Starting phenix.real_space_refine on Fri Jun 20 05:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyv_32895/06_2025/7wyv_32895.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyv_32895/06_2025/7wyv_32895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wyv_32895/06_2025/7wyv_32895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyv_32895/06_2025/7wyv_32895.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyv_32895/06_2025/7wyv_32895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyv_32895/06_2025/7wyv_32895.cif" } resolution = 3.7 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 32 5.49 5 Mg 4 5.21 5 S 118 5.16 5 Na 2 4.78 5 C 14652 2.51 5 N 3524 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 22668 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 562 Unusual residues: {' MG': 2, ' NA': 1, '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: "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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: G, K, N, L, C, D, M Time building chain proxies: 24.15, per 1000 atoms: 1.07 Number of scatterers: 22668 At special positions: 0 Unit cell: (216.276, 179.692, 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 4 11.99 Na 2 11.00 O 4336 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: 6.38 Conformation dependent library (CDL) restraints added in 2.5 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 49.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.769A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 282 through 313 removed outlier: 3.853A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.663A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.615A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 4.000A 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: 3.652A 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 removed outlier: 3.502A pdb=" N LEU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.801A 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: 3.696A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.133A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) 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: 3.655A 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: 3.756A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.977A 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: 3.653A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.646A 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: 4.227A 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: 4.041A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.553A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.789A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.534A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.450A 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: 3.796A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.548A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.909A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.363A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.755A 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: 4.203A 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 89 through 97 removed outlier: 3.768A pdb=" N GLN C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 160 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 282 through 313 removed outlier: 3.854A pdb=" N ILE C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.663A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.615A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 4.000A 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: 3.651A 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 removed outlier: 3.502A pdb=" N LEU C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) 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: 3.696A 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: 3.654A 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: 3.756A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.977A 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: 3.653A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.647A 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: 4.227A 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: 4.040A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.347A 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: 3.553A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.585A 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: 3.789A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.534A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.450A 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: 3.796A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.548A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.909A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 4.363A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.756A 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: 4.203A 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: 11.769A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.375A 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: 7.071A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.731A 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: 4.174A 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: 6.651A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.245A 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: 3.889A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.519A 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: 6.562A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.119A 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 91 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: 11.769A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.884A 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: 4.174A 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: 6.652A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.245A 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: 3.889A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.519A 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: 6.563A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.119A 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 91 Processing sheet with id=AC2, first strand: chain 'D' and resid 124 through 125 998 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.39 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6867 1.35 - 1.47: 5220 1.47 - 1.59: 10763 1.59 - 1.71: 68 1.71 - 1.83: 172 Bond restraints: 23090 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" C39 PCW A1114 " pdb=" C40 PCW A1114 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C39 PCW C1114 " pdb=" C40 PCW C1114 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C19 PCW A1110 " pdb=" C20 PCW A1110 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 29091 2.33 - 4.67: 1634 4.67 - 7.00: 289 7.00 - 9.34: 102 9.34 - 11.67: 46 Bond angle restraints: 31162 Sorted by residual: angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 113.12 106.65 6.47 1.25e+00 6.40e-01 2.68e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 113.12 106.71 6.41 1.25e+00 6.40e-01 2.63e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.46e+01 angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" C SER D 122 " pdb=" N PRO D 123 " pdb=" CA PRO D 123 " ideal model delta sigma weight residual 127.00 115.44 11.56 2.40e+00 1.74e-01 2.32e+01 ... (remaining 31157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14080 35.94 - 71.89: 796 71.89 - 107.83: 86 107.83 - 143.78: 40 143.78 - 179.72: 2 Dihedral angle restraints: 15004 sinusoidal: 7348 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E 102 " pdb=" C31 PCW E 102 " pdb=" C32 PCW E 102 " pdb=" O2 PCW E 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.55 -179.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G 102 " pdb=" C31 PCW G 102 " pdb=" C32 PCW G 102 " pdb=" O2 PCW G 102 " ideal model delta sinusoidal sigma weight residual -168.17 11.52 -179.69 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 -29.69 -138.48 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2920 0.074 - 0.148: 497 0.148 - 0.222: 59 0.222 - 0.296: 24 0.296 - 0.370: 20 Chirality restraints: 3520 Sorted by residual: chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.91e+01 chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.69e+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 -2.33 -0.07 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3517 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO C 283 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO A 283 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 594 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO A 595 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " -0.046 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 144 2.54 - 3.13: 17053 3.13 - 3.72: 31849 3.72 - 4.31: 46883 4.31 - 4.90: 76918 Nonbonded interactions: 172847 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.954 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.954 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1202 " model vdw 1.994 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 2.003 2.170 nonbonded pdb=" O THR C 378 " pdb="MG MG C1101 " model vdw 2.020 2.170 ... (remaining 172842 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 62.740 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 0.308 23134 Z= 0.540 Angle : 1.322 17.282 31288 Z= 0.620 Chirality : 0.063 0.370 3520 Planarity : 0.008 0.105 3806 Dihedral : 20.330 179.724 10074 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.97 % Favored : 91.58 % Rotamer: Outliers : 10.52 % Allowed : 8.36 % Favored : 81.12 % 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: -3.15 (0.14), residues: 2636 helix: -1.48 (0.13), residues: 1192 sheet: -2.36 (0.28), residues: 266 loop : -2.61 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 894 HIS 0.009 0.001 HIS A 493 PHE 0.023 0.002 PHE D 297 TYR 0.035 0.002 TYR D 40 ARG 0.009 0.001 ARG B 137 Details of bonding type rmsd link_NAG-ASN : bond 0.01367 ( 8) link_NAG-ASN : angle 3.42088 ( 24) link_ALPHA1-6 : bond 0.00655 ( 4) link_ALPHA1-6 : angle 1.31781 ( 12) link_BETA1-2 : bond 0.00763 ( 2) link_BETA1-2 : angle 5.45504 ( 6) link_BETA1-4 : bond 0.00837 ( 14) link_BETA1-4 : angle 5.94233 ( 42) link_ALPHA1-3 : bond 0.00760 ( 6) link_ALPHA1-3 : angle 3.08011 ( 18) hydrogen bonds : bond 0.15774 ( 998) hydrogen bonds : angle 7.01497 ( 2892) link_BETA1-6 : bond 0.00216 ( 4) link_BETA1-6 : angle 1.02265 ( 12) SS BOND : bond 0.00274 ( 6) SS BOND : angle 1.89163 ( 12) covalent geometry : bond 0.01072 (23090) covalent geometry : angle 1.29743 (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 717 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 479 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4443 (tp) REVERT: A 64 THR cc_start: 0.4283 (OUTLIER) cc_final: 0.3833 (p) REVERT: A 127 ASN cc_start: 0.3716 (OUTLIER) cc_final: 0.3475 (t0) REVERT: A 180 ILE cc_start: 0.6921 (pt) cc_final: 0.6662 (tp) REVERT: A 240 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7797 (mtt180) REVERT: A 241 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7800 (p0) REVERT: A 260 TYR cc_start: 0.7321 (m-80) cc_final: 0.6735 (m-80) REVERT: A 493 HIS cc_start: 0.4723 (OUTLIER) cc_final: 0.3433 (m-70) REVERT: A 515 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7260 (pp) REVERT: A 524 ASN cc_start: 0.8008 (t0) cc_final: 0.7593 (t0) REVERT: A 753 ASP cc_start: 0.7234 (m-30) cc_final: 0.6948 (m-30) REVERT: A 837 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7022 (ptt-90) REVERT: A 923 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 32 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7158 (t) REVERT: B 73 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7464 (p) REVERT: B 94 SER cc_start: 0.6956 (OUTLIER) cc_final: 0.6538 (p) REVERT: B 284 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7449 (p0) REVERT: C 63 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4689 (tp) REVERT: C 174 ASP cc_start: 0.7076 (t0) cc_final: 0.6305 (m-30) REVERT: C 180 ILE cc_start: 0.7228 (pt) cc_final: 0.6787 (tp) REVERT: C 240 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: C 272 THR cc_start: 0.7851 (m) cc_final: 0.7620 (p) REVERT: C 381 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 489 GLN cc_start: 0.7815 (tt0) cc_final: 0.7028 (tt0) REVERT: C 493 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.2965 (m-70) REVERT: C 515 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7261 (pp) REVERT: C 524 ASN cc_start: 0.7894 (t0) cc_final: 0.7437 (p0) REVERT: C 692 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6252 (tpt170) REVERT: C 837 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7248 (ptt-90) REVERT: C 923 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8233 (t80) REVERT: D 32 SER cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (t) REVERT: D 73 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7435 (p) REVERT: D 94 SER cc_start: 0.7062 (OUTLIER) cc_final: 0.6663 (p) REVERT: D 284 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7410 (p0) outliers start: 238 outliers final: 28 residues processed: 654 average time/residue: 0.4174 time to fit residues: 401.8428 Evaluate side-chains 272 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 837 ARG 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 B residue 32 SER Chi-restraints excluded: chain B residue 37 PHE 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 160 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 923 PHE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 434 GLN A 656 ASN A 683 HIS A 754 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN A 904 GLN A1019 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN C 225 GLN C 406 GLN C 434 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS C 754 ASN C 826 GLN C 904 GLN C1019 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.114121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085547 restraints weight = 51943.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085060 restraints weight = 36349.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085262 restraints weight = 29562.299| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 23134 Z= 0.297 Angle : 0.861 11.888 31288 Z= 0.420 Chirality : 0.052 0.462 3520 Planarity : 0.006 0.072 3806 Dihedral : 17.741 163.241 5216 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.51 % Allowed : 13.88 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.15), residues: 2636 helix: -0.04 (0.14), residues: 1204 sheet: -1.96 (0.29), residues: 248 loop : -1.86 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 392 HIS 0.006 0.002 HIS A 52 PHE 0.032 0.003 PHE C 571 TYR 0.023 0.002 TYR D 40 ARG 0.007 0.001 ARG C 889 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 8) link_NAG-ASN : angle 2.49612 ( 24) link_ALPHA1-6 : bond 0.00514 ( 4) link_ALPHA1-6 : angle 2.03587 ( 12) link_BETA1-2 : bond 0.00883 ( 2) link_BETA1-2 : angle 4.22740 ( 6) link_BETA1-4 : bond 0.00815 ( 14) link_BETA1-4 : angle 3.88002 ( 42) link_ALPHA1-3 : bond 0.00791 ( 6) link_ALPHA1-3 : angle 3.95295 ( 18) hydrogen bonds : bond 0.07082 ( 998) hydrogen bonds : angle 5.30126 ( 2892) link_BETA1-6 : bond 0.01228 ( 4) link_BETA1-6 : angle 2.00372 ( 12) SS BOND : bond 0.00113 ( 6) SS BOND : angle 1.25069 ( 12) covalent geometry : bond 0.00701 (23090) covalent geometry : angle 0.83796 (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 298 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 196 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6549 (ppp) cc_final: 0.5631 (ppp) REVERT: A 64 THR cc_start: 0.4190 (OUTLIER) cc_final: 0.3544 (t) REVERT: A 127 ASN cc_start: 0.4053 (OUTLIER) cc_final: 0.3723 (t0) REVERT: A 260 TYR cc_start: 0.7382 (m-80) cc_final: 0.7066 (m-80) REVERT: A 483 ASN cc_start: 0.5284 (t0) cc_final: 0.5080 (t0) REVERT: A 493 HIS cc_start: 0.4894 (OUTLIER) cc_final: 0.3721 (m-70) REVERT: A 494 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6212 (pm20) REVERT: A 524 ASN cc_start: 0.8238 (t0) cc_final: 0.7766 (t0) REVERT: A 837 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7652 (ptt-90) REVERT: B 284 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7452 (p0) REVERT: C 64 THR cc_start: 0.4118 (OUTLIER) cc_final: 0.3470 (t) REVERT: C 65 ASN cc_start: 0.5734 (OUTLIER) cc_final: 0.5062 (t0) REVERT: C 69 LYS cc_start: 0.6499 (mmtm) cc_final: 0.6227 (tmtt) REVERT: C 230 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: C 272 THR cc_start: 0.8283 (m) cc_final: 0.7848 (p) REVERT: C 483 ASN cc_start: 0.5517 (t0) cc_final: 0.5266 (t0) REVERT: C 493 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.3582 (m-70) REVERT: C 524 ASN cc_start: 0.7970 (t0) cc_final: 0.7403 (p0) REVERT: C 530 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6071 (tt) REVERT: C 837 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7717 (ptt-90) REVERT: D 47 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7779 (mp) REVERT: D 284 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7416 (p0) outliers start: 102 outliers final: 51 residues processed: 293 average time/residue: 0.3386 time to fit residues: 157.1790 Evaluate side-chains 222 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 120 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 826 GLN B 146 GLN C 406 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.114986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086703 restraints weight = 50796.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086383 restraints weight = 35064.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086764 restraints weight = 26680.213| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23134 Z= 0.163 Angle : 0.642 9.821 31288 Z= 0.309 Chirality : 0.045 0.427 3520 Planarity : 0.005 0.058 3806 Dihedral : 16.017 130.092 5168 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.80 % Allowed : 14.68 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2636 helix: 0.79 (0.15), residues: 1212 sheet: -1.38 (0.32), residues: 226 loop : -1.45 (0.16), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 418 HIS 0.004 0.001 HIS C 493 PHE 0.027 0.001 PHE A 184 TYR 0.012 0.001 TYR D 40 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 8) link_NAG-ASN : angle 2.31811 ( 24) link_ALPHA1-6 : bond 0.00719 ( 4) link_ALPHA1-6 : angle 1.62878 ( 12) link_BETA1-2 : bond 0.00425 ( 2) link_BETA1-2 : angle 4.38219 ( 6) link_BETA1-4 : bond 0.00746 ( 14) link_BETA1-4 : angle 3.29776 ( 42) link_ALPHA1-3 : bond 0.01138 ( 6) link_ALPHA1-3 : angle 3.30710 ( 18) hydrogen bonds : bond 0.05461 ( 998) hydrogen bonds : angle 4.60159 ( 2892) link_BETA1-6 : bond 0.00408 ( 4) link_BETA1-6 : angle 1.59999 ( 12) SS BOND : bond 0.00133 ( 6) SS BOND : angle 1.29524 ( 12) covalent geometry : bond 0.00376 (23090) covalent geometry : angle 0.61786 (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 270 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 184 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6259 (ppp) cc_final: 0.5785 (ppp) REVERT: A 64 THR cc_start: 0.3337 (OUTLIER) cc_final: 0.2928 (t) REVERT: A 173 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4434 (ptp90) REVERT: A 418 TRP cc_start: 0.6910 (t-100) cc_final: 0.6627 (t-100) REVERT: A 483 ASN cc_start: 0.5248 (t0) cc_final: 0.5018 (t0) REVERT: A 493 HIS cc_start: 0.4469 (OUTLIER) cc_final: 0.3632 (m-70) REVERT: A 524 ASN cc_start: 0.8067 (t0) cc_final: 0.7504 (t0) REVERT: A 605 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7721 (mtmt) REVERT: C 230 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: C 272 THR cc_start: 0.8256 (m) cc_final: 0.7918 (p) REVERT: C 476 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7553 (tttp) REVERT: C 483 ASN cc_start: 0.5457 (t0) cc_final: 0.5197 (t0) REVERT: C 493 HIS cc_start: 0.4428 (OUTLIER) cc_final: 0.3294 (m-70) REVERT: C 524 ASN cc_start: 0.8059 (t0) cc_final: 0.7488 (t0) REVERT: C 605 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7572 (mtmt) outliers start: 86 outliers final: 43 residues processed: 258 average time/residue: 0.3734 time to fit residues: 148.8803 Evaluate side-chains 202 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 2.528 ------------------------------------------------------------------------------- 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 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 135 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 85 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 196 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 263 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 56 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 384 ASN C 406 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.116273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088042 restraints weight = 52876.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088160 restraints weight = 34896.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089073 restraints weight = 26322.004| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23134 Z= 0.111 Angle : 0.580 9.096 31288 Z= 0.275 Chirality : 0.043 0.445 3520 Planarity : 0.004 0.050 3806 Dihedral : 14.758 116.262 5143 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.61 % Allowed : 15.92 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2636 helix: 1.25 (0.15), residues: 1226 sheet: -0.89 (0.32), residues: 246 loop : -1.22 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 418 HIS 0.005 0.001 HIS C 493 PHE 0.019 0.001 PHE A 184 TYR 0.010 0.001 TYR D 40 ARG 0.005 0.000 ARG C 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 8) link_NAG-ASN : angle 1.91134 ( 24) link_ALPHA1-6 : bond 0.00726 ( 4) link_ALPHA1-6 : angle 1.68621 ( 12) link_BETA1-2 : bond 0.00383 ( 2) link_BETA1-2 : angle 4.42566 ( 6) link_BETA1-4 : bond 0.00606 ( 14) link_BETA1-4 : angle 3.15927 ( 42) link_ALPHA1-3 : bond 0.01096 ( 6) link_ALPHA1-3 : angle 3.59310 ( 18) hydrogen bonds : bond 0.04446 ( 998) hydrogen bonds : angle 4.24162 ( 2892) link_BETA1-6 : bond 0.00190 ( 4) link_BETA1-6 : angle 1.56196 ( 12) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.99337 ( 12) covalent geometry : bond 0.00235 (23090) covalent geometry : angle 0.55461 (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 236 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.8448 (t0) cc_final: 0.8186 (t0) REVERT: A 418 TRP cc_start: 0.7022 (t-100) cc_final: 0.6699 (t-100) REVERT: A 483 ASN cc_start: 0.5519 (t0) cc_final: 0.5235 (t0) REVERT: A 493 HIS cc_start: 0.4432 (OUTLIER) cc_final: 0.3537 (m-70) REVERT: A 524 ASN cc_start: 0.8188 (t0) cc_final: 0.7578 (t0) REVERT: A 605 LYS cc_start: 0.7926 (mmtp) cc_final: 0.7653 (mtmt) REVERT: B 73 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.7749 (p) REVERT: C 96 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8720 (mp) REVERT: C 230 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: C 331 ASN cc_start: 0.8398 (t0) cc_final: 0.8153 (t0) REVERT: C 476 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7520 (tttp) REVERT: C 483 ASN cc_start: 0.5666 (t0) cc_final: 0.5357 (t0) REVERT: C 493 HIS cc_start: 0.4218 (OUTLIER) cc_final: 0.3050 (m-70) REVERT: C 524 ASN cc_start: 0.8129 (t0) cc_final: 0.7512 (t0) REVERT: C 530 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6134 (tt) REVERT: C 534 MET cc_start: 0.6274 (mmt) cc_final: 0.5902 (mpp) REVERT: C 605 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7520 (mtmt) REVERT: C 734 MET cc_start: 0.7624 (mmm) cc_final: 0.7341 (mmm) REVERT: D 73 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.7747 (p) outliers start: 59 outliers final: 40 residues processed: 227 average time/residue: 0.3531 time to fit residues: 126.3632 Evaluate side-chains 200 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 180 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 9.9990 chunk 169 optimal weight: 0.0170 chunk 102 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS C 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.113121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084714 restraints weight = 52546.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084127 restraints weight = 39867.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085131 restraints weight = 31818.876| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23134 Z= 0.163 Angle : 0.624 8.419 31288 Z= 0.296 Chirality : 0.045 0.478 3520 Planarity : 0.004 0.048 3806 Dihedral : 14.143 114.726 5135 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.14 % Allowed : 16.31 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2636 helix: 1.33 (0.15), residues: 1212 sheet: -0.68 (0.33), residues: 246 loop : -1.08 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 418 HIS 0.004 0.001 HIS C 493 PHE 0.031 0.002 PHE A 184 TYR 0.015 0.001 TYR C 869 ARG 0.004 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 8) link_NAG-ASN : angle 2.48929 ( 24) link_ALPHA1-6 : bond 0.00785 ( 4) link_ALPHA1-6 : angle 1.68158 ( 12) link_BETA1-2 : bond 0.00382 ( 2) link_BETA1-2 : angle 4.28590 ( 6) link_BETA1-4 : bond 0.00641 ( 14) link_BETA1-4 : angle 2.92705 ( 42) link_ALPHA1-3 : bond 0.01033 ( 6) link_ALPHA1-3 : angle 3.72201 ( 18) hydrogen bonds : bond 0.05121 ( 998) hydrogen bonds : angle 4.28981 ( 2892) link_BETA1-6 : bond 0.00274 ( 4) link_BETA1-6 : angle 1.60659 ( 12) SS BOND : bond 0.00094 ( 6) SS BOND : angle 0.82402 ( 12) covalent geometry : bond 0.00388 (23090) covalent geometry : angle 0.60106 (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: 71 poor density : 155 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6136 (ppp) cc_final: 0.5716 (ppp) REVERT: A 173 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4289 (ptp90) REVERT: A 483 ASN cc_start: 0.5083 (t0) cc_final: 0.4778 (t0) REVERT: A 493 HIS cc_start: 0.4589 (OUTLIER) cc_final: 0.3708 (m-70) REVERT: A 524 ASN cc_start: 0.8112 (t0) cc_final: 0.7449 (t0) REVERT: A 852 MET cc_start: 0.8330 (mmm) cc_final: 0.7814 (mmp) REVERT: C 96 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8795 (mp) REVERT: C 230 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6936 (pm20) REVERT: C 483 ASN cc_start: 0.5619 (t0) cc_final: 0.5267 (t0) REVERT: C 493 HIS cc_start: 0.4315 (OUTLIER) cc_final: 0.3347 (m-70) REVERT: C 524 ASN cc_start: 0.8009 (t0) cc_final: 0.7266 (t0) REVERT: C 530 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6199 (tt) REVERT: C 534 MET cc_start: 0.6212 (mmt) cc_final: 0.5861 (mpp) REVERT: C 605 LYS cc_start: 0.7958 (mmtp) cc_final: 0.7745 (mtmt) outliers start: 71 outliers final: 51 residues processed: 212 average time/residue: 0.3666 time to fit residues: 122.3745 Evaluate side-chains 205 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 202 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 242 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS B 146 GLN ** C 437 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 = 0.3842 r_free = 0.3842 target = 0.114856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087159 restraints weight = 52036.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086783 restraints weight = 37329.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087787 restraints weight = 28350.156| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23134 Z= 0.104 Angle : 0.557 9.260 31288 Z= 0.262 Chirality : 0.043 0.474 3520 Planarity : 0.004 0.042 3806 Dihedral : 13.584 109.619 5129 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.39 % Allowed : 17.42 % Favored : 80.19 % 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: 1.52 (0.15), residues: 1228 sheet: -0.51 (0.30), residues: 292 loop : -1.10 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 156 HIS 0.021 0.001 HIS C 52 PHE 0.022 0.001 PHE A 184 TYR 0.009 0.001 TYR D 40 ARG 0.004 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 8) link_NAG-ASN : angle 2.00974 ( 24) link_ALPHA1-6 : bond 0.00707 ( 4) link_ALPHA1-6 : angle 1.66775 ( 12) link_BETA1-2 : bond 0.00435 ( 2) link_BETA1-2 : angle 4.43746 ( 6) link_BETA1-4 : bond 0.00539 ( 14) link_BETA1-4 : angle 2.76711 ( 42) link_ALPHA1-3 : bond 0.01039 ( 6) link_ALPHA1-3 : angle 3.69687 ( 18) hydrogen bonds : bond 0.04286 ( 998) hydrogen bonds : angle 4.03683 ( 2892) link_BETA1-6 : bond 0.00153 ( 4) link_BETA1-6 : angle 1.52549 ( 12) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.67243 ( 12) covalent geometry : bond 0.00222 (23090) covalent geometry : angle 0.53342 (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 225 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6147 (ppp) cc_final: 0.5764 (ppp) REVERT: A 173 ARG cc_start: 0.5007 (OUTLIER) cc_final: 0.4485 (ptp90) REVERT: A 483 ASN cc_start: 0.5254 (t0) cc_final: 0.4990 (t0) REVERT: A 493 HIS cc_start: 0.4407 (OUTLIER) cc_final: 0.3645 (m-70) REVERT: A 524 ASN cc_start: 0.8125 (t0) cc_final: 0.7423 (t0) REVERT: A 852 MET cc_start: 0.8229 (mmm) cc_final: 0.7740 (mmp) REVERT: C 96 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8700 (mp) REVERT: C 172 ILE cc_start: 0.5741 (OUTLIER) cc_final: 0.5431 (tp) REVERT: C 230 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: C 483 ASN cc_start: 0.5678 (t0) cc_final: 0.5319 (t0) REVERT: C 524 ASN cc_start: 0.8050 (t0) cc_final: 0.7311 (t0) REVERT: C 530 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.5993 (tt) REVERT: C 534 MET cc_start: 0.6034 (mmt) cc_final: 0.5802 (mpp) REVERT: C 605 LYS cc_start: 0.7879 (mmtp) cc_final: 0.7657 (mtmt) outliers start: 54 outliers final: 36 residues processed: 215 average time/residue: 0.3568 time to fit residues: 122.2811 Evaluate side-chains 192 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 54 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083154 restraints weight = 52381.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082094 restraints weight = 42358.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083048 restraints weight = 34320.839| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23134 Z= 0.206 Angle : 0.665 10.117 31288 Z= 0.317 Chirality : 0.047 0.514 3520 Planarity : 0.004 0.046 3806 Dihedral : 13.782 119.302 5126 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.70 % Allowed : 17.73 % Favored : 79.58 % 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: 0.13 (0.16), residues: 2636 helix: 1.29 (0.15), residues: 1214 sheet: -0.73 (0.32), residues: 266 loop : -0.98 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 156 HIS 0.005 0.001 HIS C 666 PHE 0.021 0.002 PHE A 184 TYR 0.016 0.002 TYR D 248 ARG 0.003 0.001 ARG C 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 8) link_NAG-ASN : angle 2.52580 ( 24) link_ALPHA1-6 : bond 0.00799 ( 4) link_ALPHA1-6 : angle 1.64055 ( 12) link_BETA1-2 : bond 0.00344 ( 2) link_BETA1-2 : angle 4.27992 ( 6) link_BETA1-4 : bond 0.00520 ( 14) link_BETA1-4 : angle 2.74711 ( 42) link_ALPHA1-3 : bond 0.00875 ( 6) link_ALPHA1-3 : angle 3.87078 ( 18) hydrogen bonds : bond 0.05721 ( 998) hydrogen bonds : angle 4.37689 ( 2892) link_BETA1-6 : bond 0.00213 ( 4) link_BETA1-6 : angle 1.77440 ( 12) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.85250 ( 12) covalent geometry : bond 0.00493 (23090) covalent geometry : angle 0.64408 (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 215 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 154 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6359 (ppp) cc_final: 0.6014 (ppp) REVERT: A 61 ARG cc_start: 0.7108 (tpp80) cc_final: 0.6842 (tmt-80) REVERT: A 173 ARG cc_start: 0.5212 (OUTLIER) cc_final: 0.4674 (ptp90) REVERT: A 483 ASN cc_start: 0.5384 (t0) cc_final: 0.5119 (t0) REVERT: A 493 HIS cc_start: 0.4767 (OUTLIER) cc_final: 0.4061 (m-70) REVERT: A 524 ASN cc_start: 0.8296 (t0) cc_final: 0.7622 (t0) REVERT: A 585 PHE cc_start: 0.4285 (t80) cc_final: 0.3747 (t80) REVERT: C 96 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8781 (mp) REVERT: C 172 ILE cc_start: 0.5644 (OUTLIER) cc_final: 0.5280 (tp) REVERT: C 230 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: C 483 ASN cc_start: 0.5565 (t0) cc_final: 0.5264 (t0) REVERT: C 524 ASN cc_start: 0.8217 (t0) cc_final: 0.7480 (t0) REVERT: C 530 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.5980 (tt) outliers start: 61 outliers final: 46 residues processed: 208 average time/residue: 0.3530 time to fit residues: 116.3262 Evaluate side-chains 193 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 42 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 244 optimal weight: 0.0170 chunk 119 optimal weight: 7.9990 chunk 152 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.113940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086230 restraints weight = 50894.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085552 restraints weight = 32368.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086459 restraints weight = 26049.989| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23134 Z= 0.108 Angle : 0.568 10.769 31288 Z= 0.269 Chirality : 0.043 0.490 3520 Planarity : 0.004 0.042 3806 Dihedral : 13.136 108.749 5126 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.30 % Allowed : 18.35 % Favored : 79.35 % 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: 0.43 (0.16), residues: 2636 helix: 1.57 (0.15), residues: 1220 sheet: -0.32 (0.31), residues: 292 loop : -0.99 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 156 HIS 0.003 0.001 HIS A 493 PHE 0.034 0.001 PHE C 184 TYR 0.008 0.001 TYR C 569 ARG 0.011 0.000 ARG A 517 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 8) link_NAG-ASN : angle 1.93308 ( 24) link_ALPHA1-6 : bond 0.00695 ( 4) link_ALPHA1-6 : angle 1.67235 ( 12) link_BETA1-2 : bond 0.00418 ( 2) link_BETA1-2 : angle 4.43244 ( 6) link_BETA1-4 : bond 0.00553 ( 14) link_BETA1-4 : angle 2.52835 ( 42) link_ALPHA1-3 : bond 0.00938 ( 6) link_ALPHA1-3 : angle 3.70988 ( 18) hydrogen bonds : bond 0.04285 ( 998) hydrogen bonds : angle 4.03538 ( 2892) link_BETA1-6 : bond 0.00114 ( 4) link_BETA1-6 : angle 1.53679 ( 12) SS BOND : bond 0.00079 ( 6) SS BOND : angle 0.64408 ( 12) covalent geometry : bond 0.00236 (23090) covalent geometry : angle 0.54661 (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 207 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7778 (mt-10) REVERT: A 41 MET cc_start: 0.6256 (ppp) cc_final: 0.5958 (ppp) REVERT: A 173 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4613 (ptp90) REVERT: A 483 ASN cc_start: 0.5641 (t0) cc_final: 0.5407 (t0) REVERT: A 493 HIS cc_start: 0.4811 (OUTLIER) cc_final: 0.4186 (m-70) REVERT: A 524 ASN cc_start: 0.8263 (t0) cc_final: 0.7685 (t0) REVERT: A 585 PHE cc_start: 0.4245 (t80) cc_final: 0.3710 (t80) REVERT: C 96 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 172 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5547 (tp) REVERT: C 230 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: C 483 ASN cc_start: 0.5433 (t0) cc_final: 0.5141 (t0) REVERT: C 524 ASN cc_start: 0.8139 (t0) cc_final: 0.7400 (t0) REVERT: C 752 ASP cc_start: 0.7564 (t0) cc_final: 0.7302 (t0) outliers start: 52 outliers final: 34 residues processed: 199 average time/residue: 0.3366 time to fit residues: 107.5010 Evaluate side-chains 181 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 120 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 260 optimal weight: 0.1980 chunk 188 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 118 optimal weight: 0.1980 chunk 62 optimal weight: 0.3980 chunk 150 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** C 331 ASN ** 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 = 0.3846 r_free = 0.3846 target = 0.114799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087391 restraints weight = 50970.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.087014 restraints weight = 33845.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087875 restraints weight = 27229.699| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23134 Z= 0.098 Angle : 0.547 11.577 31288 Z= 0.257 Chirality : 0.043 0.499 3520 Planarity : 0.004 0.048 3806 Dihedral : 12.586 101.335 5125 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.77 % Allowed : 18.79 % Favored : 79.44 % 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: 0.64 (0.16), residues: 2636 helix: 1.74 (0.15), residues: 1224 sheet: -0.16 (0.31), residues: 292 loop : -0.89 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 894 HIS 0.003 0.001 HIS A 493 PHE 0.032 0.001 PHE C 184 TYR 0.009 0.001 TYR A 869 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 8) link_NAG-ASN : angle 1.73787 ( 24) link_ALPHA1-6 : bond 0.00727 ( 4) link_ALPHA1-6 : angle 1.59870 ( 12) link_BETA1-2 : bond 0.00459 ( 2) link_BETA1-2 : angle 4.43183 ( 6) link_BETA1-4 : bond 0.00549 ( 14) link_BETA1-4 : angle 2.49936 ( 42) link_ALPHA1-3 : bond 0.00925 ( 6) link_ALPHA1-3 : angle 3.72338 ( 18) hydrogen bonds : bond 0.03775 ( 998) hydrogen bonds : angle 3.88624 ( 2892) link_BETA1-6 : bond 0.00134 ( 4) link_BETA1-6 : angle 1.48607 ( 12) SS BOND : bond 0.00084 ( 6) SS BOND : angle 0.54794 ( 12) covalent geometry : bond 0.00207 (23090) covalent geometry : angle 0.52567 (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 200 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6238 (ppp) cc_final: 0.5974 (ppp) REVERT: A 173 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.4452 (ptp90) REVERT: A 524 ASN cc_start: 0.8242 (t0) cc_final: 0.7645 (t0) REVERT: A 585 PHE cc_start: 0.4023 (t80) cc_final: 0.3485 (t80) REVERT: A 734 MET cc_start: 0.7728 (mmm) cc_final: 0.7419 (mmm) REVERT: A 852 MET cc_start: 0.8263 (mmm) cc_final: 0.8049 (mmp) REVERT: C 96 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8549 (mp) REVERT: C 172 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5556 (tp) REVERT: C 483 ASN cc_start: 0.5519 (t0) cc_final: 0.5283 (t0) REVERT: C 524 ASN cc_start: 0.8176 (t0) cc_final: 0.7474 (t0) outliers start: 40 outliers final: 27 residues processed: 194 average time/residue: 0.4381 time to fit residues: 141.8534 Evaluate side-chains 172 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 6.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 82 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.112835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084722 restraints weight = 50177.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084979 restraints weight = 33158.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085637 restraints weight = 25638.460| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23134 Z= 0.153 Angle : 0.605 11.551 31288 Z= 0.288 Chirality : 0.045 0.513 3520 Planarity : 0.004 0.052 3806 Dihedral : 12.682 105.446 5123 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.68 % Allowed : 18.92 % Favored : 79.40 % 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: 0.53 (0.16), residues: 2636 helix: 1.58 (0.15), residues: 1220 sheet: -0.42 (0.32), residues: 266 loop : -0.79 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 894 HIS 0.004 0.001 HIS C 557 PHE 0.028 0.002 PHE C 184 TYR 0.013 0.001 TYR C 869 ARG 0.004 0.000 ARG B 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 8) link_NAG-ASN : angle 2.03841 ( 24) link_ALPHA1-6 : bond 0.00758 ( 4) link_ALPHA1-6 : angle 1.62721 ( 12) link_BETA1-2 : bond 0.00358 ( 2) link_BETA1-2 : angle 4.33770 ( 6) link_BETA1-4 : bond 0.00503 ( 14) link_BETA1-4 : angle 2.47758 ( 42) link_ALPHA1-3 : bond 0.00817 ( 6) link_ALPHA1-3 : angle 3.77389 ( 18) hydrogen bonds : bond 0.04759 ( 998) hydrogen bonds : angle 4.07197 ( 2892) link_BETA1-6 : bond 0.00146 ( 4) link_BETA1-6 : angle 1.57485 ( 12) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.68519 ( 12) covalent geometry : bond 0.00364 (23090) covalent geometry : angle 0.58464 (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 182 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7859 (mt-10) REVERT: A 41 MET cc_start: 0.6320 (ppp) cc_final: 0.6086 (ppp) REVERT: A 173 ARG cc_start: 0.5125 (OUTLIER) cc_final: 0.4521 (ptp90) REVERT: A 260 TYR cc_start: 0.7386 (m-80) cc_final: 0.7004 (m-10) REVERT: A 585 PHE cc_start: 0.3951 (t80) cc_final: 0.3385 (t80) REVERT: C 38 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7738 (mt-10) REVERT: C 96 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 172 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5580 (tp) REVERT: C 524 ASN cc_start: 0.8225 (t0) cc_final: 0.7513 (t0) REVERT: C 578 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7181 (m-80) outliers start: 38 outliers final: 33 residues processed: 177 average time/residue: 0.4539 time to fit residues: 129.5321 Evaluate side-chains 173 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 891 ASP Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 227 optimal weight: 0.1980 chunk 103 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 0.0070 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.114202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086607 restraints weight = 49616.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086409 restraints weight = 34703.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087721 restraints weight = 24484.326| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23134 Z= 0.111 Angle : 0.572 11.774 31288 Z= 0.270 Chirality : 0.043 0.499 3520 Planarity : 0.004 0.053 3806 Dihedral : 12.342 100.516 5123 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.50 % Allowed : 19.50 % Favored : 79.00 % 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: 0.70 (0.17), residues: 2636 helix: 1.73 (0.15), residues: 1220 sheet: -0.13 (0.31), residues: 292 loop : -0.78 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 894 HIS 0.003 0.001 HIS A 493 PHE 0.029 0.001 PHE C 184 TYR 0.009 0.001 TYR A 869 ARG 0.003 0.000 ARG D 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 8) link_NAG-ASN : angle 1.76408 ( 24) link_ALPHA1-6 : bond 0.00698 ( 4) link_ALPHA1-6 : angle 1.66422 ( 12) link_BETA1-2 : bond 0.00397 ( 2) link_BETA1-2 : angle 4.40304 ( 6) link_BETA1-4 : bond 0.00513 ( 14) link_BETA1-4 : angle 2.36759 ( 42) link_ALPHA1-3 : bond 0.00831 ( 6) link_ALPHA1-3 : angle 3.66759 ( 18) hydrogen bonds : bond 0.04129 ( 998) hydrogen bonds : angle 3.93490 ( 2892) link_BETA1-6 : bond 0.00108 ( 4) link_BETA1-6 : angle 1.50452 ( 12) SS BOND : bond 0.00088 ( 6) SS BOND : angle 0.62366 ( 12) covalent geometry : bond 0.00250 (23090) covalent geometry : angle 0.55232 (31162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6966.32 seconds wall clock time: 124 minutes 21.58 seconds (7461.58 seconds total)