Starting phenix.real_space_refine on Sat May 24 11:10:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxl_37910/05_2025/8wxl_37910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxl_37910/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxl_37910/05_2025/8wxl_37910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxl_37910/05_2025/8wxl_37910.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxl_37910/05_2025/8wxl_37910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxl_37910/05_2025/8wxl_37910.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.18, per 1000 atoms: 0.29 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: 7.67 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 4.25 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: 12.24 Time building geometry restraints manager: 8.82 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: 0.18 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: 35.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 53.390 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.120 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (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 TRP 0.022 0.002 TRP B 884 HIS 0.005 0.001 HIS G1062 PHE 0.041 0.001 PHE B 904 TYR 0.018 0.001 TYR B1065 ARG 0.002 0.000 ARG A1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 45) link_NAG-ASN : angle 3.02880 ( 135) link_BETA1-4 : bond 0.00500 ( 6) link_BETA1-4 : angle 0.88282 ( 18) hydrogen bonds : bond 0.11983 ( 999) hydrogen bonds : angle 6.09065 ( 2835) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.50801 ( 78) covalent geometry : bond 0.00456 (25773) covalent geometry : angle 0.59383 (35079) Misc. bond : bond 0.00239 ( 9) *********************** 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 : 2.924 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: 0.6950 (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: 1.2276 time to fit residues: 403.9864 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 : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 chunk 148 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1008 GLN G 359 ASN G 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.130741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079243 restraints weight = 43983.367| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.97 r_work: 0.2946 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25872 Z= 0.114 Angle : 0.572 10.766 35310 Z= 0.296 Chirality : 0.046 0.376 4116 Planarity : 0.004 0.054 4452 Dihedral : 8.385 100.129 4410 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.84 % Allowed : 6.22 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3078 helix: 1.81 (0.20), residues: 714 sheet: 1.27 (0.19), residues: 729 loop : -1.29 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 884 HIS 0.005 0.001 HIS A 338 PHE 0.018 0.001 PHE B 937 TYR 0.016 0.001 TYR A1065 ARG 0.007 0.000 ARG G 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 45) link_NAG-ASN : angle 2.70834 ( 135) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 0.81442 ( 18) hydrogen bonds : bond 0.05306 ( 999) hydrogen bonds : angle 5.11344 ( 2835) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.24221 ( 78) covalent geometry : bond 0.00239 (25773) covalent geometry : angle 0.54490 (35079) Misc. bond : bond 0.00135 ( 9) *********************** 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 215 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7715 (m-40) cc_final: 0.7150 (t0) REVERT: A 140 PHE cc_start: 0.8035 (p90) cc_final: 0.7133 (p90) REVERT: A 200 TYR cc_start: 0.8227 (m-80) cc_final: 0.7998 (m-80) REVERT: A 359 ASN cc_start: 0.8830 (m-40) cc_final: 0.8589 (m-40) REVERT: A 377 LYS cc_start: 0.8588 (tppp) cc_final: 0.8348 (tppp) REVERT: A 626 GLN cc_start: 0.8094 (mt0) cc_final: 0.7878 (mt0) REVERT: A 644 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.8179 (mtm180) REVERT: A 866 GLU cc_start: 0.8378 (mp0) cc_final: 0.8093 (mp0) REVERT: B 140 PHE cc_start: 0.7976 (p90) cc_final: 0.7639 (p90) REVERT: B 164 ASN cc_start: 0.7604 (t0) cc_final: 0.7129 (t0) REVERT: B 171 VAL cc_start: 0.8769 (p) cc_final: 0.8505 (t) REVERT: B 377 LYS cc_start: 0.8429 (tppp) cc_final: 0.8184 (tppp) REVERT: B 463 PHE cc_start: 0.8846 (m-10) cc_final: 0.8555 (m-10) REVERT: B 623 HIS cc_start: 0.8242 (m-70) cc_final: 0.8016 (m-70) REVERT: G 26 GLN cc_start: 0.7680 (mp10) cc_final: 0.7476 (mp10) REVERT: G 100 ILE cc_start: 0.8395 (mm) cc_final: 0.8194 (mp) REVERT: G 121 ASN cc_start: 0.7556 (m-40) cc_final: 0.6911 (t0) REVERT: G 140 PHE cc_start: 0.8082 (p90) cc_final: 0.7634 (p90) REVERT: G 584 ASP cc_start: 0.8041 (m-30) cc_final: 0.7813 (m-30) REVERT: G 623 HIS cc_start: 0.8146 (m-70) cc_final: 0.7828 (m-70) outliers start: 23 outliers final: 9 residues processed: 203 average time/residue: 0.9746 time to fit residues: 239.7306 Evaluate side-chains 176 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 703 VAL 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 958 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 281 optimal weight: 0.0670 chunk 111 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN G 338 HIS G 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.077767 restraints weight = 43623.020| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.98 r_work: 0.2915 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25872 Z= 0.135 Angle : 0.581 10.397 35310 Z= 0.299 Chirality : 0.047 0.368 4116 Planarity : 0.004 0.039 4452 Dihedral : 8.099 95.647 4410 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.99 % Allowed : 8.16 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3078 helix: 1.76 (0.20), residues: 717 sheet: 1.30 (0.19), residues: 726 loop : -1.31 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 884 HIS 0.005 0.001 HIS G1062 PHE 0.025 0.001 PHE B 937 TYR 0.018 0.001 TYR A1065 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 45) link_NAG-ASN : angle 2.68900 ( 135) link_BETA1-4 : bond 0.00313 ( 6) link_BETA1-4 : angle 0.96579 ( 18) hydrogen bonds : bond 0.05665 ( 999) hydrogen bonds : angle 5.00783 ( 2835) SS BOND : bond 0.00317 ( 39) SS BOND : angle 1.27103 ( 78) covalent geometry : bond 0.00316 (25773) covalent geometry : angle 0.55529 (35079) Misc. bond : bond 0.00117 ( 9) *********************** 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 196 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7849 (m-40) cc_final: 0.7239 (t0) REVERT: A 140 PHE cc_start: 0.8090 (p90) cc_final: 0.7288 (p90) REVERT: A 346 PHE cc_start: 0.7566 (m-80) cc_final: 0.7239 (m-80) REVERT: A 359 ASN cc_start: 0.8850 (m-40) cc_final: 0.8611 (m-40) REVERT: A 626 GLN cc_start: 0.8138 (mt0) cc_final: 0.7918 (mt0) REVERT: A 644 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8163 (mtm180) REVERT: A 866 GLU cc_start: 0.8394 (mp0) cc_final: 0.8100 (mp0) REVERT: B 140 PHE cc_start: 0.7990 (p90) cc_final: 0.7631 (p90) REVERT: B 164 ASN cc_start: 0.7577 (t0) cc_final: 0.7123 (t0) REVERT: B 171 VAL cc_start: 0.8748 (p) cc_final: 0.8446 (t) REVERT: B 463 PHE cc_start: 0.8853 (m-10) cc_final: 0.8548 (m-10) REVERT: B 623 HIS cc_start: 0.8364 (m-70) cc_final: 0.8108 (m-70) REVERT: G 26 GLN cc_start: 0.7695 (mp10) cc_final: 0.7430 (mp10) REVERT: G 100 ILE cc_start: 0.8329 (mm) cc_final: 0.8111 (mp) REVERT: G 121 ASN cc_start: 0.7588 (m-40) cc_final: 0.6934 (t0) REVERT: G 140 PHE cc_start: 0.8097 (p90) cc_final: 0.7643 (p90) REVERT: G 164 ASN cc_start: 0.7600 (t0) cc_final: 0.7251 (t0) REVERT: G 200 TYR cc_start: 0.8163 (m-80) cc_final: 0.7962 (m-80) REVERT: G 584 ASP cc_start: 0.8082 (m-30) cc_final: 0.7840 (m-30) REVERT: G 623 HIS cc_start: 0.8185 (m-70) cc_final: 0.7921 (m-70) outliers start: 27 outliers final: 19 residues processed: 188 average time/residue: 1.0329 time to fit residues: 233.8661 Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 513 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 B residue 127 PHE 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 127 PHE 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 1090 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 279 optimal weight: 0.0970 chunk 71 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079282 restraints weight = 44098.398| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.98 r_work: 0.2964 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25872 Z= 0.105 Angle : 0.553 10.314 35310 Z= 0.282 Chirality : 0.045 0.348 4116 Planarity : 0.004 0.039 4452 Dihedral : 7.803 91.026 4410 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.10 % Allowed : 9.22 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3078 helix: 1.87 (0.21), residues: 708 sheet: 1.35 (0.19), residues: 726 loop : -1.26 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 884 HIS 0.003 0.001 HIS G1062 PHE 0.025 0.001 PHE B 937 TYR 0.016 0.001 TYR B1065 ARG 0.004 0.000 ARG G 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 45) link_NAG-ASN : angle 2.61705 ( 135) link_BETA1-4 : bond 0.00377 ( 6) link_BETA1-4 : angle 0.85806 ( 18) hydrogen bonds : bond 0.04808 ( 999) hydrogen bonds : angle 4.83121 ( 2835) SS BOND : bond 0.00298 ( 39) SS BOND : angle 1.18184 ( 78) covalent geometry : bond 0.00223 (25773) covalent geometry : angle 0.52678 (35079) Misc. bond : bond 0.00087 ( 9) *********************** 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 205 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 2.601 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 102 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7836 (mtp85) REVERT: A 121 ASN cc_start: 0.7973 (m-40) cc_final: 0.7233 (t0) REVERT: A 140 PHE cc_start: 0.8071 (p90) cc_final: 0.7258 (p90) REVERT: A 177 MET cc_start: 0.4599 (mmt) cc_final: 0.3288 (pp-130) REVERT: A 359 ASN cc_start: 0.8867 (m-40) cc_final: 0.8623 (m-40) REVERT: A 626 GLN cc_start: 0.8157 (mt0) cc_final: 0.7936 (mt0) REVERT: A 644 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8167 (mtm180) REVERT: A 866 GLU cc_start: 0.8359 (mp0) cc_final: 0.8082 (mp0) REVERT: B 102 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7920 (mtp85) REVERT: B 121 ASN cc_start: 0.7682 (m-40) cc_final: 0.7020 (t0) REVERT: B 140 PHE cc_start: 0.7992 (p90) cc_final: 0.7616 (p90) REVERT: B 164 ASN cc_start: 0.7580 (t0) cc_final: 0.7128 (t0) REVERT: B 569 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8033 (t0) REVERT: B 623 HIS cc_start: 0.8359 (m-70) cc_final: 0.8088 (m-70) REVERT: G 121 ASN cc_start: 0.7665 (m-40) cc_final: 0.6907 (t0) REVERT: G 140 PHE cc_start: 0.8093 (p90) cc_final: 0.7641 (p90) REVERT: G 164 ASN cc_start: 0.7601 (t0) cc_final: 0.7257 (t0) REVERT: G 345 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7999 (tpp-160) REVERT: G 450 TYR cc_start: 0.7204 (m-80) cc_final: 0.5646 (m-10) REVERT: G 584 ASP cc_start: 0.8059 (m-30) cc_final: 0.7806 (m-30) REVERT: G 623 HIS cc_start: 0.8167 (m-70) cc_final: 0.7862 (m-70) outliers start: 30 outliers final: 19 residues processed: 197 average time/residue: 1.1355 time to fit residues: 268.0735 Evaluate side-chains 180 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 513 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 958 ASN 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 569 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 567 ILE 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 1090 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 119 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 217 GLN G 338 HIS G 538 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075872 restraints weight = 43905.121| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.97 r_work: 0.2888 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25872 Z= 0.190 Angle : 0.633 10.023 35310 Z= 0.326 Chirality : 0.049 0.366 4116 Planarity : 0.004 0.040 4452 Dihedral : 7.829 89.890 4410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.32 % Allowed : 9.99 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3078 helix: 1.70 (0.20), residues: 711 sheet: 1.17 (0.18), residues: 750 loop : -1.41 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 884 HIS 0.007 0.001 HIS G1062 PHE 0.026 0.002 PHE B 937 TYR 0.020 0.001 TYR A1065 ARG 0.004 0.000 ARG A 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 45) link_NAG-ASN : angle 2.78948 ( 135) link_BETA1-4 : bond 0.00336 ( 6) link_BETA1-4 : angle 1.09969 ( 18) hydrogen bonds : bond 0.06659 ( 999) hydrogen bonds : angle 5.06452 ( 2835) SS BOND : bond 0.00306 ( 39) SS BOND : angle 1.56273 ( 78) covalent geometry : bond 0.00467 (25773) covalent geometry : angle 0.60615 (35079) Misc. bond : bond 0.00170 ( 9) *********************** 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 194 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 2.651 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: 0.7904 (m-40) cc_final: 0.7287 (t0) REVERT: A 140 PHE cc_start: 0.8139 (p90) cc_final: 0.7343 (p90) REVERT: A 177 MET cc_start: 0.4779 (mmt) cc_final: 0.3520 (pp-130) REVERT: A 346 PHE cc_start: 0.7701 (m-80) cc_final: 0.7323 (m-80) REVERT: A 359 ASN cc_start: 0.8893 (m-40) cc_final: 0.8636 (m-40) REVERT: A 626 GLN cc_start: 0.8197 (mt0) cc_final: 0.7941 (mt0) REVERT: A 644 ARG cc_start: 0.8741 (mtp-110) cc_final: 0.8178 (mtm180) REVERT: A 866 GLU cc_start: 0.8426 (mp0) cc_final: 0.8114 (mp0) REVERT: B 121 ASN cc_start: 0.7592 (m-40) cc_final: 0.6943 (t0) REVERT: B 140 PHE cc_start: 0.8017 (p90) cc_final: 0.7646 (p90) REVERT: B 171 VAL cc_start: 0.8768 (p) cc_final: 0.8474 (t) REVERT: B 177 MET cc_start: 0.4892 (mmt) cc_final: 0.3202 (ppp) REVERT: B 377 LYS cc_start: 0.8461 (tppp) cc_final: 0.8243 (tppp) REVERT: B 450 TYR cc_start: 0.6965 (m-80) cc_final: 0.6708 (m-80) REVERT: B 644 ARG cc_start: 0.8648 (mtp-110) cc_final: 0.8113 (mtm180) REVERT: B 986 GLU cc_start: 0.8366 (mp0) cc_final: 0.7673 (mp0) REVERT: G 121 ASN cc_start: 0.7628 (m-40) cc_final: 0.6874 (t0) REVERT: G 140 PHE cc_start: 0.8141 (p90) cc_final: 0.7682 (p90) REVERT: G 346 PHE cc_start: 0.7639 (m-80) cc_final: 0.6941 (m-80) REVERT: G 450 TYR cc_start: 0.7162 (m-80) cc_final: 0.5843 (m-10) REVERT: G 623 HIS cc_start: 0.8174 (m-70) cc_final: 0.7903 (m-70) REVERT: G 738 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8364 (tmm) outliers start: 36 outliers final: 22 residues processed: 185 average time/residue: 1.0751 time to fit residues: 240.3793 Evaluate side-chains 173 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 513 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 B residue 105 ILE 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 958 ASN Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 567 ILE 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 1090 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 338 HIS 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 = 0.3840 r_free = 0.3840 target = 0.126971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074711 restraints weight = 43775.068| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.96 r_work: 0.2871 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25872 Z= 0.221 Angle : 0.669 10.433 35310 Z= 0.345 Chirality : 0.050 0.378 4116 Planarity : 0.005 0.041 4452 Dihedral : 7.893 89.457 4410 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.68 % Allowed : 10.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3078 helix: 1.48 (0.20), residues: 711 sheet: 1.03 (0.19), residues: 747 loop : -1.55 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 884 HIS 0.008 0.001 HIS G1062 PHE 0.031 0.002 PHE B 937 TYR 0.019 0.002 TYR A1065 ARG 0.005 0.001 ARG G 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 45) link_NAG-ASN : angle 2.97451 ( 135) link_BETA1-4 : bond 0.00314 ( 6) link_BETA1-4 : angle 1.22367 ( 18) hydrogen bonds : bond 0.07171 ( 999) hydrogen bonds : angle 5.20427 ( 2835) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.80663 ( 78) covalent geometry : bond 0.00549 (25773) covalent geometry : angle 0.63872 (35079) Misc. bond : bond 0.00141 ( 9) *********************** 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 212 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7954 (m-40) cc_final: 0.7395 (t0) REVERT: A 140 PHE cc_start: 0.8177 (p90) cc_final: 0.7371 (p90) REVERT: A 177 MET cc_start: 0.4841 (mmt) cc_final: 0.3577 (pp-130) REVERT: A 215 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: A 346 PHE cc_start: 0.7875 (m-80) cc_final: 0.7156 (m-80) REVERT: A 359 ASN cc_start: 0.8883 (m-40) cc_final: 0.8627 (m-40) REVERT: A 450 TYR cc_start: 0.7050 (m-80) cc_final: 0.5847 (m-10) REVERT: A 626 GLN cc_start: 0.8235 (mt0) cc_final: 0.7941 (mt0) REVERT: A 644 ARG cc_start: 0.8769 (mtp-110) cc_final: 0.8211 (mtm180) REVERT: A 866 GLU cc_start: 0.8538 (mp0) cc_final: 0.8220 (mp0) REVERT: A 937 PHE cc_start: 0.8459 (t80) cc_final: 0.8232 (t80) REVERT: A 981 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8113 (ptp-170) REVERT: B 140 PHE cc_start: 0.8044 (p90) cc_final: 0.7672 (p90) REVERT: B 171 VAL cc_start: 0.8781 (p) cc_final: 0.8488 (t) REVERT: B 346 PHE cc_start: 0.7722 (m-80) cc_final: 0.6885 (m-80) REVERT: B 377 LYS cc_start: 0.8459 (tppp) cc_final: 0.8240 (tppp) REVERT: B 450 TYR cc_start: 0.7127 (m-80) cc_final: 0.6066 (m-10) REVERT: B 644 ARG cc_start: 0.8668 (mtp-110) cc_final: 0.8166 (mtm180) REVERT: B 986 GLU cc_start: 0.8343 (mp0) cc_final: 0.8138 (mp0) REVERT: G 121 ASN cc_start: 0.7468 (m-40) cc_final: 0.6843 (t0) REVERT: G 140 PHE cc_start: 0.8166 (p90) cc_final: 0.7699 (p90) REVERT: G 346 PHE cc_start: 0.7578 (m-80) cc_final: 0.6545 (m-80) REVERT: G 450 TYR cc_start: 0.7058 (m-80) cc_final: 0.5704 (m-10) REVERT: G 623 HIS cc_start: 0.8065 (m-70) cc_final: 0.7838 (m-70) REVERT: G 738 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8417 (tmm) outliers start: 46 outliers final: 26 residues processed: 196 average time/residue: 1.0184 time to fit residues: 243.1952 Evaluate side-chains 183 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 513 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 981 ARG Chi-restraints excluded: chain A residue 1124 CYS Chi-restraints excluded: chain B residue 105 ILE 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 958 ASN Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 626 GLN Chi-restraints excluded: chain G residue 628 THR 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 Chi-restraints excluded: chain G residue 1126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 304 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 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 = 0.3854 r_free = 0.3854 target = 0.128089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076177 restraints weight = 44059.897| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.97 r_work: 0.2898 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25872 Z= 0.158 Angle : 0.641 12.467 35310 Z= 0.328 Chirality : 0.048 0.361 4116 Planarity : 0.004 0.041 4452 Dihedral : 7.675 86.463 4410 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.35 % Allowed : 11.12 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3078 helix: 1.61 (0.20), residues: 708 sheet: 1.00 (0.19), residues: 774 loop : -1.61 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 631 HIS 0.005 0.001 HIS G1062 PHE 0.031 0.001 PHE B 937 TYR 0.018 0.001 TYR G 160 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 45) link_NAG-ASN : angle 2.83335 ( 135) link_BETA1-4 : bond 0.00253 ( 6) link_BETA1-4 : angle 1.05366 ( 18) hydrogen bonds : bond 0.06147 ( 999) hydrogen bonds : angle 5.04431 ( 2835) SS BOND : bond 0.00303 ( 39) SS BOND : angle 2.62414 ( 78) covalent geometry : bond 0.00376 (25773) covalent geometry : angle 0.60589 (35079) Misc. bond : bond 0.00105 ( 9) *********************** 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 195 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7919 (m-40) cc_final: 0.7404 (t0) REVERT: A 140 PHE cc_start: 0.8200 (p90) cc_final: 0.7416 (p90) REVERT: A 177 MET cc_start: 0.4673 (mmt) cc_final: 0.3677 (ppp) REVERT: A 215 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: A 346 PHE cc_start: 0.8099 (m-80) cc_final: 0.7436 (m-80) REVERT: A 359 ASN cc_start: 0.8872 (m-40) cc_final: 0.8617 (m-40) REVERT: A 450 TYR cc_start: 0.6777 (m-80) cc_final: 0.6422 (m-10) REVERT: A 452 TYR cc_start: 0.6798 (p90) cc_final: 0.6535 (p90) REVERT: A 492 SER cc_start: 0.8937 (p) cc_final: 0.8705 (t) REVERT: A 626 GLN cc_start: 0.8209 (mt0) cc_final: 0.7933 (mt0) REVERT: A 644 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8184 (mtm180) REVERT: A 738 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8729 (tpt) REVERT: A 866 GLU cc_start: 0.8498 (mp0) cc_final: 0.8206 (mp0) REVERT: A 937 PHE cc_start: 0.8452 (t80) cc_final: 0.8212 (t80) REVERT: A 981 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8016 (ptp90) REVERT: B 121 ASN cc_start: 0.7608 (m-40) cc_final: 0.7003 (t0) REVERT: B 140 PHE cc_start: 0.8076 (p90) cc_final: 0.7730 (p90) REVERT: B 171 VAL cc_start: 0.8747 (p) cc_final: 0.8461 (t) REVERT: B 177 MET cc_start: 0.4761 (mmt) cc_final: 0.3322 (ppp) REVERT: B 377 LYS cc_start: 0.8472 (tppp) cc_final: 0.8192 (tppp) REVERT: B 450 TYR cc_start: 0.7072 (m-80) cc_final: 0.6247 (m-10) REVERT: B 644 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8158 (mtm180) REVERT: B 986 GLU cc_start: 0.8379 (mp0) cc_final: 0.8147 (mp0) REVERT: G 121 ASN cc_start: 0.7423 (m-40) cc_final: 0.6800 (t0) REVERT: G 140 PHE cc_start: 0.8121 (p90) cc_final: 0.7691 (p90) REVERT: G 177 MET cc_start: 0.4826 (mmt) cc_final: 0.3370 (ppp) REVERT: G 450 TYR cc_start: 0.7080 (m-80) cc_final: 0.5941 (m-10) REVERT: G 623 HIS cc_start: 0.8043 (m-70) cc_final: 0.7819 (m-70) outliers start: 37 outliers final: 26 residues processed: 187 average time/residue: 1.0648 time to fit residues: 240.4629 Evaluate side-chains 180 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 628 THR 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 A residue 1124 CYS 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 574 VAL Chi-restraints excluded: chain B residue 626 GLN Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 205 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 11 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 0.0070 chunk 189 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078065 restraints weight = 43720.300| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.97 r_work: 0.2912 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1719 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= 0.116 Angle : 0.611 11.107 35310 Z= 0.309 Chirality : 0.046 0.342 4116 Planarity : 0.004 0.048 4452 Dihedral : 7.256 80.235 4410 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.80 % Allowed : 12.11 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3078 helix: 1.75 (0.20), residues: 708 sheet: 1.10 (0.19), residues: 777 loop : -1.55 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 631 HIS 0.003 0.001 HIS G1062 PHE 0.029 0.001 PHE B 937 TYR 0.015 0.001 TYR B1065 ARG 0.003 0.000 ARG G 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 45) link_NAG-ASN : angle 2.72296 ( 135) link_BETA1-4 : bond 0.00350 ( 6) link_BETA1-4 : angle 0.89447 ( 18) hydrogen bonds : bond 0.05114 ( 999) hydrogen bonds : angle 4.85439 ( 2835) SS BOND : bond 0.00277 ( 39) SS BOND : angle 2.73313 ( 78) covalent geometry : bond 0.00254 (25773) covalent geometry : angle 0.57496 (35079) Misc. bond : bond 0.00094 ( 9) *********************** 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 182 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7953 (m-40) cc_final: 0.7417 (t0) REVERT: A 140 PHE cc_start: 0.8180 (p90) cc_final: 0.7378 (p90) REVERT: A 177 MET cc_start: 0.4924 (mmt) cc_final: 0.3867 (ppp) REVERT: A 215 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: A 346 PHE cc_start: 0.8091 (m-80) cc_final: 0.7597 (m-80) REVERT: A 359 ASN cc_start: 0.8902 (m-40) cc_final: 0.8638 (m-40) REVERT: A 450 TYR cc_start: 0.7345 (m-80) cc_final: 0.7119 (m-80) REVERT: A 626 GLN cc_start: 0.8180 (mt0) cc_final: 0.7979 (mt0) REVERT: A 644 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8176 (mtm180) REVERT: A 866 GLU cc_start: 0.8461 (mp0) cc_final: 0.8175 (mp0) REVERT: A 937 PHE cc_start: 0.8376 (t80) cc_final: 0.8142 (t80) REVERT: A 981 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8050 (ptp-170) REVERT: B 121 ASN cc_start: 0.7671 (m-40) cc_final: 0.7128 (t0) REVERT: B 140 PHE cc_start: 0.8055 (p90) cc_final: 0.7674 (p90) REVERT: B 171 VAL cc_start: 0.8666 (p) cc_final: 0.8376 (t) REVERT: B 177 MET cc_start: 0.4700 (OUTLIER) cc_final: 0.3402 (ppp) REVERT: B 377 LYS cc_start: 0.8461 (tppp) cc_final: 0.8179 (tppp) REVERT: B 450 TYR cc_start: 0.7088 (m-80) cc_final: 0.6199 (m-10) REVERT: B 644 ARG cc_start: 0.8663 (mtp-110) cc_final: 0.8140 (mtm180) REVERT: B 986 GLU cc_start: 0.8401 (mp0) cc_final: 0.7632 (mp0) REVERT: B 1048 MET cc_start: 0.9498 (ptm) cc_final: 0.9258 (ptp) REVERT: G 121 ASN cc_start: 0.7519 (m-40) cc_final: 0.6881 (t0) REVERT: G 140 PHE cc_start: 0.8102 (p90) cc_final: 0.7665 (p90) REVERT: G 177 MET cc_start: 0.4863 (mmt) cc_final: 0.3450 (ppp) REVERT: G 346 PHE cc_start: 0.7882 (m-80) cc_final: 0.7264 (m-80) REVERT: G 450 TYR cc_start: 0.7147 (m-80) cc_final: 0.6305 (m-10) REVERT: G 569 ASP cc_start: 0.8466 (m-30) cc_final: 0.8151 (t0) REVERT: G 623 HIS cc_start: 0.8050 (m-70) cc_final: 0.7811 (m-70) outliers start: 22 outliers final: 20 residues processed: 176 average time/residue: 1.0067 time to fit residues: 215.7144 Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 513 PHE 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 A residue 1124 CYS 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 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 127 PHE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 147 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 0.0000 chunk 97 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 282 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077521 restraints weight = 44055.978| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.98 r_work: 0.2902 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25872 Z= 0.129 Angle : 0.616 11.412 35310 Z= 0.313 Chirality : 0.046 0.339 4116 Planarity : 0.004 0.052 4452 Dihedral : 6.955 73.394 4410 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.17 % Allowed : 12.00 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3078 helix: 1.78 (0.20), residues: 708 sheet: 1.16 (0.19), residues: 753 loop : -1.52 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 631 HIS 0.005 0.001 HIS G1062 PHE 0.029 0.001 PHE B 937 TYR 0.017 0.001 TYR G1065 ARG 0.003 0.000 ARG G 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 45) link_NAG-ASN : angle 2.74520 ( 135) link_BETA1-4 : bond 0.00323 ( 6) link_BETA1-4 : angle 0.91296 ( 18) hydrogen bonds : bond 0.05376 ( 999) hydrogen bonds : angle 4.83937 ( 2835) SS BOND : bond 0.00248 ( 39) SS BOND : angle 2.47368 ( 78) covalent geometry : bond 0.00297 (25773) covalent geometry : angle 0.58242 (35079) Misc. bond : bond 0.00095 ( 9) *********************** 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 193 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7917 (m-40) cc_final: 0.7485 (t0) REVERT: A 140 PHE cc_start: 0.8180 (p90) cc_final: 0.7398 (p90) REVERT: A 177 MET cc_start: 0.4967 (mmt) cc_final: 0.3937 (ppp) REVERT: A 346 PHE cc_start: 0.8056 (m-80) cc_final: 0.7524 (m-80) REVERT: A 359 ASN cc_start: 0.8911 (m-40) cc_final: 0.8647 (m-40) REVERT: A 452 TYR cc_start: 0.6992 (p90) cc_final: 0.6696 (p90) REVERT: A 626 GLN cc_start: 0.8205 (mt0) cc_final: 0.7995 (mt0) REVERT: A 644 ARG cc_start: 0.8730 (mtp-110) cc_final: 0.8158 (mtm180) REVERT: A 866 GLU cc_start: 0.8475 (mp0) cc_final: 0.8181 (mp0) REVERT: A 937 PHE cc_start: 0.8426 (t80) cc_final: 0.8194 (t80) REVERT: A 981 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8051 (ptp-170) REVERT: B 121 ASN cc_start: 0.7700 (m-40) cc_final: 0.7133 (t0) REVERT: B 140 PHE cc_start: 0.8053 (p90) cc_final: 0.7669 (p90) REVERT: B 171 VAL cc_start: 0.8688 (p) cc_final: 0.8400 (t) REVERT: B 177 MET cc_start: 0.4809 (OUTLIER) cc_final: 0.3622 (ppp) REVERT: B 377 LYS cc_start: 0.8459 (tppp) cc_final: 0.8174 (tppp) REVERT: B 450 TYR cc_start: 0.7116 (m-80) cc_final: 0.6223 (m-10) REVERT: B 644 ARG cc_start: 0.8627 (mtp-110) cc_final: 0.8088 (mtm180) REVERT: B 981 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8011 (ptp90) REVERT: B 986 GLU cc_start: 0.8401 (mp0) cc_final: 0.7620 (mp0) REVERT: B 1048 MET cc_start: 0.9487 (ptm) cc_final: 0.9257 (ptp) REVERT: G 121 ASN cc_start: 0.7477 (m-40) cc_final: 0.6858 (t0) REVERT: G 140 PHE cc_start: 0.8101 (p90) cc_final: 0.7663 (p90) REVERT: G 177 MET cc_start: 0.4784 (mmt) cc_final: 0.3500 (ppp) REVERT: G 346 PHE cc_start: 0.7905 (m-80) cc_final: 0.7204 (m-80) REVERT: G 450 TYR cc_start: 0.7248 (m-80) cc_final: 0.6324 (m-10) REVERT: G 569 ASP cc_start: 0.8447 (m-30) cc_final: 0.8152 (t0) REVERT: G 623 HIS cc_start: 0.8054 (m-70) cc_final: 0.7822 (m-70) outliers start: 32 outliers final: 25 residues processed: 185 average time/residue: 1.0286 time to fit residues: 232.2583 Evaluate side-chains 180 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 628 THR 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 A residue 1124 CYS 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 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 127 PHE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain G residue 574 VAL Chi-restraints excluded: chain G residue 628 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 238 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 233 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079378 restraints weight = 43743.647| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.98 r_work: 0.2932 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25872 Z= 0.109 Angle : 0.589 11.462 35310 Z= 0.297 Chirality : 0.045 0.332 4116 Planarity : 0.004 0.053 4452 Dihedral : 6.376 55.762 4410 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.06 % Allowed : 12.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3078 helix: 1.83 (0.21), residues: 708 sheet: 1.33 (0.19), residues: 717 loop : -1.46 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 631 HIS 0.007 0.001 HIS B 338 PHE 0.029 0.001 PHE G 937 TYR 0.016 0.001 TYR B1065 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.82174 ( 135) link_BETA1-4 : bond 0.00368 ( 6) link_BETA1-4 : angle 0.85292 ( 18) hydrogen bonds : bond 0.04623 ( 999) hydrogen bonds : angle 4.71342 ( 2835) SS BOND : bond 0.00260 ( 39) SS BOND : angle 2.20558 ( 78) covalent geometry : bond 0.00241 (25773) covalent geometry : angle 0.55450 (35079) Misc. bond : bond 0.00088 ( 9) ********************** 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 192 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7897 (m-40) cc_final: 0.7446 (t0) REVERT: A 140 PHE cc_start: 0.8157 (p90) cc_final: 0.7380 (p90) REVERT: A 177 MET cc_start: 0.4885 (mmt) cc_final: 0.3978 (ppp) REVERT: A 346 PHE cc_start: 0.7966 (m-80) cc_final: 0.7443 (m-80) REVERT: A 359 ASN cc_start: 0.8954 (m-40) cc_final: 0.8707 (m-40) REVERT: A 452 TYR cc_start: 0.7177 (p90) cc_final: 0.6802 (p90) REVERT: A 644 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8155 (mtm180) REVERT: A 866 GLU cc_start: 0.8468 (mp0) cc_final: 0.8166 (mp0) REVERT: A 937 PHE cc_start: 0.8307 (t80) cc_final: 0.8075 (t80) REVERT: A 981 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7997 (ptp-170) REVERT: B 102 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7597 (mtp85) REVERT: B 121 ASN cc_start: 0.7670 (m-40) cc_final: 0.7009 (t0) REVERT: B 140 PHE cc_start: 0.8046 (p90) cc_final: 0.7670 (p90) REVERT: B 177 MET cc_start: 0.4778 (OUTLIER) cc_final: 0.3792 (ppp) REVERT: B 377 LYS cc_start: 0.8445 (tppp) cc_final: 0.8163 (tppp) REVERT: B 450 TYR cc_start: 0.7140 (m-80) cc_final: 0.6260 (m-10) REVERT: B 626 GLN cc_start: 0.8324 (mt0) cc_final: 0.7989 (pt0) REVERT: B 644 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8043 (mtm180) REVERT: B 981 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (ptp90) REVERT: B 986 GLU cc_start: 0.8405 (mp0) cc_final: 0.7670 (mp0) REVERT: B 1048 MET cc_start: 0.9479 (ptm) cc_final: 0.9173 (ptp) REVERT: G 121 ASN cc_start: 0.7473 (m-40) cc_final: 0.6829 (t0) REVERT: G 140 PHE cc_start: 0.8083 (p90) cc_final: 0.7643 (p90) REVERT: G 177 MET cc_start: 0.4810 (mmt) cc_final: 0.3606 (ppp) REVERT: G 346 PHE cc_start: 0.8050 (m-80) cc_final: 0.7376 (m-80) REVERT: G 450 TYR cc_start: 0.7241 (m-80) cc_final: 0.6275 (m-10) REVERT: G 569 ASP cc_start: 0.8306 (m-30) cc_final: 0.8103 (t0) REVERT: G 584 ASP cc_start: 0.8025 (m-30) cc_final: 0.7758 (m-30) REVERT: G 623 HIS cc_start: 0.8098 (m-70) cc_final: 0.7842 (m-70) outliers start: 29 outliers final: 21 residues processed: 183 average time/residue: 1.0146 time to fit residues: 225.0126 Evaluate side-chains 181 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 628 THR 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 A residue 1124 CYS 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 958 ASN Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 567 ILE Chi-restraints excluded: chain G residue 574 VAL Chi-restraints excluded: chain G residue 703 VAL Chi-restraints excluded: chain G residue 738 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 275 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.128702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076488 restraints weight = 43774.783| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.97 r_work: 0.2880 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25872 Z= 0.175 Angle : 0.638 10.276 35310 Z= 0.325 Chirality : 0.047 0.343 4116 Planarity : 0.004 0.054 4452 Dihedral : 6.334 56.040 4410 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.06 % Allowed : 12.40 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3078 helix: 1.76 (0.20), residues: 708 sheet: 1.11 (0.19), residues: 756 loop : -1.56 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 884 HIS 0.007 0.001 HIS G1062 PHE 0.030 0.002 PHE B 937 TYR 0.018 0.001 TYR A1065 ARG 0.002 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 45) link_NAG-ASN : angle 2.98761 ( 135) link_BETA1-4 : bond 0.00380 ( 6) link_BETA1-4 : angle 1.02708 ( 18) hydrogen bonds : bond 0.06095 ( 999) hydrogen bonds : angle 4.91333 ( 2835) SS BOND : bond 0.00291 ( 39) SS BOND : angle 2.52387 ( 78) covalent geometry : bond 0.00428 (25773) covalent geometry : angle 0.60055 (35079) Misc. bond : bond 0.00098 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22533.06 seconds wall clock time: 389 minutes 32.98 seconds (23372.98 seconds total)