-10) REVERT: C 589 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7724 (mtt) REVERT: D 18 TRP cc_start: 0.8677 (t-100) cc_final: 0.7923 (t60) REVERT: D 23 LYS cc_start: 0.8533 (mttt) cc_final: 0.8151 (ptmt) REVERT: D 97 LYS cc_start: 0.8826 (tppt) cc_final: 0.8349 (tppt) outliers start: 42 outliers final: 36 residues processed: 188 average time/residue: 0.1455 time to fit residues: 44.5860 Evaluate side-chains 191 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 203 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 331 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082983 restraints weight = 39487.838| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.30 r_work: 0.2870 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23134 Z= 0.114 Angle : 0.547 8.223 31288 Z= 0.262 Chirality : 0.043 0.474 3520 Planarity : 0.004 0.045 3806 Dihedral : 12.085 110.718 5128 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.95 % Allowed : 17.90 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2636 helix: 1.78 (0.15), residues: 1230 sheet: -0.11 (0.28), residues: 318 loop : -0.77 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 11 TYR 0.020 0.001 TYR A 488 PHE 0.023 0.001 PHE C 793 TRP 0.032 0.001 TRP A 392 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00258 (23090) covalent geometry : angle 0.52600 (31162) SS BOND : bond 0.00069 ( 6) SS BOND : angle 0.66168 ( 12) hydrogen bonds : bond 0.04614 ( 1005) hydrogen bonds : angle 4.13153 ( 2913) link_ALPHA1-3 : bond 0.01016 ( 6) link_ALPHA1-3 : angle 3.44092 ( 18) link_ALPHA1-6 : bond 0.00803 ( 4) link_ALPHA1-6 : angle 1.65007 ( 12) link_BETA1-2 : bond 0.00333 ( 2) link_BETA1-2 : angle 4.71905 ( 6) link_BETA1-4 : bond 0.00530 ( 14) link_BETA1-4 : angle 2.55940 ( 42) link_BETA1-6 : bond 0.00032 ( 4) link_BETA1-6 : angle 1.61836 ( 12) link_NAG-ASN : bond 0.00394 ( 8) link_NAG-ASN : angle 1.40008 ( 24) ********************** 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 198 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8139 (t70) cc_final: 0.7757 (p0) REVERT: A 493 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6205 (m-70) REVERT: A 555 PHE cc_start: 0.8414 (m-10) cc_final: 0.8195 (m-10) REVERT: A 589 MET cc_start: 0.8430 (tpp) cc_final: 0.7932 (mtt) REVERT: A 676 GLU cc_start: 0.7839 (mp0) cc_final: 0.7499 (tp30) REVERT: B 23 LYS cc_start: 0.8484 (mttt) cc_final: 0.8097 (ptpt) REVERT: B 97 LYS cc_start: 0.8865 (tppt) cc_final: 0.8467 (tppt) REVERT: B 106 MET cc_start: 0.9137 (mmm) cc_final: 0.8838 (mmm) REVERT: C 391 MET cc_start: 0.8471 (mtm) cc_final: 0.8109 (mtm) REVERT: C 493 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6360 (m-70) REVERT: C 555 PHE cc_start: 0.8370 (m-10) cc_final: 0.8159 (m-10) REVERT: C 589 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7713 (mtt) REVERT: D 18 TRP cc_start: 0.8686 (t-100) cc_final: 0.7890 (t60) REVERT: D 23 LYS cc_start: 0.8517 (mttt) cc_final: 0.8030 (ptmt) outliers start: 44 outliers final: 37 residues processed: 186 average time/residue: 0.1423 time to fit residues: 43.0752 Evaluate side-chains 189 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 158 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 437 GLN C 331 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.081891 restraints weight = 39599.801| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.35 r_work: 0.2845 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 23134 Z= 0.137 Angle : 0.568 11.706 31288 Z= 0.271 Chirality : 0.044 0.467 3520 Planarity : 0.004 0.045 3806 Dihedral : 12.034 110.379 5128 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.95 % Allowed : 18.04 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2636 helix: 1.69 (0.15), residues: 1242 sheet: -0.11 (0.28), residues: 318 loop : -0.82 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1010 TYR 0.022 0.001 TYR A 488 PHE 0.025 0.002 PHE A 793 TRP 0.024 0.001 TRP A 392 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00324 (23090) covalent geometry : angle 0.54740 (31162) SS BOND : bond 0.00108 ( 6) SS BOND : angle 0.77981 ( 12) hydrogen bonds : bond 0.04948 ( 1005) hydrogen bonds : angle 4.16418 ( 2913) link_ALPHA1-3 : bond 0.00895 ( 6) link_ALPHA1-3 : angle 3.40156 ( 18) link_ALPHA1-6 : bond 0.00799 ( 4) link_ALPHA1-6 : angle 1.65611 ( 12) link_BETA1-2 : bond 0.00295 ( 2) link_BETA1-2 : angle 4.73423 ( 6) link_BETA1-4 : bond 0.00522 ( 14) link_BETA1-4 : angle 2.52728 ( 42) link_BETA1-6 : bond 0.00047 ( 4) link_BETA1-6 : angle 1.65329 ( 12) link_NAG-ASN : bond 0.00599 ( 8) link_NAG-ASN : angle 1.87225 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.57 seconds wall clock time: 102 minutes 12.17 seconds (6132.17 seconds total)