Starting phenix.real_space_refine on Fri Jun 20 04:37:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyu_32894/06_2025/7wyu_32894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyu_32894/06_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_32894/06_2025/7wyu_32894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyu_32894/06_2025/7wyu_32894.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyu_32894/06_2025/7wyu_32894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyu_32894/06_2025/7wyu_32894.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.43, per 1000 atoms: 0.55 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: 6.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 20 sheets defined 49.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 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: 9.20 Time building geometry restraints manager: 7.44 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: 0.10 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.450 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (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 TRP 0.024 0.002 TRP A 894 HIS 0.009 0.002 HIS A 493 PHE 0.025 0.002 PHE B 297 TYR 0.033 0.002 TYR A 131 ARG 0.009 0.001 ARG A 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01042 ( 8) link_NAG-ASN : angle 2.67792 ( 24) 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_ALPHA1-3 : bond 0.00671 ( 6) link_ALPHA1-3 : angle 2.89573 ( 18) hydrogen bonds : bond 0.16048 ( 1005) hydrogen bonds : angle 6.82334 ( 2913) link_BETA1-6 : bond 0.00203 ( 4) link_BETA1-6 : angle 0.88966 ( 12) SS BOND : bond 0.00120 ( 6) SS BOND : angle 1.76746 ( 12) covalent geometry : bond 0.01094 (23090) covalent geometry : angle 1.29726 (31162) *********************** 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 : 2.545 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: 0.6972 (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: 0.7033 (m-70) REVERT: A 523 LEU cc_start: 0.8533 (tp) cc_final: 0.8317 (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: 0.7459 (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: 0.7032 (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: 0.4130 time to fit residues: 360.8301 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 2.220 ------------------------------------------------------------------------------- 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 222 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 474 ASN A 486 ASN A 524 ASN A 904 GLN B 56 GLN B 146 GLN B 258 GLN B 284 ASN C 52 HIS C 129 ASN C 474 ASN C 486 ASN C 524 ASN C 904 GLN D 56 GLN D 258 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087672 restraints weight = 39308.625| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.53 r_work: 0.3012 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23134 Z= 0.157 Angle : 0.684 11.370 31288 Z= 0.332 Chirality : 0.045 0.429 3520 Planarity : 0.005 0.071 3806 Dihedral : 17.342 176.756 5206 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 13.40 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2636 helix: 0.45 (0.15), residues: 1218 sheet: -1.76 (0.28), residues: 262 loop : -1.80 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 392 HIS 0.006 0.001 HIS D 80 PHE 0.024 0.002 PHE C 793 TYR 0.024 0.002 TYR A 684 ARG 0.007 0.000 ARG C1006 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 8) link_NAG-ASN : angle 2.06348 ( 24) link_ALPHA1-6 : bond 0.00718 ( 4) link_ALPHA1-6 : angle 2.18668 ( 12) link_BETA1-2 : bond 0.00684 ( 2) link_BETA1-2 : angle 4.93675 ( 6) link_BETA1-4 : bond 0.00816 ( 14) link_BETA1-4 : angle 3.72797 ( 42) link_ALPHA1-3 : bond 0.00891 ( 6) link_ALPHA1-3 : angle 3.75858 ( 18) hydrogen bonds : bond 0.06065 ( 1005) hydrogen bonds : angle 5.07673 ( 2913) link_BETA1-6 : bond 0.00589 ( 4) link_BETA1-6 : angle 1.57684 ( 12) SS BOND : bond 0.00225 ( 6) SS BOND : angle 1.20934 ( 12) covalent geometry : bond 0.00350 (23090) covalent geometry : angle 0.65691 (31162) *********************** 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 295 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 214 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: A 170 LEU cc_start: 0.8066 (tp) cc_final: 0.7784 (tt) REVERT: A 231 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6493 (t80) REVERT: A 442 ILE cc_start: 0.8474 (mm) cc_final: 0.8182 (tt) REVERT: A 493 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6785 (m-70) REVERT: A 822 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8854 (mt) REVERT: B 73 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 106 MET cc_start: 0.9077 (mmm) cc_final: 0.8552 (mmt) REVERT: B 142 ASP cc_start: 0.8431 (t0) cc_final: 0.8101 (t70) REVERT: B 160 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (m) REVERT: B 180 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8616 (ttpt) REVERT: G 11 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8830 (ttt180) REVERT: C 100 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: C 231 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6576 (t80) REVERT: C 493 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6748 (m-70) REVERT: C 561 PRO cc_start: 0.5651 (Cg_endo) cc_final: 0.5366 (Cg_exo) REVERT: C 589 MET cc_start: 0.8688 (tpp) cc_final: 0.8102 (tpp) REVERT: C 658 ARG cc_start: 0.7270 (mmt-90) cc_final: 0.6990 (mmp80) REVERT: C 822 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9109 (mt) REVERT: D 142 ASP cc_start: 0.8382 (t0) cc_final: 0.8094 (t70) REVERT: D 180 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8611 (ptpt) outliers start: 81 outliers final: 33 residues processed: 277 average time/residue: 0.3630 time to fit residues: 158.7295 Evaluate side-chains 216 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 552 VAL 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 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 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 180 LYS Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 A 697 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 = 0.3652 r_free = 0.3652 target = 0.116956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078791 restraints weight = 39433.646| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.54 r_work: 0.2816 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23134 Z= 0.232 Angle : 0.713 10.969 31288 Z= 0.348 Chirality : 0.047 0.416 3520 Planarity : 0.005 0.052 3806 Dihedral : 15.816 164.176 5153 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.32 % Allowed : 13.97 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2636 helix: 0.81 (0.15), residues: 1226 sheet: -1.14 (0.31), residues: 262 loop : -1.21 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 156 HIS 0.005 0.001 HIS C 919 PHE 0.031 0.002 PHE A 793 TYR 0.024 0.002 TYR D 44 ARG 0.008 0.001 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.01175 ( 8) link_NAG-ASN : angle 2.19740 ( 24) link_ALPHA1-6 : bond 0.00777 ( 4) link_ALPHA1-6 : angle 1.74867 ( 12) link_BETA1-2 : bond 0.00357 ( 2) link_BETA1-2 : angle 4.58098 ( 6) link_BETA1-4 : bond 0.00786 ( 14) link_BETA1-4 : angle 3.52609 ( 42) link_ALPHA1-3 : bond 0.01270 ( 6) link_ALPHA1-3 : angle 3.21853 ( 18) hydrogen bonds : bond 0.06840 ( 1005) hydrogen bonds : angle 4.75912 ( 2913) link_BETA1-6 : bond 0.00356 ( 4) link_BETA1-6 : angle 1.66994 ( 12) SS BOND : bond 0.00234 ( 6) SS BOND : angle 1.79408 ( 12) covalent geometry : bond 0.00561 (23090) covalent geometry : angle 0.68975 (31162) *********************** 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 250 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 175 time to evaluate : 2.383 Fit side-chains REVERT: A 100 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: A 442 ILE cc_start: 0.8769 (mm) cc_final: 0.8509 (tt) REVERT: A 488 TYR cc_start: 0.8187 (p90) cc_final: 0.7878 (p90) REVERT: A 493 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6664 (m-70) REVERT: A 555 PHE cc_start: 0.8368 (m-80) cc_final: 0.8119 (m-10) REVERT: A 589 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: B 106 MET cc_start: 0.9123 (mmm) cc_final: 0.8909 (mmm) REVERT: B 142 ASP cc_start: 0.8711 (t0) cc_final: 0.8479 (t70) REVERT: C 100 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: C 445 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: C 493 HIS cc_start: 0.7036 (OUTLIER) cc_final: 0.6726 (m-70) REVERT: C 558 PHE cc_start: 0.7883 (t80) cc_final: 0.7618 (t80) REVERT: C 658 ARG cc_start: 0.7517 (mmt-90) cc_final: 0.7271 (mmp80) REVERT: D 18 TRP cc_start: 0.7787 (t-100) cc_final: 0.7466 (t60) REVERT: D 97 LYS cc_start: 0.8554 (tppt) cc_final: 0.8260 (tppt) REVERT: D 106 MET cc_start: 0.9036 (mmm) cc_final: 0.8710 (mmm) REVERT: D 180 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8803 (ttpt) REVERT: E 11 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8552 (ttt180) outliers start: 75 outliers final: 44 residues processed: 235 average time/residue: 0.3339 time to fit residues: 126.5610 Evaluate side-chains 204 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 THR 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 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 266 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 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 402 THR Chi-restraints excluded: chain C residue 445 ARG 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 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 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 121 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 285 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 203 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN C 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.119068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082443 restraints weight = 39516.138| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.50 r_work: 0.2874 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23134 Z= 0.127 Angle : 0.577 9.748 31288 Z= 0.277 Chirality : 0.044 0.431 3520 Planarity : 0.004 0.046 3806 Dihedral : 14.658 153.530 5141 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.56 % Allowed : 15.74 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2636 helix: 1.27 (0.15), residues: 1226 sheet: -0.75 (0.31), residues: 262 loop : -1.07 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 392 HIS 0.003 0.001 HIS C 290 PHE 0.024 0.001 PHE C 793 TYR 0.016 0.001 TYR C 488 ARG 0.011 0.000 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 8) link_NAG-ASN : angle 1.48095 ( 24) link_ALPHA1-6 : bond 0.00749 ( 4) link_ALPHA1-6 : angle 1.69327 ( 12) link_BETA1-2 : bond 0.00297 ( 2) link_BETA1-2 : angle 4.66069 ( 6) link_BETA1-4 : bond 0.00631 ( 14) link_BETA1-4 : angle 3.08040 ( 42) link_ALPHA1-3 : bond 0.01172 ( 6) link_ALPHA1-3 : angle 3.67765 ( 18) hydrogen bonds : bond 0.05124 ( 1005) hydrogen bonds : angle 4.40505 ( 2913) link_BETA1-6 : bond 0.00109 ( 4) link_BETA1-6 : angle 1.61292 ( 12) SS BOND : bond 0.00099 ( 6) SS BOND : angle 1.07171 ( 12) covalent geometry : bond 0.00288 (23090) covalent geometry : angle 0.55246 (31162) *********************** 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 224 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 ILE cc_start: 0.8692 (mm) cc_final: 0.8370 (tt) REVERT: A 488 TYR cc_start: 0.8230 (p90) cc_final: 0.7765 (p90) REVERT: A 493 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6474 (m-70) REVERT: A 676 GLU cc_start: 0.7763 (mp0) cc_final: 0.7527 (tp30) REVERT: B 97 LYS cc_start: 0.8639 (tppt) cc_final: 0.8354 (tppt) REVERT: B 106 MET cc_start: 0.9132 (mmm) cc_final: 0.8895 (mmm) REVERT: B 142 ASP cc_start: 0.8752 (t0) cc_final: 0.8401 (t70) REVERT: C 74 ARG cc_start: 0.8165 (ptt180) cc_final: 0.7624 (ptm160) REVERT: C 493 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6506 (m-70) REVERT: C 558 PHE cc_start: 0.7810 (t80) cc_final: 0.7464 (t80) REVERT: C 658 ARG cc_start: 0.7512 (mmt-90) cc_final: 0.6970 (mmp80) REVERT: D 18 TRP cc_start: 0.7846 (t-100) cc_final: 0.7418 (t60) REVERT: D 97 LYS cc_start: 0.8605 (tppt) cc_final: 0.8324 (tppt) REVERT: D 180 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8505 (ttpt) REVERT: E 11 ARG cc_start: 0.8908 (ttt90) cc_final: 0.8645 (ttt180) outliers start: 58 outliers final: 35 residues processed: 210 average time/residue: 0.3327 time to fit residues: 111.6342 Evaluate side-chains 190 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 2.215 ------------------------------------------------------------------------------- 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 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 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 85 ILE 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 184 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 VAL 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 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 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LYS 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 34 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 254 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 654 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 = 0.3651 r_free = 0.3651 target = 0.116547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.079923 restraints weight = 39646.155| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.44 r_work: 0.2831 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23134 Z= 0.181 Angle : 0.610 9.258 31288 Z= 0.295 Chirality : 0.045 0.442 3520 Planarity : 0.004 0.046 3806 Dihedral : 14.126 137.620 5138 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.05 % Allowed : 15.69 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2636 helix: 1.37 (0.15), residues: 1224 sheet: -0.77 (0.29), residues: 284 loop : -1.06 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 894 HIS 0.004 0.001 HIS C 290 PHE 0.028 0.002 PHE C 793 TYR 0.020 0.002 TYR C 488 ARG 0.006 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 8) link_NAG-ASN : angle 1.66994 ( 24) link_ALPHA1-6 : bond 0.00844 ( 4) link_ALPHA1-6 : angle 1.63085 ( 12) link_BETA1-2 : bond 0.00359 ( 2) link_BETA1-2 : angle 4.71411 ( 6) link_BETA1-4 : bond 0.00567 ( 14) link_BETA1-4 : angle 3.01028 ( 42) link_ALPHA1-3 : bond 0.01234 ( 6) link_ALPHA1-3 : angle 3.60646 ( 18) hydrogen bonds : bond 0.05759 ( 1005) hydrogen bonds : angle 4.41607 ( 2913) link_BETA1-6 : bond 0.00155 ( 4) link_BETA1-6 : angle 1.71475 ( 12) SS BOND : bond 0.00150 ( 6) SS BOND : angle 1.03605 ( 12) covalent geometry : bond 0.00439 (23090) covalent geometry : angle 0.58773 (31162) *********************** 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 226 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.8473 (mtm) cc_final: 0.8173 (mtm) REVERT: A 493 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6607 (m90) REVERT: A 589 MET cc_start: 0.8524 (tpp) cc_final: 0.8250 (mtt) REVERT: B 97 LYS cc_start: 0.8715 (tppt) cc_final: 0.8497 (tppt) REVERT: B 106 MET cc_start: 0.9159 (mmm) cc_final: 0.8910 (mmm) REVERT: B 142 ASP cc_start: 0.8852 (t0) cc_final: 0.8543 (t70) REVERT: C 445 ARG cc_start: 0.8455 (mtp180) cc_final: 0.8206 (mtp85) REVERT: C 493 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6576 (m-70) REVERT: C 658 ARG cc_start: 0.7622 (mmt-90) cc_final: 0.7141 (mmp80) REVERT: C 1002 ASP cc_start: 0.8417 (t0) cc_final: 0.8205 (m-30) REVERT: D 18 TRP cc_start: 0.8201 (t-100) cc_final: 0.7670 (t60) REVERT: D 97 LYS cc_start: 0.8690 (tppt) cc_final: 0.8407 (tppt) REVERT: D 106 MET cc_start: 0.9055 (mmm) cc_final: 0.8745 (mmm) REVERT: D 180 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8755 (ttpt) REVERT: E 11 ARG cc_start: 0.8804 (ttt90) cc_final: 0.8513 (ttt180) outliers start: 69 outliers final: 48 residues processed: 209 average time/residue: 0.3204 time to fit residues: 108.2047 Evaluate side-chains 199 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU 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 402 THR 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 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 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 219 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 277 LEU 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 402 THR Chi-restraints excluded: chain C residue 440 VAL 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 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 178 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 145 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080782 restraints weight = 39336.628| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.41 r_work: 0.2839 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23134 Z= 0.148 Angle : 0.570 8.827 31288 Z= 0.274 Chirality : 0.044 0.455 3520 Planarity : 0.004 0.043 3806 Dihedral : 13.445 122.397 5136 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.83 % Allowed : 16.40 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2636 helix: 1.54 (0.15), residues: 1224 sheet: -0.68 (0.29), residues: 284 loop : -0.97 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 392 HIS 0.003 0.001 HIS A 290 PHE 0.026 0.002 PHE C 793 TYR 0.019 0.001 TYR C 488 ARG 0.005 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 8) link_NAG-ASN : angle 1.49038 ( 24) link_ALPHA1-6 : bond 0.00852 ( 4) link_ALPHA1-6 : angle 1.60225 ( 12) link_BETA1-2 : bond 0.00328 ( 2) link_BETA1-2 : angle 4.74622 ( 6) link_BETA1-4 : bond 0.00573 ( 14) link_BETA1-4 : angle 2.80968 ( 42) link_ALPHA1-3 : bond 0.01120 ( 6) link_ALPHA1-3 : angle 3.60697 ( 18) hydrogen bonds : bond 0.05232 ( 1005) hydrogen bonds : angle 4.30933 ( 2913) link_BETA1-6 : bond 0.00056 ( 4) link_BETA1-6 : angle 1.69333 ( 12) SS BOND : bond 0.00103 ( 6) SS BOND : angle 0.93536 ( 12) covalent geometry : bond 0.00353 (23090) covalent geometry : angle 0.54755 (31162) *********************** 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 224 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6358 (m-70) REVERT: A 589 MET cc_start: 0.8497 (tpp) cc_final: 0.8183 (mtt) REVERT: A 1002 ASP cc_start: 0.8436 (t0) cc_final: 0.8232 (m-30) REVERT: B 97 LYS cc_start: 0.8827 (tppt) cc_final: 0.8517 (tppt) REVERT: B 106 MET cc_start: 0.9136 (mmm) cc_final: 0.8868 (mmm) REVERT: C 493 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6451 (m-70) REVERT: C 507 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8094 (tpt) REVERT: C 658 ARG cc_start: 0.7604 (mmt-90) cc_final: 0.7158 (mmp80) REVERT: C 1002 ASP cc_start: 0.8419 (t0) cc_final: 0.8217 (m-30) REVERT: D 18 TRP cc_start: 0.8426 (t-100) cc_final: 0.7740 (t60) REVERT: D 23 LYS cc_start: 0.8490 (mttt) cc_final: 0.8104 (ptmt) REVERT: D 97 LYS cc_start: 0.8707 (tppt) cc_final: 0.8380 (tppt) REVERT: D 106 MET cc_start: 0.9068 (mmm) cc_final: 0.8747 (mmm) REVERT: D 180 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8509 (ttpt) outliers start: 64 outliers final: 42 residues processed: 212 average time/residue: 0.3193 time to fit residues: 111.2004 Evaluate side-chains 191 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 2.346 ------------------------------------------------------------------------------- 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 282 THR Chi-restraints excluded: chain A residue 300 VAL 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 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 85 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 277 LEU 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 402 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET 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 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 178 VAL Chi-restraints excluded: chain D residue 180 LYS 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 224 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** 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 = 0.3645 r_free = 0.3645 target = 0.116115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079939 restraints weight = 39593.347| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.39 r_work: 0.2825 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23134 Z= 0.173 Angle : 0.592 8.595 31288 Z= 0.286 Chirality : 0.044 0.456 3520 Planarity : 0.004 0.044 3806 Dihedral : 13.123 116.659 5132 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 16.49 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2636 helix: 1.51 (0.15), residues: 1224 sheet: -0.65 (0.30), residues: 276 loop : -0.92 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 392 HIS 0.004 0.001 HIS A 290 PHE 0.028 0.002 PHE C 793 TYR 0.021 0.001 TYR C 488 ARG 0.003 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 8) link_NAG-ASN : angle 1.55298 ( 24) link_ALPHA1-6 : bond 0.00856 ( 4) link_ALPHA1-6 : angle 1.61712 ( 12) link_BETA1-2 : bond 0.00309 ( 2) link_BETA1-2 : angle 4.77119 ( 6) link_BETA1-4 : bond 0.00547 ( 14) link_BETA1-4 : angle 2.77715 ( 42) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 3.50529 ( 18) hydrogen bonds : bond 0.05591 ( 1005) hydrogen bonds : angle 4.33376 ( 2913) link_BETA1-6 : bond 0.00070 ( 4) link_BETA1-6 : angle 1.72736 ( 12) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.95343 ( 12) covalent geometry : bond 0.00420 (23090) covalent geometry : angle 0.57106 (31162) *********************** 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 219 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 493 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6361 (m-70) REVERT: A 555 PHE cc_start: 0.8447 (m-10) cc_final: 0.8237 (m-10) REVERT: A 589 MET cc_start: 0.8483 (tpp) cc_final: 0.8188 (mtt) REVERT: A 889 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8134 (mmp80) REVERT: B 23 LYS cc_start: 0.8414 (mttt) cc_final: 0.8014 (ptmt) REVERT: B 97 LYS cc_start: 0.8817 (tppt) cc_final: 0.8512 (tppt) REVERT: B 106 MET cc_start: 0.9134 (mmm) cc_final: 0.8892 (mmm) REVERT: C 493 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6460 (m-70) REVERT: C 507 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8181 (tpt) REVERT: C 658 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7236 (mmp80) REVERT: D 18 TRP cc_start: 0.8569 (t-100) cc_final: 0.7791 (t60) REVERT: D 23 LYS cc_start: 0.8414 (mttt) cc_final: 0.8055 (ptmt) REVERT: D 97 LYS cc_start: 0.8792 (tppt) cc_final: 0.8427 (tppt) REVERT: D 106 MET cc_start: 0.9072 (mmm) cc_final: 0.8779 (mmm) REVERT: D 180 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8744 (ttpt) outliers start: 64 outliers final: 49 residues processed: 205 average time/residue: 0.4146 time to fit residues: 138.2909 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 : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 402 THR 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 889 ARG Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE 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 117 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 277 LEU 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 402 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET 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 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 178 VAL Chi-restraints excluded: chain D residue 180 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 216 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 654 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.114971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079054 restraints weight = 39660.257| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.45 r_work: 0.2804 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23134 Z= 0.198 Angle : 0.619 8.651 31288 Z= 0.300 Chirality : 0.045 0.453 3520 Planarity : 0.004 0.044 3806 Dihedral : 13.076 118.061 5131 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.01 % Allowed : 16.40 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2636 helix: 1.41 (0.15), residues: 1228 sheet: -0.66 (0.29), residues: 284 loop : -0.89 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 317 HIS 0.004 0.001 HIS A 290 PHE 0.030 0.002 PHE A 793 TYR 0.022 0.002 TYR A 488 ARG 0.004 0.000 ARG D 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 8) link_NAG-ASN : angle 1.60663 ( 24) link_ALPHA1-6 : bond 0.00871 ( 4) link_ALPHA1-6 : angle 1.64591 ( 12) link_BETA1-2 : bond 0.00272 ( 2) link_BETA1-2 : angle 4.88687 ( 6) link_BETA1-4 : bond 0.00528 ( 14) link_BETA1-4 : angle 2.74866 ( 42) link_ALPHA1-3 : bond 0.00912 ( 6) link_ALPHA1-3 : angle 3.43472 ( 18) hydrogen bonds : bond 0.06001 ( 1005) hydrogen bonds : angle 4.39671 ( 2913) link_BETA1-6 : bond 0.00220 ( 4) link_BETA1-6 : angle 1.79877 ( 12) SS BOND : bond 0.00163 ( 6) SS BOND : angle 1.12098 ( 12) covalent geometry : bond 0.00485 (23090) covalent geometry : angle 0.59859 (31162) *********************** 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 223 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 155 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8262 (t70) cc_final: 0.7884 (p0) REVERT: A 473 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7744 (mtt180) REVERT: A 493 HIS cc_start: 0.6688 (OUTLIER) cc_final: 0.6264 (m-70) REVERT: A 589 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8134 (mtt) REVERT: A 889 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8186 (mmp80) REVERT: B 23 LYS cc_start: 0.8497 (mttt) cc_final: 0.8036 (ptmt) REVERT: B 97 LYS cc_start: 0.8873 (tppt) cc_final: 0.8532 (tppt) REVERT: B 106 MET cc_start: 0.9151 (mmm) cc_final: 0.8923 (mmm) REVERT: C 493 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6400 (m-70) REVERT: C 507 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8126 (tpt) REVERT: D 18 TRP cc_start: 0.8756 (t-100) cc_final: 0.7944 (t60) REVERT: D 23 LYS cc_start: 0.8569 (mttt) cc_final: 0.8047 (ptmt) REVERT: D 97 LYS cc_start: 0.8889 (tppt) cc_final: 0.8480 (tppt) REVERT: D 106 MET cc_start: 0.9099 (mmm) cc_final: 0.8806 (mmm) REVERT: D 140 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8477 (mt) REVERT: D 180 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8782 (ttpt) outliers start: 68 outliers final: 45 residues processed: 207 average time/residue: 0.3411 time to fit residues: 114.9578 Evaluate side-chains 201 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 402 THR 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 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 975 ASP Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE 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 75 ASP Chi-restraints excluded: chain C residue 219 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 402 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET 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 671 LYS Chi-restraints excluded: chain C residue 677 VAL 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 178 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 285 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN C 331 ASN C 685 HIS C 946 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.081617 restraints weight = 39395.514| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.40 r_work: 0.2859 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 23134 Z= 0.110 Angle : 0.550 8.371 31288 Z= 0.264 Chirality : 0.043 0.466 3520 Planarity : 0.004 0.042 3806 Dihedral : 12.493 113.563 5128 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.17 % Allowed : 17.77 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2636 helix: 1.75 (0.15), residues: 1216 sheet: -0.31 (0.28), residues: 318 loop : -0.75 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 392 HIS 0.002 0.001 HIS C 290 PHE 0.023 0.001 PHE C 793 TYR 0.021 0.001 TYR C 488 ARG 0.004 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 8) link_NAG-ASN : angle 1.47241 ( 24) link_ALPHA1-6 : bond 0.00804 ( 4) link_ALPHA1-6 : angle 1.64843 ( 12) link_BETA1-2 : bond 0.00314 ( 2) link_BETA1-2 : angle 4.79929 ( 6) link_BETA1-4 : bond 0.00533 ( 14) link_BETA1-4 : angle 2.57893 ( 42) link_ALPHA1-3 : bond 0.00905 ( 6) link_ALPHA1-3 : angle 3.46881 ( 18) hydrogen bonds : bond 0.04691 ( 1005) hydrogen bonds : angle 4.16493 ( 2913) link_BETA1-6 : bond 0.00057 ( 4) link_BETA1-6 : angle 1.63582 ( 12) SS BOND : bond 0.00073 ( 6) SS BOND : angle 0.67039 ( 12) covalent geometry : bond 0.00241 (23090) covalent geometry : angle 0.52836 (31162) *********************** 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 218 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8205 (t70) cc_final: 0.7826 (p0) REVERT: A 493 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6284 (m-70) REVERT: A 555 PHE cc_start: 0.8394 (m-10) cc_final: 0.8180 (m-10) REVERT: A 583 LEU cc_start: 0.7173 (mm) cc_final: 0.6931 (mm) REVERT: A 589 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: B 23 LYS cc_start: 0.8513 (mttt) cc_final: 0.8025 (ptmt) REVERT: B 97 LYS cc_start: 0.8815 (tppt) cc_final: 0.8343 (tppt) REVERT: B 106 MET cc_start: 0.9142 (mmm) cc_final: 0.8868 (mmm) REVERT: B 140 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 493 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6453 (m-70) REVERT: C 507 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8194 (tpt) REVERT: D 18 TRP cc_start: 0.8757 (t-100) cc_final: 0.7947 (t60) REVERT: D 23 LYS cc_start: 0.8570 (mttt) cc_final: 0.8106 (ptmt) REVERT: D 106 MET cc_start: 0.9069 (mmm) cc_final: 0.8743 (mmm) REVERT: D 140 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8488 (mt) REVERT: D 180 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8510 (ttpt) outliers start: 49 outliers final: 34 residues processed: 204 average time/residue: 0.3100 time to fit residues: 103.1572 Evaluate side-chains 194 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 557 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 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 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 75 ASP 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 493 HIS Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 677 VAL 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 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LYS 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 177 optimal weight: 30.0000 chunk 178 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.080583 restraints weight = 39800.220| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.27 r_work: 0.2834 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23134 Z= 0.145 Angle : 0.576 10.518 31288 Z= 0.276 Chirality : 0.044 0.466 3520 Planarity : 0.004 0.042 3806 Dihedral : 12.393 113.189 5128 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 17.99 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2636 helix: 1.70 (0.15), residues: 1216 sheet: -0.27 (0.28), residues: 322 loop : -0.76 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 392 HIS 0.003 0.001 HIS C 290 PHE 0.027 0.002 PHE A 793 TYR 0.025 0.001 TYR A 488 ARG 0.003 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 8) link_NAG-ASN : angle 1.99754 ( 24) link_ALPHA1-6 : bond 0.00803 ( 4) link_ALPHA1-6 : angle 1.65943 ( 12) link_BETA1-2 : bond 0.00294 ( 2) link_BETA1-2 : angle 4.77349 ( 6) link_BETA1-4 : bond 0.00543 ( 14) link_BETA1-4 : angle 2.60584 ( 42) link_ALPHA1-3 : bond 0.00852 ( 6) link_ALPHA1-3 : angle 3.45591 ( 18) hydrogen bonds : bond 0.05088 ( 1005) hydrogen bonds : angle 4.20755 ( 2913) link_BETA1-6 : bond 0.00076 ( 4) link_BETA1-6 : angle 1.67484 ( 12) SS BOND : bond 0.00166 ( 6) SS BOND : angle 0.81369 ( 12) covalent geometry : bond 0.00346 (23090) covalent geometry : angle 0.55377 (31162) ********************** 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 200 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8214 (t70) cc_final: 0.7860 (p0) REVERT: A 493 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.6294 (m-70) REVERT: A 555 PHE cc_start: 0.8418 (m-10) cc_final: 0.8204 (m-10) REVERT: A 583 LEU cc_start: 0.7144 (mm) cc_final: 0.6916 (mm) REVERT: A 589 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: A 889 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8098 (mmp80) REVERT: B 23 LYS cc_start: 0.8511 (mttt) cc_final: 0.8012 (ptmt) REVERT: B 97 LYS cc_start: 0.8848 (tppt) cc_final: 0.8370 (tppt) REVERT: B 106 MET cc_start: 0.9131 (mmm) cc_final: 0.8862 (mmm) REVERT: C 493 HIS cc_start: 0.6801 (OUTLIER) cc_final: 0.6409 (m-70) REVERT: C 507 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8149 (tpt) REVERT: D 18 TRP cc_start: 0.8785 (t-100) cc_final: 0.8022 (t60) REVERT: D 23 LYS cc_start: 0.8604 (mttt) cc_final: 0.8129 (ptmt) REVERT: D 106 MET cc_start: 0.9084 (mmm) cc_final: 0.8779 (mmm) REVERT: D 140 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8514 (mt) REVERT: D 180 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8533 (ttpt) outliers start: 48 outliers final: 39 residues processed: 187 average time/residue: 0.3238 time to fit residues: 98.4035 Evaluate side-chains 197 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 331 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 557 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 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 41 LEU 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 75 ASP 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 308 ILE 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 402 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET 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 671 LYS Chi-restraints excluded: chain C residue 677 VAL 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 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LYS 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 50 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 20 optimal weight: 30.0000 chunk 173 optimal weight: 0.0020 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- 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 A 946 GLN C 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.081389 restraints weight = 39551.925| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.43 r_work: 0.2854 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5209 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= 0.113 Angle : 0.550 9.614 31288 Z= 0.262 Chirality : 0.043 0.468 3520 Planarity : 0.004 0.038 3806 Dihedral : 12.155 111.244 5128 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.08 % Allowed : 18.13 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2636 helix: 1.82 (0.15), residues: 1216 sheet: -0.22 (0.28), residues: 328 loop : -0.71 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.003 0.001 HIS C 290 PHE 0.024 0.001 PHE C 793 TYR 0.023 0.001 TYR A 488 ARG 0.004 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 8) link_NAG-ASN : angle 1.75018 ( 24) link_ALPHA1-6 : bond 0.00785 ( 4) link_ALPHA1-6 : angle 1.65839 ( 12) link_BETA1-2 : bond 0.00323 ( 2) link_BETA1-2 : angle 4.75904 ( 6) link_BETA1-4 : bond 0.00507 ( 14) link_BETA1-4 : angle 2.56737 ( 42) link_ALPHA1-3 : bond 0.00866 ( 6) link_ALPHA1-3 : angle 3.40332 ( 18) hydrogen bonds : bond 0.04661 ( 1005) hydrogen bonds : angle 4.13011 ( 2913) link_BETA1-6 : bond 0.00040 ( 4) link_BETA1-6 : angle 1.60876 ( 12) SS BOND : bond 0.00097 ( 6) SS BOND : angle 0.66417 ( 12) covalent geometry : bond 0.00255 (23090) covalent geometry : angle 0.52892 (31162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13387.93 seconds wall clock time: 231 minutes 58.12 seconds (13918.12 seconds total)