Starting phenix.real_space_refine on Sun Oct 12 15:30:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxl_37910/10_2025/8wxl_37910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxl_37910/10_2025/8wxl_37910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wxl_37910/10_2025/8wxl_37910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxl_37910/10_2025/8wxl_37910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wxl_37910/10_2025/8wxl_37910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxl_37910/10_2025/8wxl_37910.map" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16089 2.51 5 N 4113 2.21 5 O 4869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25179 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8155 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 6 Chain: "D" 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: "E" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 8155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8155 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 6 Chain: "C" 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: "F" 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: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "G" Number of atoms: 8155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8155 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 6 Chain: "H" 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: "I" 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: "G" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.08, per 1000 atoms: 0.24 Number of scatterers: 25179 At special positions: 0 Unit cell: (135.675, 139.695, 170.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4869 8.00 N 4113 7.00 C 16089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.04 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.04 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.04 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.02 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 290 " - pdb=" SG CYS G 300 " distance=2.03 Simple disulfide: pdb=" SG CYS G 335 " - pdb=" SG CYS G 360 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 431 " distance=2.03 Simple disulfide: pdb=" SG CYS G 390 " - pdb=" SG CYS G 523 " distance=2.03 Simple disulfide: pdb=" SG CYS G 479 " - pdb=" SG CYS G 486 " distance=2.03 Simple disulfide: pdb=" SG CYS G 536 " - pdb=" SG CYS G 588 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 647 " distance=2.04 Simple disulfide: pdb=" SG CYS G 660 " - pdb=" SG CYS G 669 " distance=2.04 Simple disulfide: pdb=" SG CYS G 736 " - pdb=" SG CYS G 758 " distance=2.02 Simple disulfide: pdb=" SG CYS G 741 " - pdb=" SG CYS G 747 " distance=2.03 Simple disulfide: pdb=" SG CYS G1030 " - pdb=" SG CYS G1041 " distance=2.03 Simple disulfide: pdb=" SG CYS G1080 " - pdb=" SG CYS G1124 " 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=9, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1300 " - " ASN A 61 " " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 655 " " NAG A1304 " - " ASN A 707 " " NAG A1305 " - " ASN A1072 " " NAG A1306 " - " ASN A1096 " " NAG A1307 " - " ASN A1132 " " NAG A1308 " - " ASN A 342 " " NAG A1309 " - " ASN A 353 " " NAG A1310 " - " ASN A 281 " " NAG A1311 " - " ASN A 614 " " NAG A1312 " - " ASN A 330 " " NAG B1300 " - " ASN B 61 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 655 " " NAG B1304 " - " ASN B 707 " " NAG B1305 " - " ASN B1072 " " NAG B1306 " - " ASN B1096 " " NAG B1307 " - " ASN B1132 " " NAG B1308 " - " ASN B 342 " " NAG B1309 " - " ASN B 353 " " NAG B1310 " - " ASN B 281 " " NAG B1311 " - " ASN B 614 " " NAG B1312 " - " ASN B 330 " " NAG C 1 " - " ASN B 715 " " NAG D 1 " - " ASN A 715 " " NAG E 1 " - " ASN A 799 " " NAG F 1 " - " ASN B 799 " " NAG G1300 " - " ASN G 61 " " NAG G1301 " - " ASN G 122 " " NAG G1302 " - " ASN G 165 " " NAG G1303 " - " ASN G 655 " " NAG G1304 " - " ASN G 707 " " NAG G1305 " - " ASN G1072 " " NAG G1306 " - " ASN G1096 " " NAG G1307 " - " ASN G1132 " " NAG G1308 " - " ASN G 342 " " NAG G1309 " - " ASN G 353 " " NAG G1310 " - " ASN G 281 " " NAG G1311 " - " ASN G 614 " " NAG G1312 " - " ASN G 330 " " NAG H 1 " - " ASN G 715 " " NAG I 1 " - " ASN G 799 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 974.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 39 sheets defined 26.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.031A pdb=" N GLY A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.602A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 removed outlier: 4.201A pdb=" N ASN A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 388 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 389 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.965A pdb=" N SER A 407 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 614 through 625 removed outlier: 3.607A pdb=" N VAL A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.780A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.549A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.526A pdb=" N GLY A 887 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 908 Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.322A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 938 removed outlier: 3.550A pdb=" N ILE A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 942 removed outlier: 3.751A pdb=" N ALA A 942 " --> pdb=" O THR A 939 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 939 through 942' Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.979A pdb=" N VAL A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.667A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 3.912A pdb=" N GLU A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A1015 " --> pdb=" O ILE A1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.032A pdb=" N GLY B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.602A pdb=" N TYR B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 removed outlier: 4.201A pdb=" N ASN B 387 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 388 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.965A pdb=" N SER B 407 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.606A pdb=" N VAL B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 742 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.779A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 776 " --> pdb=" O GLN B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.549A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.527A pdb=" N GLY B 887 " --> pdb=" O TRP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 908 Processing helix chain 'B' and resid 910 through 917 removed outlier: 4.323A pdb=" N LEU B 914 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 removed outlier: 3.551A pdb=" N ILE B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 942 removed outlier: 3.751A pdb=" N ALA B 942 " --> pdb=" O THR B 939 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 939 through 942' Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.979A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.667A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 3.911A pdb=" N GLU B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B1015 " --> pdb=" O ILE B1011 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.032A pdb=" N GLY G 158 " --> pdb=" O SER G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 303 Processing helix chain 'G' and resid 336 through 341 Processing helix chain 'G' and resid 364 through 371 removed outlier: 3.602A pdb=" N TYR G 368 " --> pdb=" O TYR G 364 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 389 removed outlier: 4.201A pdb=" N ASN G 387 " --> pdb=" O THR G 384 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP G 388 " --> pdb=" O LYS G 385 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU G 389 " --> pdb=" O LEU G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 409 removed outlier: 3.965A pdb=" N SER G 407 " --> pdb=" O ASN G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 421 Processing helix chain 'G' and resid 614 through 625 removed outlier: 3.607A pdb=" N VAL G 618 " --> pdb=" O ASN G 614 " (cutoff:3.500A) Processing helix chain 'G' and resid 735 through 742 Processing helix chain 'G' and resid 744 through 752 Processing helix chain 'G' and resid 753 through 755 No H-bonds generated for 'chain 'G' and resid 753 through 755' Processing helix chain 'G' and resid 756 through 781 removed outlier: 3.780A pdb=" N GLN G 760 " --> pdb=" O SER G 756 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR G 776 " --> pdb=" O GLN G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 removed outlier: 3.549A pdb=" N VAL G 824 " --> pdb=" O LEU G 820 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 882 Processing helix chain 'G' and resid 884 through 888 removed outlier: 3.526A pdb=" N GLY G 887 " --> pdb=" O TRP G 884 " (cutoff:3.500A) Processing helix chain 'G' and resid 895 through 908 Processing helix chain 'G' and resid 910 through 917 removed outlier: 4.322A pdb=" N LEU G 914 " --> pdb=" O THR G 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 917 through 938 removed outlier: 3.551A pdb=" N ILE G 932 " --> pdb=" O ALA G 928 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN G 933 " --> pdb=" O ILE G 929 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP G 934 " --> pdb=" O GLY G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 939 through 942 removed outlier: 3.750A pdb=" N ALA G 942 " --> pdb=" O THR G 939 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 939 through 942' Processing helix chain 'G' and resid 943 through 963 removed outlier: 3.979A pdb=" N VAL G 949 " --> pdb=" O LYS G 945 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL G 950 " --> pdb=" O LEU G 946 " (cutoff:3.500A) Processing helix chain 'G' and resid 964 through 966 No H-bonds generated for 'chain 'G' and resid 964 through 966' Processing helix chain 'G' and resid 974 through 982 removed outlier: 3.667A pdb=" N ILE G 978 " --> pdb=" O VAL G 974 " (cutoff:3.500A) Processing helix chain 'G' and resid 983 through 1031 removed outlier: 3.912A pdb=" N GLU G 988 " --> pdb=" O PRO G 984 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL G 989 " --> pdb=" O PRO G 985 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN G 990 " --> pdb=" O GLU G 986 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG G 993 " --> pdb=" O VAL G 989 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU G 994 " --> pdb=" O GLN G 990 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU G1015 " --> pdb=" O ILE G1011 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 268 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 205 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS A 207 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 36 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.113A pdb=" N ASP A 286 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.473A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 310 through 318 removed outlier: 6.937A pdb=" N VAL A 593 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN A 316 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY A 591 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 324 through 327 Processing sheet with id=6, first strand: chain 'A' and resid 353 through 357 Processing sheet with id=7, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=8, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=9, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.080A pdb=" N THR A 694 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN A 656 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.705A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.705A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.591A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 1118 through 1119 Processing sheet with id=14, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.789A pdb=" N ASN B 61 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR B 268 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER B 205 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS B 207 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N LEU B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 36 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.112A pdb=" N ASP B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.473A pdb=" N GLY B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 310 through 318 removed outlier: 6.937A pdb=" N VAL B 593 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN B 316 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY B 591 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 324 through 327 Processing sheet with id=19, first strand: chain 'B' and resid 353 through 357 Processing sheet with id=20, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=21, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=22, first strand: chain 'B' and resid 652 through 658 removed outlier: 5.080A pdb=" N THR B 694 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B 656 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.705A pdb=" N SER B 709 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR B1074 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 711 " --> pdb=" O ASN B1072 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1072 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.705A pdb=" N SER B 709 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR B1074 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 711 " --> pdb=" O ASN B1072 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1072 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.591A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'B' and resid 1118 through 1119 Processing sheet with id=27, first strand: chain 'G' and resid 25 through 30 removed outlier: 7.789A pdb=" N ASN G 61 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR G 268 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER G 205 " --> pdb=" O PRO G 224 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS G 207 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU G 222 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL G 36 " --> pdb=" O LEU G 222 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 47 through 55 removed outlier: 4.113A pdb=" N ASP G 286 " --> pdb=" O LYS G 277 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'G' and resid 84 through 85 removed outlier: 4.473A pdb=" N GLY G 103 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN G 121 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'G' and resid 310 through 318 removed outlier: 6.936A pdb=" N VAL G 593 " --> pdb=" O THR G 314 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN G 316 " --> pdb=" O GLY G 591 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY G 591 " --> pdb=" O ASN G 316 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY G 592 " --> pdb=" O GLN G 611 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'G' and resid 324 through 327 Processing sheet with id=32, first strand: chain 'G' and resid 353 through 357 Processing sheet with id=33, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=34, first strand: chain 'G' and resid 472 through 473 Processing sheet with id=35, first strand: chain 'G' and resid 652 through 658 removed outlier: 5.081A pdb=" N THR G 694 " --> pdb=" O VAL G 654 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN G 656 " --> pdb=" O THR G 694 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'G' and resid 709 through 726 removed outlier: 6.705A pdb=" N SER G 709 " --> pdb=" O THR G1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR G1074 " --> pdb=" O SER G 709 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA G 711 " --> pdb=" O ASN G1072 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN G1072 " --> pdb=" O ALA G 711 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU G1070 " --> pdb=" O PRO G 713 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET G1048 " --> pdb=" O VAL G1063 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR G1065 " --> pdb=" O HIS G1046 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS G1046 " --> pdb=" O TYR G1065 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'G' and resid 709 through 726 removed outlier: 6.705A pdb=" N SER G 709 " --> pdb=" O THR G1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR G1074 " --> pdb=" O SER G 709 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA G 711 " --> pdb=" O ASN G1072 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN G1072 " --> pdb=" O ALA G 711 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU G1070 " --> pdb=" O PRO G 713 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G1074 " --> pdb=" O SER G1095 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA G1076 " --> pdb=" O PHE G1093 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE G1093 " --> pdb=" O ALA G1076 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'G' and resid 731 through 734 removed outlier: 4.591A pdb=" N LYS G 731 " --> pdb=" O LEU G 859 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 1118 through 1119 1035 hydrogen bonds defined for protein. 2835 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: 6.55 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7926 1.34 - 1.46: 6043 1.46 - 1.58: 11669 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 25773 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 NAG G1303 " pdb=" O5 NAG G1303 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.82e+00 bond pdb=" CB CYS G 736 " pdb=" SG CYS G 736 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 25768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 33379 1.25 - 2.50: 1361 2.50 - 3.75: 285 3.75 - 5.00: 35 5.00 - 6.25: 19 Bond angle restraints: 35079 Sorted by residual: angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 111.91 106.57 5.34 8.90e-01 1.26e+00 3.60e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 111.91 106.57 5.34 8.90e-01 1.26e+00 3.60e+01 angle pdb=" N VAL G 130 " pdb=" CA VAL G 130 " pdb=" C VAL G 130 " ideal model delta sigma weight residual 111.91 106.59 5.32 8.90e-01 1.26e+00 3.57e+01 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.82 127.07 -4.25 1.42e+00 4.96e-01 8.98e+00 angle pdb=" C ILE G 197 " pdb=" N ASP G 198 " pdb=" CA ASP G 198 " ideal model delta sigma weight residual 122.82 127.06 -4.24 1.42e+00 4.96e-01 8.92e+00 ... (remaining 35074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.16: 15206 23.16 - 46.33: 661 46.33 - 69.49: 90 69.49 - 92.65: 18 92.65 - 115.81: 9 Dihedral angle restraints: 15984 sinusoidal: 6894 harmonic: 9090 Sorted by residual: dihedral pdb=" CB CYS B1080 " pdb=" SG CYS B1080 " pdb=" SG CYS B1124 " pdb=" CB CYS B1124 " ideal model delta sinusoidal sigma weight residual -86.00 -139.01 53.01 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -139.00 53.00 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS G1080 " pdb=" SG CYS G1080 " pdb=" SG CYS G1124 " pdb=" CB CYS G1124 " ideal model delta sinusoidal sigma weight residual -86.00 -138.98 52.98 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 15981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3661 0.082 - 0.164: 443 0.164 - 0.246: 9 0.246 - 0.328: 0 0.328 - 0.410: 3 Chirality restraints: 4116 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 707 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C1 NAG G1304 " pdb=" ND2 ASN G 707 " pdb=" C2 NAG G1304 " pdb=" O5 NAG G1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 707 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 4113 not shown) Planarity restraints: 4497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 904 " 0.015 2.00e-02 2.50e+03 1.81e-02 5.70e+00 pdb=" CG PHE B 904 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 904 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 904 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 904 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 904 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 904 " 0.015 2.00e-02 2.50e+03 1.79e-02 5.62e+00 pdb=" CG PHE A 904 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 904 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 904 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 904 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 904 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 904 " -0.015 2.00e-02 2.50e+03 1.79e-02 5.59e+00 pdb=" CG PHE G 904 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE G 904 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE G 904 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE G 904 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE G 904 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE G 904 " -0.000 2.00e-02 2.50e+03 ... (remaining 4494 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 78 2.47 - 3.07: 16613 3.07 - 3.68: 34347 3.68 - 4.29: 51537 4.29 - 4.90: 88991 Nonbonded interactions: 191566 Sorted by model distance: nonbonded pdb=" O ALA B 704 " pdb=" OE1 GLN G 893 " model vdw 1.858 3.040 nonbonded pdb=" O ALA A 704 " pdb=" OE1 GLN B 893 " model vdw 1.864 3.040 nonbonded pdb=" OE1 GLN A 893 " pdb=" O ALA G 704 " model vdw 1.866 3.040 nonbonded pdb=" NZ LYS G 809 " pdb=" OG SER G 811 " model vdw 2.136 3.120 nonbonded pdb=" NZ LYS A 809 " pdb=" OG SER A 811 " model vdw 2.136 3.120 ... (remaining 191561 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.950 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 0.005 0.078 25872 Z= 0.204 Angle : 0.625 11.231 35310 Z= 0.324 Chirality : 0.048 0.410 4116 Planarity : 0.004 0.037 4452 Dihedral : 13.063 115.813 10017 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3078 helix: 1.58 (0.20), residues: 711 sheet: 1.04 (0.19), residues: 717 loop : -1.35 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1037 TYR 0.018 0.001 TYR B1065 PHE 0.041 0.001 PHE B 904 TRP 0.022 0.002 TRP B 884 HIS 0.005 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00456 (25773) covalent geometry : angle 0.59383 (35079) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.50801 ( 78) hydrogen bonds : bond 0.11983 ( 999) hydrogen bonds : angle 6.09065 ( 2835) Misc. bond : bond 0.00239 ( 9) link_BETA1-4 : bond 0.00500 ( 6) link_BETA1-4 : angle 0.88282 ( 18) link_NAG-ASN : bond 0.00406 ( 45) link_NAG-ASN : angle 3.02880 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7593 (mp10) cc_final: 0.7362 (mp10) REVERT: A 121 ASN cc_start: 0.7480 (m-40) cc_final: 0.7114 (t0) REVERT: A 140 PHE cc_start: 0.8115 (p90) cc_final: 0.7262 (p90) REVERT: A 359 ASN cc_start: 0.8872 (m-40) cc_final: 0.8621 (m-40) REVERT: A 377 LYS cc_start: 0.8555 (tppp) cc_final: 0.8349 (tppp) REVERT: A 623 HIS cc_start: 0.8161 (m-70) cc_final: 0.7899 (m-70) REVERT: A 626 GLN cc_start: 0.8272 (mt0) cc_final: 0.7989 (mt0) REVERT: A 866 GLU cc_start: 0.8351 (mp0) cc_final: 0.8036 (mp0) REVERT: B 118 LEU cc_start: 0.8345 (tp) cc_final: 0.8143 (tm) REVERT: B 140 PHE cc_start: 0.8002 (p90) cc_final: 0.7681 (p90) REVERT: B 171 VAL cc_start: 0.8803 (p) cc_final: 0.8587 (t) REVERT: B 377 LYS cc_start: 0.8395 (tppp) cc_final: 0.8171 (tppp) REVERT: B 463 PHE cc_start: 0.8974 (m-10) cc_final: 0.8624 (m-10) REVERT: B 623 HIS cc_start: 0.8073 (m-70) cc_final: 0.7855 (m-70) REVERT: B 626 GLN cc_start: 0.8245 (mt0) cc_final: 0.8042 (mt0) REVERT: G 121 ASN cc_start: 0.7496 (m-40) cc_final: 0.6949 (t0) REVERT: G 140 PHE cc_start: 0.8095 (p90) cc_final: 0.7674 (p90) REVERT: G 584 ASP cc_start: 0.8266 (m-30) cc_final: 0.8048 (m-30) REVERT: G 623 HIS cc_start: 0.7939 (m-70) cc_final: 0.7679 (m-70) REVERT: G 866 GLU cc_start: 0.8276 (mp0) cc_final: 0.8042 (mp0) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.6224 time to fit residues: 203.8811 Evaluate side-chains 166 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0040 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A1008 GLN G 359 ASN G 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076949 restraints weight = 44147.163| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.98 r_work: 0.2898 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25872 Z= 0.154 Angle : 0.607 10.660 35310 Z= 0.316 Chirality : 0.048 0.391 4116 Planarity : 0.004 0.051 4452 Dihedral : 8.472 100.799 4410 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.88 % Allowed : 6.26 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3078 helix: 1.69 (0.20), residues: 717 sheet: 1.19 (0.18), residues: 747 loop : -1.37 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 632 TYR 0.018 0.001 TYR A1065 PHE 0.023 0.001 PHE A 904 TRP 0.014 0.001 TRP G 884 HIS 0.006 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00362 (25773) covalent geometry : angle 0.58028 (35079) SS BOND : bond 0.00334 ( 39) SS BOND : angle 1.42294 ( 78) hydrogen bonds : bond 0.06221 ( 999) hydrogen bonds : angle 5.22733 ( 2835) Misc. bond : bond 0.00307 ( 9) link_BETA1-4 : bond 0.00339 ( 6) link_BETA1-4 : angle 0.91303 ( 18) link_NAG-ASN : bond 0.00317 ( 45) link_NAG-ASN : angle 2.76694 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7743 (m-40) cc_final: 0.7187 (t0) REVERT: A 140 PHE cc_start: 0.8080 (p90) cc_final: 0.7198 (p90) REVERT: A 200 TYR cc_start: 0.8249 (m-80) cc_final: 0.8021 (m-80) REVERT: A 359 ASN cc_start: 0.8823 (m-40) cc_final: 0.8621 (m-40) REVERT: A 377 LYS cc_start: 0.8574 (tppp) cc_final: 0.8331 (tppp) REVERT: A 623 HIS cc_start: 0.8209 (m-70) cc_final: 0.7890 (m-70) REVERT: A 626 GLN cc_start: 0.8122 (mt0) cc_final: 0.7897 (mt0) REVERT: A 644 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8184 (mtm180) REVERT: A 866 GLU cc_start: 0.8425 (mp0) cc_final: 0.8125 (mp0) REVERT: A 981 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8043 (ptp90) REVERT: B 140 PHE cc_start: 0.8004 (p90) cc_final: 0.7640 (p90) REVERT: B 164 ASN cc_start: 0.7618 (t0) cc_final: 0.7149 (t0) REVERT: B 171 VAL cc_start: 0.8769 (p) cc_final: 0.8501 (t) REVERT: B 377 LYS cc_start: 0.8421 (tppp) cc_final: 0.8168 (tppp) REVERT: B 463 PHE cc_start: 0.8840 (m-10) cc_final: 0.8572 (m-10) REVERT: B 623 HIS cc_start: 0.8243 (m-70) cc_final: 0.8039 (m-70) REVERT: B 626 GLN cc_start: 0.8172 (mt0) cc_final: 0.7967 (mt0) REVERT: G 121 ASN cc_start: 0.7594 (m-40) cc_final: 0.6944 (t0) REVERT: G 140 PHE cc_start: 0.8105 (p90) cc_final: 0.7648 (p90) REVERT: G 623 HIS cc_start: 0.8140 (m-70) cc_final: 0.7854 (m-70) outliers start: 24 outliers final: 10 residues processed: 188 average time/residue: 0.5167 time to fit residues: 116.5471 Evaluate side-chains 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 1090 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN G 338 HIS G 359 ASN G 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075510 restraints weight = 44007.838| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.98 r_work: 0.2872 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25872 Z= 0.186 Angle : 0.632 10.554 35310 Z= 0.328 Chirality : 0.049 0.386 4116 Planarity : 0.004 0.040 4452 Dihedral : 8.258 96.828 4410 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.39 % Allowed : 7.98 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 3078 helix: 1.74 (0.20), residues: 696 sheet: 1.10 (0.18), residues: 747 loop : -1.46 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 345 TYR 0.018 0.001 TYR A1065 PHE 0.026 0.002 PHE B 937 TRP 0.011 0.001 TRP B 884 HIS 0.007 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00456 (25773) covalent geometry : angle 0.60398 (35079) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.52234 ( 78) hydrogen bonds : bond 0.06801 ( 999) hydrogen bonds : angle 5.18171 ( 2835) Misc. bond : bond 0.00128 ( 9) link_BETA1-4 : bond 0.00341 ( 6) link_BETA1-4 : angle 1.09209 ( 18) link_NAG-ASN : bond 0.00308 ( 45) link_NAG-ASN : angle 2.85758 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.947 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 121 ASN cc_start: 0.7819 (m-40) cc_final: 0.7216 (t0) REVERT: A 133 PHE cc_start: 0.8156 (m-80) cc_final: 0.6947 (m-80) REVERT: A 140 PHE cc_start: 0.8144 (p90) cc_final: 0.7310 (p90) REVERT: A 177 MET cc_start: 0.4559 (mmt) cc_final: 0.3314 (pp-130) REVERT: A 200 TYR cc_start: 0.8258 (m-80) cc_final: 0.8021 (m-80) REVERT: A 346 PHE cc_start: 0.7737 (m-80) cc_final: 0.7368 (m-80) REVERT: A 359 ASN cc_start: 0.8847 (m-40) cc_final: 0.8615 (m-40) REVERT: A 623 HIS cc_start: 0.8246 (m-70) cc_final: 0.7966 (m-70) REVERT: A 626 GLN cc_start: 0.8165 (mt0) cc_final: 0.7912 (mt0) REVERT: A 644 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.8198 (mtm180) REVERT: A 866 GLU cc_start: 0.8420 (mp0) cc_final: 0.8110 (mp0) REVERT: A 981 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8041 (ptp90) REVERT: B 135 PHE cc_start: 0.7734 (m-80) cc_final: 0.7503 (m-80) REVERT: B 140 PHE cc_start: 0.8030 (p90) cc_final: 0.7637 (p90) REVERT: B 164 ASN cc_start: 0.7561 (t0) cc_final: 0.7106 (t0) REVERT: B 171 VAL cc_start: 0.8798 (p) cc_final: 0.8511 (t) REVERT: B 377 LYS cc_start: 0.8410 (tppp) cc_final: 0.8139 (tppp) REVERT: B 452 TYR cc_start: 0.7754 (p90) cc_final: 0.7552 (p90) REVERT: B 463 PHE cc_start: 0.8794 (m-10) cc_final: 0.8500 (m-10) REVERT: B 626 GLN cc_start: 0.8218 (mt0) cc_final: 0.8013 (mt0) REVERT: G 121 ASN cc_start: 0.7598 (m-40) cc_final: 0.6861 (t0) REVERT: G 140 PHE cc_start: 0.8150 (p90) cc_final: 0.7686 (p90) REVERT: G 164 ASN cc_start: 0.7619 (t0) cc_final: 0.7277 (t0) REVERT: G 337 PHE cc_start: 0.9167 (m-80) cc_final: 0.8951 (m-80) REVERT: G 623 HIS cc_start: 0.8145 (m-70) cc_final: 0.7885 (m-70) REVERT: G 738 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8301 (tmm) outliers start: 38 outliers final: 20 residues processed: 197 average time/residue: 0.5170 time to fit residues: 122.4682 Evaluate side-chains 185 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 569 ASP Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 1090 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 187 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 280 optimal weight: 0.3980 chunk 226 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 217 GLN B 338 HIS G 217 GLN G 338 HIS G 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.128252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076261 restraints weight = 43822.447| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.96 r_work: 0.2897 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25872 Z= 0.154 Angle : 0.606 10.489 35310 Z= 0.313 Chirality : 0.047 0.368 4116 Planarity : 0.004 0.039 4452 Dihedral : 8.070 94.184 4410 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.50 % Allowed : 9.07 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3078 helix: 1.79 (0.20), residues: 693 sheet: 1.07 (0.18), residues: 747 loop : -1.45 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 632 TYR 0.017 0.001 TYR A1065 PHE 0.029 0.001 PHE B 937 TRP 0.009 0.001 TRP A 631 HIS 0.005 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00368 (25773) covalent geometry : angle 0.57725 (35079) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.50893 ( 78) hydrogen bonds : bond 0.06189 ( 999) hydrogen bonds : angle 5.07203 ( 2835) Misc. bond : bond 0.00093 ( 9) link_BETA1-4 : bond 0.00343 ( 6) link_BETA1-4 : angle 1.00162 ( 18) link_NAG-ASN : bond 0.00319 ( 45) link_NAG-ASN : angle 2.83378 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7882 (m-40) cc_final: 0.7294 (t0) REVERT: A 133 PHE cc_start: 0.8225 (m-80) cc_final: 0.7005 (m-80) REVERT: A 140 PHE cc_start: 0.8164 (p90) cc_final: 0.7346 (p90) REVERT: A 177 MET cc_start: 0.4800 (mmt) cc_final: 0.3503 (pp-130) REVERT: A 200 TYR cc_start: 0.8251 (m-80) cc_final: 0.8028 (m-80) REVERT: A 359 ASN cc_start: 0.8878 (m-40) cc_final: 0.8620 (m-40) REVERT: A 623 HIS cc_start: 0.8193 (m-70) cc_final: 0.7864 (m-70) REVERT: A 626 GLN cc_start: 0.8155 (mt0) cc_final: 0.7856 (mt0) REVERT: A 644 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8177 (mtm180) REVERT: A 866 GLU cc_start: 0.8408 (mp0) cc_final: 0.8123 (mp0) REVERT: A 981 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8006 (ptp90) REVERT: B 135 PHE cc_start: 0.7717 (m-80) cc_final: 0.7455 (m-80) REVERT: B 140 PHE cc_start: 0.8040 (p90) cc_final: 0.7657 (p90) REVERT: B 164 ASN cc_start: 0.7536 (t0) cc_final: 0.7076 (t0) REVERT: B 171 VAL cc_start: 0.8761 (p) cc_final: 0.8469 (t) REVERT: B 377 LYS cc_start: 0.8448 (tppp) cc_final: 0.8170 (tppp) REVERT: B 463 PHE cc_start: 0.8815 (m-10) cc_final: 0.8552 (m-10) REVERT: B 626 GLN cc_start: 0.8217 (mt0) cc_final: 0.8013 (mt0) REVERT: B 644 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8091 (mtm180) REVERT: B 898 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8801 (mtp) REVERT: B 981 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7785 (ptt180) REVERT: G 121 ASN cc_start: 0.7700 (m-40) cc_final: 0.7023 (t0) REVERT: G 140 PHE cc_start: 0.8142 (p90) cc_final: 0.7682 (p90) REVERT: G 164 ASN cc_start: 0.7685 (t0) cc_final: 0.7392 (t0) REVERT: G 346 PHE cc_start: 0.7693 (m-80) cc_final: 0.6931 (m-80) REVERT: G 450 TYR cc_start: 0.7183 (m-80) cc_final: 0.5890 (m-10) REVERT: G 623 HIS cc_start: 0.8120 (m-70) cc_final: 0.7874 (m-70) REVERT: G 738 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8961 (tpp) REVERT: G 981 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7794 (ptt180) outliers start: 41 outliers final: 22 residues processed: 199 average time/residue: 0.5357 time to fit residues: 127.2913 Evaluate side-chains 187 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain G residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 231 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 338 HIS B 134 GLN B 338 HIS G 134 GLN G 338 HIS G 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.129566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077907 restraints weight = 43772.255| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.97 r_work: 0.2908 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25872 Z= 0.119 Angle : 0.580 10.362 35310 Z= 0.297 Chirality : 0.046 0.346 4116 Planarity : 0.004 0.038 4452 Dihedral : 7.711 89.732 4410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.43 % Allowed : 10.14 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3078 helix: 1.75 (0.20), residues: 711 sheet: 1.17 (0.18), residues: 747 loop : -1.38 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 345 TYR 0.015 0.001 TYR G1065 PHE 0.028 0.001 PHE B 937 TRP 0.008 0.001 TRP G 631 HIS 0.004 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00264 (25773) covalent geometry : angle 0.55286 (35079) SS BOND : bond 0.00315 ( 39) SS BOND : angle 1.25208 ( 78) hydrogen bonds : bond 0.05212 ( 999) hydrogen bonds : angle 4.88182 ( 2835) Misc. bond : bond 0.00084 ( 9) link_BETA1-4 : bond 0.00283 ( 6) link_BETA1-4 : angle 0.86958 ( 18) link_NAG-ASN : bond 0.00356 ( 45) link_NAG-ASN : angle 2.72330 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7868 (m-40) cc_final: 0.7297 (t0) REVERT: A 140 PHE cc_start: 0.8130 (p90) cc_final: 0.7334 (p90) REVERT: A 177 MET cc_start: 0.4941 (mmt) cc_final: 0.3668 (pp-130) REVERT: A 215 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: A 346 PHE cc_start: 0.7785 (m-80) cc_final: 0.7233 (m-80) REVERT: A 359 ASN cc_start: 0.8893 (m-40) cc_final: 0.8627 (m-40) REVERT: A 623 HIS cc_start: 0.8189 (m-70) cc_final: 0.7864 (m-70) REVERT: A 626 GLN cc_start: 0.8154 (mt0) cc_final: 0.7868 (mt0) REVERT: A 644 ARG cc_start: 0.8730 (mtp-110) cc_final: 0.8157 (mtm180) REVERT: A 866 GLU cc_start: 0.8393 (mp0) cc_final: 0.8122 (mp0) REVERT: B 135 PHE cc_start: 0.7711 (m-80) cc_final: 0.7404 (m-80) REVERT: B 140 PHE cc_start: 0.8044 (p90) cc_final: 0.7659 (p90) REVERT: B 164 ASN cc_start: 0.7532 (t0) cc_final: 0.7060 (t0) REVERT: B 171 VAL cc_start: 0.8735 (p) cc_final: 0.8443 (t) REVERT: B 177 MET cc_start: 0.4704 (OUTLIER) cc_final: 0.3016 (pp-130) REVERT: B 377 LYS cc_start: 0.8458 (tppp) cc_final: 0.8178 (tppp) REVERT: B 450 TYR cc_start: 0.6964 (m-80) cc_final: 0.6048 (m-10) REVERT: B 569 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 626 GLN cc_start: 0.8179 (mt0) cc_final: 0.7970 (mt0) REVERT: B 981 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7774 (ptt180) REVERT: B 986 GLU cc_start: 0.8417 (mp0) cc_final: 0.7702 (mp0) REVERT: B 1048 MET cc_start: 0.9471 (ptm) cc_final: 0.9213 (ptp) REVERT: G 121 ASN cc_start: 0.7757 (m-40) cc_final: 0.7107 (t0) REVERT: G 140 PHE cc_start: 0.8116 (p90) cc_final: 0.7663 (p90) REVERT: G 345 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7998 (tpp-160) REVERT: G 450 TYR cc_start: 0.7167 (m-80) cc_final: 0.5608 (m-10) REVERT: G 569 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8132 (t0) REVERT: G 623 HIS cc_start: 0.8096 (m-70) cc_final: 0.7846 (m-70) outliers start: 39 outliers final: 20 residues processed: 189 average time/residue: 0.5083 time to fit residues: 115.4783 Evaluate side-chains 173 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 569 ASP Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Chi-restraints excluded: chain G residue 1090 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 310 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 282 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 338 HIS B 134 GLN B 338 HIS G 134 GLN G 338 HIS G 538 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078337 restraints weight = 44023.600| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.97 r_work: 0.2924 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25872 Z= 0.117 Angle : 0.577 10.124 35310 Z= 0.294 Chirality : 0.046 0.338 4116 Planarity : 0.004 0.038 4452 Dihedral : 7.435 86.070 4410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.35 % Allowed : 10.57 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3078 helix: 1.81 (0.21), residues: 708 sheet: 1.22 (0.18), residues: 747 loop : -1.38 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 345 TYR 0.016 0.001 TYR G1065 PHE 0.027 0.001 PHE B 937 TRP 0.008 0.001 TRP A 631 HIS 0.004 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00260 (25773) covalent geometry : angle 0.55078 (35079) SS BOND : bond 0.00289 ( 39) SS BOND : angle 1.22848 ( 78) hydrogen bonds : bond 0.05065 ( 999) hydrogen bonds : angle 4.81615 ( 2835) Misc. bond : bond 0.00104 ( 9) link_BETA1-4 : bond 0.00399 ( 6) link_BETA1-4 : angle 0.89976 ( 18) link_NAG-ASN : bond 0.00345 ( 45) link_NAG-ASN : angle 2.67831 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7794 (mtp85) REVERT: A 121 ASN cc_start: 0.7868 (m-40) cc_final: 0.7363 (t0) REVERT: A 140 PHE cc_start: 0.8138 (p90) cc_final: 0.7346 (p90) REVERT: A 177 MET cc_start: 0.4917 (mmt) cc_final: 0.3765 (pp-130) REVERT: A 346 PHE cc_start: 0.7730 (m-80) cc_final: 0.7103 (m-80) REVERT: A 359 ASN cc_start: 0.8955 (m-40) cc_final: 0.8703 (m-40) REVERT: A 450 TYR cc_start: 0.7111 (m-80) cc_final: 0.6082 (m-10) REVERT: A 623 HIS cc_start: 0.8215 (m-70) cc_final: 0.7891 (m-70) REVERT: A 626 GLN cc_start: 0.8153 (mt0) cc_final: 0.7917 (mt0) REVERT: A 644 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8149 (mtm180) REVERT: A 866 GLU cc_start: 0.8479 (mp0) cc_final: 0.8185 (mp0) REVERT: A 981 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7982 (ptp90) REVERT: B 135 PHE cc_start: 0.7818 (m-80) cc_final: 0.7514 (m-80) REVERT: B 140 PHE cc_start: 0.8021 (p90) cc_final: 0.7654 (p90) REVERT: B 171 VAL cc_start: 0.8750 (p) cc_final: 0.8467 (t) REVERT: B 177 MET cc_start: 0.4844 (OUTLIER) cc_final: 0.3172 (pp-130) REVERT: B 377 LYS cc_start: 0.8467 (tppp) cc_final: 0.8182 (tppp) REVERT: B 450 TYR cc_start: 0.7169 (m-80) cc_final: 0.6227 (m-10) REVERT: B 626 GLN cc_start: 0.8173 (mt0) cc_final: 0.7966 (mt0) REVERT: B 986 GLU cc_start: 0.8378 (mp0) cc_final: 0.7638 (mp0) REVERT: B 1027 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.7772 (tpp) REVERT: B 1048 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9245 (ptp) REVERT: G 121 ASN cc_start: 0.7780 (m-40) cc_final: 0.7098 (t0) REVERT: G 140 PHE cc_start: 0.8116 (p90) cc_final: 0.7663 (p90) REVERT: G 345 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.8083 (tpp-160) REVERT: G 346 PHE cc_start: 0.7728 (m-80) cc_final: 0.6671 (m-80) REVERT: G 450 TYR cc_start: 0.6788 (m-80) cc_final: 0.6106 (m-10) REVERT: G 452 TYR cc_start: 0.6931 (p90) cc_final: 0.6512 (p90) REVERT: G 492 SER cc_start: 0.8821 (p) cc_final: 0.8534 (t) REVERT: G 584 ASP cc_start: 0.8047 (m-30) cc_final: 0.7814 (m-30) REVERT: G 623 HIS cc_start: 0.8131 (m-70) cc_final: 0.7877 (m-70) outliers start: 37 outliers final: 21 residues processed: 187 average time/residue: 0.5280 time to fit residues: 118.2211 Evaluate side-chains 176 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 274 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 241 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 338 HIS B 134 GLN B 338 HIS G 134 GLN G 338 HIS G 538 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.076595 restraints weight = 43804.187| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.96 r_work: 0.2893 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25872 Z= 0.157 Angle : 0.613 10.500 35310 Z= 0.314 Chirality : 0.047 0.349 4116 Planarity : 0.004 0.039 4452 Dihedral : 7.334 83.130 4410 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.28 % Allowed : 11.12 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.15), residues: 3078 helix: 1.75 (0.20), residues: 708 sheet: 1.20 (0.19), residues: 738 loop : -1.48 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.018 0.001 TYR A1065 PHE 0.027 0.001 PHE B 937 TRP 0.007 0.001 TRP A 631 HIS 0.006 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00376 (25773) covalent geometry : angle 0.58588 (35079) SS BOND : bond 0.00328 ( 39) SS BOND : angle 1.49800 ( 78) hydrogen bonds : bond 0.06006 ( 999) hydrogen bonds : angle 4.94940 ( 2835) Misc. bond : bond 0.00125 ( 9) link_BETA1-4 : bond 0.00369 ( 6) link_BETA1-4 : angle 1.01005 ( 18) link_NAG-ASN : bond 0.00298 ( 45) link_NAG-ASN : angle 2.75448 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7894 (m-40) cc_final: 0.7366 (t0) REVERT: A 140 PHE cc_start: 0.8159 (p90) cc_final: 0.7359 (p90) REVERT: A 177 MET cc_start: 0.4956 (mmt) cc_final: 0.3820 (pp-130) REVERT: A 346 PHE cc_start: 0.8055 (m-80) cc_final: 0.7338 (m-80) REVERT: A 359 ASN cc_start: 0.8944 (m-40) cc_final: 0.8669 (m-40) REVERT: A 450 TYR cc_start: 0.6771 (m-80) cc_final: 0.6045 (m-10) REVERT: A 623 HIS cc_start: 0.8230 (m-70) cc_final: 0.7922 (m-70) REVERT: A 626 GLN cc_start: 0.8176 (mt0) cc_final: 0.7900 (mt0) REVERT: A 644 ARG cc_start: 0.8743 (mtp-110) cc_final: 0.8169 (mtm180) REVERT: A 866 GLU cc_start: 0.8461 (mp0) cc_final: 0.8148 (mp0) REVERT: A 981 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8069 (ptp-170) REVERT: B 135 PHE cc_start: 0.7837 (m-80) cc_final: 0.7529 (m-80) REVERT: B 140 PHE cc_start: 0.8029 (p90) cc_final: 0.7664 (p90) REVERT: B 171 VAL cc_start: 0.8766 (p) cc_final: 0.8485 (t) REVERT: B 177 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.3117 (pp-130) REVERT: B 377 LYS cc_start: 0.8476 (tppp) cc_final: 0.8197 (tppp) REVERT: B 450 TYR cc_start: 0.7011 (m-80) cc_final: 0.6027 (m-10) REVERT: B 626 GLN cc_start: 0.8198 (mt0) cc_final: 0.7989 (mt0) REVERT: B 644 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8091 (mtm180) REVERT: B 898 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8757 (mtm) REVERT: B 981 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7960 (ptp90) REVERT: B 986 GLU cc_start: 0.8403 (mp0) cc_final: 0.8194 (mp0) REVERT: G 121 ASN cc_start: 0.7569 (m-40) cc_final: 0.7026 (t0) REVERT: G 140 PHE cc_start: 0.8105 (p90) cc_final: 0.7671 (p90) REVERT: G 346 PHE cc_start: 0.7680 (m-80) cc_final: 0.7236 (m-80) REVERT: G 623 HIS cc_start: 0.8050 (m-70) cc_final: 0.7814 (m-70) outliers start: 35 outliers final: 23 residues processed: 185 average time/residue: 0.5016 time to fit residues: 112.0928 Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 574 VAL Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Chi-restraints excluded: chain G residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 155 optimal weight: 6.9990 chunk 273 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 275 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 802 GLN B 134 GLN B 217 GLN B 338 HIS G 134 GLN G 338 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.130676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079302 restraints weight = 43992.556| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.98 r_work: 0.2946 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25872 Z= 0.108 Angle : 0.584 11.446 35310 Z= 0.296 Chirality : 0.045 0.331 4116 Planarity : 0.004 0.037 4452 Dihedral : 6.905 74.323 4410 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.99 % Allowed : 11.96 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.15), residues: 3078 helix: 2.01 (0.21), residues: 687 sheet: 1.33 (0.19), residues: 717 loop : -1.33 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 345 TYR 0.018 0.001 TYR G 160 PHE 0.027 0.001 PHE G 133 TRP 0.008 0.001 TRP A 631 HIS 0.002 0.000 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00230 (25773) covalent geometry : angle 0.55246 (35079) SS BOND : bond 0.00279 ( 39) SS BOND : angle 2.14655 ( 78) hydrogen bonds : bond 0.04654 ( 999) hydrogen bonds : angle 4.72669 ( 2835) Misc. bond : bond 0.00100 ( 9) link_BETA1-4 : bond 0.00369 ( 6) link_BETA1-4 : angle 0.84734 ( 18) link_NAG-ASN : bond 0.00383 ( 45) link_NAG-ASN : angle 2.66651 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7890 (m-40) cc_final: 0.7376 (t0) REVERT: A 140 PHE cc_start: 0.8140 (p90) cc_final: 0.7350 (p90) REVERT: A 177 MET cc_start: 0.4938 (mmt) cc_final: 0.3945 (pp-130) REVERT: A 215 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 346 PHE cc_start: 0.8073 (m-80) cc_final: 0.7364 (m-80) REVERT: A 623 HIS cc_start: 0.8204 (m-70) cc_final: 0.8001 (m-70) REVERT: A 626 GLN cc_start: 0.8164 (mt0) cc_final: 0.7937 (mt0) REVERT: A 644 ARG cc_start: 0.8727 (mtp-110) cc_final: 0.8176 (mtm180) REVERT: A 866 GLU cc_start: 0.8455 (mp0) cc_final: 0.8168 (mp0) REVERT: A 981 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8050 (ptp-170) REVERT: B 133 PHE cc_start: 0.8010 (m-80) cc_final: 0.6924 (m-80) REVERT: B 140 PHE cc_start: 0.8035 (p90) cc_final: 0.7643 (p90) REVERT: B 171 VAL cc_start: 0.8732 (p) cc_final: 0.8459 (t) REVERT: B 177 MET cc_start: 0.4683 (OUTLIER) cc_final: 0.3051 (ppp) REVERT: B 377 LYS cc_start: 0.8483 (tppp) cc_final: 0.8202 (tppp) REVERT: B 450 TYR cc_start: 0.7080 (m-80) cc_final: 0.6137 (m-10) REVERT: B 569 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8058 (OUTLIER) REVERT: B 626 GLN cc_start: 0.8189 (mt0) cc_final: 0.7979 (mt0) REVERT: B 644 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8062 (mtm180) REVERT: B 986 GLU cc_start: 0.8418 (mp0) cc_final: 0.7672 (mp0) REVERT: B 1048 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9219 (ptp) REVERT: G 121 ASN cc_start: 0.7790 (m-40) cc_final: 0.7330 (t0) REVERT: G 140 PHE cc_start: 0.8095 (p90) cc_final: 0.7663 (p90) REVERT: G 346 PHE cc_start: 0.7827 (m-80) cc_final: 0.7051 (m-80) REVERT: G 450 TYR cc_start: 0.7312 (m-80) cc_final: 0.6401 (m-10) REVERT: G 452 TYR cc_start: 0.7267 (p90) cc_final: 0.6916 (p90) REVERT: G 569 ASP cc_start: 0.8424 (m-30) cc_final: 0.8140 (t0) REVERT: G 584 ASP cc_start: 0.8024 (m-30) cc_final: 0.7780 (m-30) REVERT: G 623 HIS cc_start: 0.8157 (m-70) cc_final: 0.7908 (m-70) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 0.5012 time to fit residues: 114.5940 Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain G residue 574 VAL Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 736 CYS Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 179 optimal weight: 0.0770 chunk 201 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 303 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 217 GLN B 338 HIS G 338 HIS G 538 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.079942 restraints weight = 43833.652| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.96 r_work: 0.2944 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25872 Z= 0.105 Angle : 0.584 11.440 35310 Z= 0.294 Chirality : 0.045 0.326 4116 Planarity : 0.004 0.038 4452 Dihedral : 6.334 57.191 4410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.95 % Allowed : 12.26 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3078 helix: 2.08 (0.21), residues: 687 sheet: 1.17 (0.19), residues: 747 loop : -1.28 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 632 TYR 0.018 0.001 TYR G 634 PHE 0.026 0.001 PHE B 937 TRP 0.008 0.001 TRP A 631 HIS 0.003 0.000 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00227 (25773) covalent geometry : angle 0.55104 (35079) SS BOND : bond 0.00293 ( 39) SS BOND : angle 2.11695 ( 78) hydrogen bonds : bond 0.04481 ( 999) hydrogen bonds : angle 4.64765 ( 2835) Misc. bond : bond 0.00095 ( 9) link_BETA1-4 : bond 0.00424 ( 6) link_BETA1-4 : angle 0.88798 ( 18) link_NAG-ASN : bond 0.00336 ( 45) link_NAG-ASN : angle 2.74772 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7879 (m-40) cc_final: 0.7386 (t0) REVERT: A 140 PHE cc_start: 0.8137 (p90) cc_final: 0.7346 (p90) REVERT: A 177 MET cc_start: 0.4862 (mmt) cc_final: 0.3897 (pp-130) REVERT: A 346 PHE cc_start: 0.7797 (m-80) cc_final: 0.7594 (m-80) REVERT: A 452 TYR cc_start: 0.7013 (p90) cc_final: 0.6763 (p90) REVERT: A 623 HIS cc_start: 0.8205 (m-70) cc_final: 0.7996 (m-70) REVERT: A 626 GLN cc_start: 0.8181 (mt0) cc_final: 0.7961 (mt0) REVERT: A 644 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8109 (mtm180) REVERT: A 866 GLU cc_start: 0.8445 (mp0) cc_final: 0.8158 (mp0) REVERT: A 981 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8048 (ptp-170) REVERT: B 133 PHE cc_start: 0.7970 (m-80) cc_final: 0.6826 (m-80) REVERT: B 140 PHE cc_start: 0.8027 (p90) cc_final: 0.7636 (p90) REVERT: B 171 VAL cc_start: 0.8720 (p) cc_final: 0.8442 (t) REVERT: B 177 MET cc_start: 0.4665 (OUTLIER) cc_final: 0.3246 (pp-130) REVERT: B 377 LYS cc_start: 0.8480 (tppp) cc_final: 0.8196 (tppp) REVERT: B 450 TYR cc_start: 0.7115 (m-80) cc_final: 0.6179 (m-10) REVERT: B 452 TYR cc_start: 0.6660 (p90) cc_final: 0.6445 (p90) REVERT: B 981 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7943 (ptp90) REVERT: B 986 GLU cc_start: 0.8410 (mp0) cc_final: 0.7643 (mp0) REVERT: B 1048 MET cc_start: 0.9471 (ptm) cc_final: 0.9202 (ptp) REVERT: G 121 ASN cc_start: 0.7837 (m-40) cc_final: 0.7231 (t0) REVERT: G 140 PHE cc_start: 0.8090 (p90) cc_final: 0.7657 (p90) REVERT: G 346 PHE cc_start: 0.7887 (m-80) cc_final: 0.7031 (m-80) REVERT: G 450 TYR cc_start: 0.7561 (m-80) cc_final: 0.6191 (m-10) REVERT: G 452 TYR cc_start: 0.7259 (p90) cc_final: 0.6873 (p90) REVERT: G 569 ASP cc_start: 0.8329 (m-30) cc_final: 0.8120 (t0) REVERT: G 584 ASP cc_start: 0.8043 (m-30) cc_final: 0.7811 (m-30) REVERT: G 623 HIS cc_start: 0.8162 (m-70) cc_final: 0.7907 (m-70) outliers start: 26 outliers final: 14 residues processed: 179 average time/residue: 0.5342 time to fit residues: 114.6909 Evaluate side-chains 169 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 574 VAL Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 286 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 338 HIS G 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.079753 restraints weight = 43997.090| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.98 r_work: 0.2944 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25872 Z= 0.107 Angle : 0.571 11.594 35310 Z= 0.289 Chirality : 0.045 0.324 4116 Planarity : 0.004 0.037 4452 Dihedral : 5.974 56.375 4410 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.73 % Allowed : 12.55 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3078 helix: 2.14 (0.21), residues: 684 sheet: 1.19 (0.19), residues: 747 loop : -1.27 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 632 TYR 0.016 0.001 TYR G1065 PHE 0.026 0.001 PHE B 937 TRP 0.008 0.001 TRP B 631 HIS 0.003 0.000 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00235 (25773) covalent geometry : angle 0.53779 (35079) SS BOND : bond 0.00326 ( 39) SS BOND : angle 1.92273 ( 78) hydrogen bonds : bond 0.04491 ( 999) hydrogen bonds : angle 4.63168 ( 2835) Misc. bond : bond 0.00095 ( 9) link_BETA1-4 : bond 0.00378 ( 6) link_BETA1-4 : angle 0.84977 ( 18) link_NAG-ASN : bond 0.00346 ( 45) link_NAG-ASN : angle 2.79431 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7950 (m-40) cc_final: 0.7433 (t0) REVERT: A 140 PHE cc_start: 0.8150 (p90) cc_final: 0.7359 (p90) REVERT: A 177 MET cc_start: 0.4885 (mmt) cc_final: 0.4191 (ppp) REVERT: A 346 PHE cc_start: 0.7999 (m-80) cc_final: 0.7602 (m-80) REVERT: A 623 HIS cc_start: 0.8177 (m-70) cc_final: 0.7852 (m-70) REVERT: A 626 GLN cc_start: 0.8170 (mt0) cc_final: 0.7958 (mt0) REVERT: A 644 ARG cc_start: 0.8669 (mtp-110) cc_final: 0.8108 (mtm180) REVERT: A 866 GLU cc_start: 0.8443 (mp0) cc_final: 0.8154 (mp0) REVERT: A 937 PHE cc_start: 0.8138 (t80) cc_final: 0.7930 (t80) REVERT: A 981 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.8030 (ptp-170) REVERT: B 140 PHE cc_start: 0.8050 (p90) cc_final: 0.7661 (p90) REVERT: B 171 VAL cc_start: 0.8756 (p) cc_final: 0.8480 (t) REVERT: B 177 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.3347 (ppp) REVERT: B 377 LYS cc_start: 0.8493 (tppp) cc_final: 0.8206 (tppp) REVERT: B 450 TYR cc_start: 0.7098 (m-80) cc_final: 0.6073 (m-10) REVERT: B 644 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.8049 (mtm180) REVERT: B 981 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7951 (ptp90) REVERT: B 986 GLU cc_start: 0.8420 (mp0) cc_final: 0.7646 (mp0) REVERT: B 1027 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7541 (tpp) REVERT: B 1048 MET cc_start: 0.9457 (ptm) cc_final: 0.9142 (ptp) REVERT: G 121 ASN cc_start: 0.7859 (m-40) cc_final: 0.7260 (t0) REVERT: G 140 PHE cc_start: 0.8101 (p90) cc_final: 0.7668 (p90) REVERT: G 164 ASN cc_start: 0.8025 (t0) cc_final: 0.7686 (t0) REVERT: G 346 PHE cc_start: 0.7699 (m-80) cc_final: 0.7279 (m-80) REVERT: G 452 TYR cc_start: 0.7265 (p90) cc_final: 0.6894 (p90) REVERT: G 584 ASP cc_start: 0.8041 (m-30) cc_final: 0.7812 (m-30) REVERT: G 623 HIS cc_start: 0.8161 (m-70) cc_final: 0.7898 (m-70) outliers start: 20 outliers final: 14 residues processed: 179 average time/residue: 0.5334 time to fit residues: 114.4847 Evaluate side-chains 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 574 VAL Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 981 ARG Chi-restraints excluded: chain G residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 22 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 338 HIS G 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076153 restraints weight = 43735.065| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.97 r_work: 0.2874 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25872 Z= 0.171 Angle : 0.632 11.168 35310 Z= 0.326 Chirality : 0.047 0.340 4116 Planarity : 0.004 0.040 4452 Dihedral : 5.970 56.106 4410 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.84 % Allowed : 12.59 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3078 helix: 1.80 (0.20), residues: 708 sheet: 1.20 (0.19), residues: 747 loop : -1.49 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.020 0.001 TYR A1065 PHE 0.030 0.002 PHE B 937 TRP 0.006 0.001 TRP B 884 HIS 0.006 0.001 HIS G1062 Details of bonding type rmsd covalent geometry : bond 0.00414 (25773) covalent geometry : angle 0.59981 (35079) SS BOND : bond 0.00295 ( 39) SS BOND : angle 2.28972 ( 78) hydrogen bonds : bond 0.06313 ( 999) hydrogen bonds : angle 4.94656 ( 2835) Misc. bond : bond 0.00103 ( 9) link_BETA1-4 : bond 0.00317 ( 6) link_BETA1-4 : angle 1.04219 ( 18) link_NAG-ASN : bond 0.00281 ( 45) link_NAG-ASN : angle 2.82351 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11304.61 seconds wall clock time: 192 minutes 30.19 seconds (11550.19 seconds total)