Starting phenix.real_space_refine on Sun Jun 22 00:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxl_37910/06_2025/8wxl_37910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxl_37910/06_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_37910/06_2025/8wxl_37910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxl_37910/06_2025/8wxl_37910.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxl_37910/06_2025/8wxl_37910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxl_37910/06_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-5710/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: 13.95, per 1000 atoms: 0.55 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: 5.94 Conformation dependent library (CDL) restraints added in 3.2 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: 3.69 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: 10.53 Time building geometry restraints manager: 7.13 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: 0.22 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.230 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:35.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.240 ------------------------------------------------------------------------------- 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 : 2.894 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: 1.3567 time to fit residues: 450.1774 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 : 2.803 ------------------------------------------------------------------------------- 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 = 0.130728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079205 restraints weight = 43980.183| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.97 r_work: 0.2957 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 8.385 100.128 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 0.00545 ( 6) link_BETA1-4 : angle 0.81447 ( 18) hydrogen bonds : bond 0.05306 ( 999) hydrogen bonds : angle 5.11342 ( 2835) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.24226 ( 78) covalent geometry : bond 0.00239 (25773) covalent geometry : angle 0.54489 (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 : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7721 (m-40) cc_final: 0.7154 (t0) REVERT: A 140 PHE cc_start: 0.8037 (p90) cc_final: 0.7136 (p90) REVERT: A 200 TYR cc_start: 0.8226 (m-80) cc_final: 0.7996 (m-80) REVERT: A 359 ASN cc_start: 0.8829 (m-40) cc_final: 0.8588 (m-40) REVERT: A 377 LYS cc_start: 0.8585 (tppp) cc_final: 0.8345 (tppp) REVERT: A 626 GLN cc_start: 0.8090 (mt0) cc_final: 0.7873 (mt0) REVERT: A 644 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8176 (mtm180) REVERT: A 866 GLU cc_start: 0.8376 (mp0) cc_final: 0.8090 (mp0) REVERT: B 140 PHE cc_start: 0.7977 (p90) cc_final: 0.7640 (p90) REVERT: B 164 ASN cc_start: 0.7607 (t0) cc_final: 0.7130 (t0) REVERT: B 171 VAL cc_start: 0.8768 (p) cc_final: 0.8504 (t) REVERT: B 377 LYS cc_start: 0.8425 (tppp) cc_final: 0.8180 (tppp) REVERT: B 463 PHE cc_start: 0.8843 (m-10) cc_final: 0.8553 (m-10) REVERT: B 623 HIS cc_start: 0.8241 (m-70) cc_final: 0.8014 (m-70) REVERT: G 26 GLN cc_start: 0.7685 (mp10) cc_final: 0.7482 (mp10) REVERT: G 100 ILE cc_start: 0.8397 (mm) cc_final: 0.8197 (mp) REVERT: G 121 ASN cc_start: 0.7562 (m-40) cc_final: 0.6916 (t0) REVERT: G 140 PHE cc_start: 0.8084 (p90) cc_final: 0.7634 (p90) REVERT: G 584 ASP cc_start: 0.8034 (m-30) cc_final: 0.7807 (m-30) REVERT: G 623 HIS cc_start: 0.8143 (m-70) cc_final: 0.7824 (m-70) outliers start: 23 outliers final: 9 residues processed: 203 average time/residue: 1.3579 time to fit residues: 336.4233 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 : 4.024 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.128978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076747 restraints weight = 43576.205| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.98 r_work: 0.2902 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25872 Z= 0.148 Angle : 0.595 10.347 35310 Z= 0.307 Chirality : 0.047 0.372 4116 Planarity : 0.004 0.039 4452 Dihedral : 8.115 95.562 4410 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.02 % Allowed : 8.16 % Favored : 90.82 % 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: 0.13 (0.15), residues: 3078 helix: 1.73 (0.20), residues: 717 sheet: 1.26 (0.18), residues: 741 loop : -1.32 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 884 HIS 0.006 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 0.00326 ( 45) link_NAG-ASN : angle 2.71999 ( 135) link_BETA1-4 : bond 0.00331 ( 6) link_BETA1-4 : angle 0.98324 ( 18) hydrogen bonds : bond 0.05981 ( 999) hydrogen bonds : angle 5.04184 ( 2835) SS BOND : bond 0.00392 ( 39) SS BOND : angle 1.35120 ( 78) covalent geometry : bond 0.00350 (25773) covalent geometry : angle 0.56841 (35079) Misc. bond : bond 0.00144 ( 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 199 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.784 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: 0.7866 (m-40) cc_final: 0.7263 (t0) REVERT: A 133 PHE cc_start: 0.7922 (m-80) cc_final: 0.7715 (m-80) REVERT: A 140 PHE cc_start: 0.8108 (p90) cc_final: 0.7307 (p90) REVERT: A 346 PHE cc_start: 0.7609 (m-80) cc_final: 0.7250 (m-80) REVERT: A 359 ASN cc_start: 0.8851 (m-40) cc_final: 0.8611 (m-40) REVERT: A 626 GLN cc_start: 0.8167 (mt0) cc_final: 0.7951 (mt0) REVERT: A 644 ARG cc_start: 0.8729 (mtp-110) cc_final: 0.8171 (mtm180) REVERT: A 866 GLU cc_start: 0.8405 (mp0) cc_final: 0.8104 (mp0) REVERT: B 135 PHE cc_start: 0.7668 (m-80) cc_final: 0.7449 (m-80) REVERT: B 140 PHE cc_start: 0.7997 (p90) cc_final: 0.7640 (p90) REVERT: B 164 ASN cc_start: 0.7594 (t0) cc_final: 0.7145 (t0) REVERT: B 171 VAL cc_start: 0.8756 (p) cc_final: 0.8454 (t) REVERT: B 463 PHE cc_start: 0.8851 (m-10) cc_final: 0.8543 (m-10) REVERT: B 623 HIS cc_start: 0.8332 (m-70) cc_final: 0.8080 (m-70) REVERT: G 26 GLN cc_start: 0.7733 (mp10) cc_final: 0.7527 (mp10) REVERT: G 121 ASN cc_start: 0.7515 (m-40) cc_final: 0.6851 (t0) REVERT: G 140 PHE cc_start: 0.8092 (p90) cc_final: 0.7632 (p90) REVERT: G 164 ASN cc_start: 0.7617 (t0) cc_final: 0.7268 (t0) REVERT: G 200 TYR cc_start: 0.8148 (m-80) cc_final: 0.7923 (m-80) REVERT: G 623 HIS cc_start: 0.8180 (m-70) cc_final: 0.7921 (m-70) outliers start: 28 outliers final: 19 residues processed: 190 average time/residue: 1.0183 time to fit residues: 234.9546 Evaluate side-chains 176 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.128878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.076867 restraints weight = 44060.965| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.98 r_work: 0.2897 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25872 Z= 0.152 Angle : 0.597 10.242 35310 Z= 0.308 Chirality : 0.047 0.366 4116 Planarity : 0.004 0.039 4452 Dihedral : 7.976 92.866 4410 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.32 % Allowed : 9.37 % Favored : 89.32 % 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: 0.08 (0.15), residues: 3078 helix: 1.72 (0.20), residues: 711 sheet: 1.23 (0.18), residues: 747 loop : -1.37 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 884 HIS 0.006 0.001 HIS G1062 PHE 0.026 0.001 PHE B 937 TYR 0.018 0.001 TYR A1065 ARG 0.004 0.000 ARG G 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 45) link_NAG-ASN : angle 2.74688 ( 135) link_BETA1-4 : bond 0.00341 ( 6) link_BETA1-4 : angle 0.97507 ( 18) hydrogen bonds : bond 0.05997 ( 999) hydrogen bonds : angle 5.01548 ( 2835) SS BOND : bond 0.00306 ( 39) SS BOND : angle 1.44842 ( 78) covalent geometry : bond 0.00364 (25773) covalent geometry : angle 0.56979 (35079) Misc. bond : bond 0.00094 ( 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 203 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7955 (m-40) cc_final: 0.7360 (t0) REVERT: A 140 PHE cc_start: 0.8121 (p90) cc_final: 0.7327 (p90) REVERT: A 177 MET cc_start: 0.4667 (mmt) cc_final: 0.3355 (pp-130) REVERT: A 359 ASN cc_start: 0.8878 (m-40) cc_final: 0.8627 (m-40) REVERT: A 439 LYS cc_start: 0.9443 (ttpp) cc_final: 0.9242 (tmmt) REVERT: A 626 GLN cc_start: 0.8200 (mt0) cc_final: 0.7929 (mt0) REVERT: A 644 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8166 (mtm180) REVERT: A 866 GLU cc_start: 0.8406 (mp0) cc_final: 0.8112 (mp0) REVERT: A 981 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (ptp90) REVERT: B 121 ASN cc_start: 0.7605 (m-40) cc_final: 0.6920 (t0) REVERT: B 135 PHE cc_start: 0.7687 (m-80) cc_final: 0.7432 (m-80) REVERT: B 140 PHE cc_start: 0.8014 (p90) cc_final: 0.7675 (p90) REVERT: B 164 ASN cc_start: 0.7522 (t0) cc_final: 0.7043 (t0) REVERT: B 171 VAL cc_start: 0.8758 (p) cc_final: 0.8460 (t) REVERT: B 377 LYS cc_start: 0.8456 (tppp) cc_final: 0.8174 (tppp) REVERT: B 450 TYR cc_start: 0.6986 (m-80) cc_final: 0.6162 (m-10) REVERT: B 644 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8089 (mtm180) REVERT: G 121 ASN cc_start: 0.7534 (m-40) cc_final: 0.6806 (t0) REVERT: G 140 PHE cc_start: 0.8118 (p90) cc_final: 0.7659 (p90) REVERT: G 164 ASN cc_start: 0.7630 (t0) cc_final: 0.7289 (t0) REVERT: G 450 TYR cc_start: 0.7180 (m-80) cc_final: 0.5892 (m-10) REVERT: G 623 HIS cc_start: 0.8154 (m-70) cc_final: 0.7882 (m-70) outliers start: 36 outliers final: 22 residues processed: 193 average time/residue: 1.1294 time to fit residues: 262.7237 Evaluate side-chains 178 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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 A residue 738 MET Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1090 GLU 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 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: 0.5980 chunk 245 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 217 GLN A 338 HIS B 134 GLN B 338 HIS G 134 GLN G 217 GLN G 338 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076612 restraints weight = 43908.076| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.98 r_work: 0.2886 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25872 Z= 0.152 Angle : 0.605 10.245 35310 Z= 0.310 Chirality : 0.047 0.359 4116 Planarity : 0.004 0.040 4452 Dihedral : 7.849 90.515 4410 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.24 % Allowed : 9.77 % Favored : 88.99 % 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: 1.20 (0.18), residues: 747 loop : -1.42 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 631 HIS 0.006 0.001 HIS G1062 PHE 0.026 0.001 PHE B 937 TYR 0.017 0.001 TYR A1065 ARG 0.005 0.000 ARG G 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 45) link_NAG-ASN : angle 2.75966 ( 135) link_BETA1-4 : bond 0.00360 ( 6) link_BETA1-4 : angle 0.99692 ( 18) hydrogen bonds : bond 0.06001 ( 999) hydrogen bonds : angle 4.99258 ( 2835) SS BOND : bond 0.00295 ( 39) SS BOND : angle 1.39783 ( 78) covalent geometry : bond 0.00362 (25773) covalent geometry : angle 0.57775 (35079) Misc. bond : bond 0.00173 ( 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 196 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 3.056 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: 0.7929 (m-40) cc_final: 0.7311 (t0) REVERT: A 140 PHE cc_start: 0.8138 (p90) cc_final: 0.7327 (p90) REVERT: A 177 MET cc_start: 0.4813 (mmt) cc_final: 0.3600 (pp-130) REVERT: A 215 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: A 346 PHE cc_start: 0.7733 (m-80) cc_final: 0.7309 (m-80) REVERT: A 359 ASN cc_start: 0.8884 (m-40) cc_final: 0.8626 (m-40) REVERT: A 626 GLN cc_start: 0.8194 (mt0) cc_final: 0.7950 (mt0) REVERT: A 644 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8171 (mtm180) REVERT: A 866 GLU cc_start: 0.8425 (mp0) cc_final: 0.8133 (mp0) REVERT: A 981 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (ptp-170) REVERT: B 135 PHE cc_start: 0.7716 (m-80) cc_final: 0.7486 (m-80) REVERT: B 140 PHE cc_start: 0.8047 (p90) cc_final: 0.7681 (p90) REVERT: B 171 VAL cc_start: 0.8757 (p) cc_final: 0.8472 (t) REVERT: B 377 LYS cc_start: 0.8463 (tppp) cc_final: 0.8179 (tppp) REVERT: B 450 TYR cc_start: 0.7130 (m-80) cc_final: 0.6207 (m-10) REVERT: B 644 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8101 (mtm180) REVERT: B 986 GLU cc_start: 0.8390 (mp0) cc_final: 0.7742 (mp0) REVERT: B 1048 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.9258 (ptp) REVERT: G 121 ASN cc_start: 0.7690 (m-40) cc_final: 0.6965 (t0) REVERT: G 140 PHE cc_start: 0.8134 (p90) cc_final: 0.7679 (p90) REVERT: G 346 PHE cc_start: 0.7633 (m-80) cc_final: 0.7133 (m-80) REVERT: G 623 HIS cc_start: 0.8157 (m-70) cc_final: 0.7892 (m-70) outliers start: 34 outliers final: 22 residues processed: 188 average time/residue: 1.0094 time to fit residues: 231.9052 Evaluate side-chains 175 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 2.801 ------------------------------------------------------------------------------- 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 568 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 981 ARG Chi-restraints excluded: chain 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 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1048 MET 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 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 958 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: 6.9990 chunk 236 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 134 GLN B 338 HIS G 134 GLN G 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074591 restraints weight = 43734.113| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.96 r_work: 0.2869 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 25872 Z= 0.227 Angle : 0.678 10.833 35310 Z= 0.349 Chirality : 0.050 0.378 4116 Planarity : 0.005 0.042 4452 Dihedral : 7.952 90.538 4410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.87 % Allowed : 9.99 % Favored : 88.14 % 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: -0.21 (0.15), residues: 3078 helix: 1.50 (0.20), residues: 711 sheet: 1.02 (0.19), residues: 747 loop : -1.55 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 884 HIS 0.008 0.001 HIS G1062 PHE 0.030 0.002 PHE B 937 TYR 0.019 0.002 TYR G 278 ARG 0.005 0.000 ARG A 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 45) link_NAG-ASN : angle 3.00893 ( 135) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 1.25894 ( 18) hydrogen bonds : bond 0.07323 ( 999) hydrogen bonds : angle 5.21369 ( 2835) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.80089 ( 78) covalent geometry : bond 0.00564 (25773) covalent geometry : angle 0.64807 (35079) Misc. bond : bond 0.00333 ( 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 213 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 2.680 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: 0.7992 (m-40) cc_final: 0.7420 (t0) REVERT: A 140 PHE cc_start: 0.8146 (p90) cc_final: 0.7285 (p90) REVERT: A 177 MET cc_start: 0.4840 (mmt) cc_final: 0.3591 (pp-130) REVERT: A 346 PHE cc_start: 0.7864 (m-80) cc_final: 0.7035 (m-80) REVERT: A 359 ASN cc_start: 0.8894 (m-40) cc_final: 0.8651 (m-40) REVERT: A 450 TYR cc_start: 0.6975 (m-80) cc_final: 0.5838 (m-10) REVERT: A 626 GLN cc_start: 0.8219 (mt0) cc_final: 0.7923 (mt0) REVERT: A 644 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8197 (mtm180) REVERT: A 866 GLU cc_start: 0.8546 (mp0) cc_final: 0.8206 (mp0) REVERT: A 981 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8106 (ptp90) REVERT: B 135 PHE cc_start: 0.7866 (m-80) cc_final: 0.7553 (m-80) REVERT: B 140 PHE cc_start: 0.8077 (p90) cc_final: 0.7715 (p90) REVERT: B 171 VAL cc_start: 0.8790 (p) cc_final: 0.8508 (t) REVERT: B 177 MET cc_start: 0.4744 (mmt) cc_final: 0.3105 (pp-130) REVERT: B 377 LYS cc_start: 0.8467 (tppp) cc_final: 0.8242 (tppp) REVERT: B 450 TYR cc_start: 0.7117 (m-80) cc_final: 0.6288 (m-10) REVERT: B 644 ARG cc_start: 0.8669 (mtp-110) cc_final: 0.8170 (mtm180) REVERT: B 986 GLU cc_start: 0.8346 (mp0) cc_final: 0.8135 (mp0) REVERT: G 121 ASN cc_start: 0.7463 (m-40) cc_final: 0.6860 (t0) REVERT: G 140 PHE cc_start: 0.8167 (p90) cc_final: 0.7699 (p90) REVERT: G 346 PHE cc_start: 0.7404 (m-80) cc_final: 0.6814 (m-80) REVERT: G 450 TYR cc_start: 0.7137 (m-80) cc_final: 0.6219 (m-10) REVERT: G 623 HIS cc_start: 0.8071 (m-70) cc_final: 0.7838 (m-70) outliers start: 51 outliers final: 32 residues processed: 200 average time/residue: 1.0280 time to fit residues: 250.7874 Evaluate side-chains 187 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 628 THR 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 574 VAL 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 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 981 ARG Chi-restraints excluded: chain G residue 1090 GLU Chi-restraints excluded: chain G residue 1094 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: 0.9990 chunk 311 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 305 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 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 = 0.3860 r_free = 0.3860 target = 0.128578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076729 restraints weight = 43967.781| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.97 r_work: 0.2884 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25872 Z= 0.139 Angle : 0.631 11.837 35310 Z= 0.322 Chirality : 0.047 0.352 4116 Planarity : 0.004 0.041 4452 Dihedral : 7.678 87.458 4410 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.21 % Allowed : 11.31 % Favored : 87.49 % 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: -0.10 (0.15), residues: 3078 helix: 1.66 (0.20), residues: 708 sheet: 1.13 (0.19), residues: 744 loop : -1.54 (0.14), residues: 1626 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 0.018 0.001 TYR G 160 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 45) link_NAG-ASN : angle 2.81016 ( 135) link_BETA1-4 : bond 0.00319 ( 6) link_BETA1-4 : angle 0.96312 ( 18) hydrogen bonds : bond 0.05759 ( 999) hydrogen bonds : angle 4.98834 ( 2835) SS BOND : bond 0.00307 ( 39) SS BOND : angle 2.73226 ( 78) covalent geometry : bond 0.00321 (25773) covalent geometry : angle 0.59447 (35079) Misc. bond : bond 0.00199 ( 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 189 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7901 (m-40) cc_final: 0.7374 (t0) REVERT: A 140 PHE cc_start: 0.8163 (p90) cc_final: 0.7376 (p90) REVERT: A 177 MET cc_start: 0.4809 (mmt) cc_final: 0.3702 (ppp) REVERT: A 346 PHE cc_start: 0.8017 (m-80) cc_final: 0.7354 (m-80) REVERT: A 359 ASN cc_start: 0.8877 (m-40) cc_final: 0.8602 (m-40) REVERT: A 450 TYR cc_start: 0.6687 (m-80) cc_final: 0.6338 (m-10) REVERT: A 452 TYR cc_start: 0.6801 (p90) cc_final: 0.6509 (p90) REVERT: A 492 SER cc_start: 0.8925 (p) cc_final: 0.8682 (t) REVERT: A 626 GLN cc_start: 0.8180 (mt0) cc_final: 0.7904 (mt0) REVERT: A 644 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.8154 (mtm180) REVERT: A 866 GLU cc_start: 0.8481 (mp0) cc_final: 0.8184 (mp0) REVERT: A 937 PHE cc_start: 0.8285 (t80) cc_final: 0.8073 (t80) REVERT: B 121 ASN cc_start: 0.7725 (m-40) cc_final: 0.7091 (t0) REVERT: B 135 PHE cc_start: 0.7836 (m-80) cc_final: 0.7542 (m-80) REVERT: B 140 PHE cc_start: 0.8039 (p90) cc_final: 0.7687 (p90) REVERT: B 171 VAL cc_start: 0.8706 (p) cc_final: 0.8410 (t) REVERT: B 177 MET cc_start: 0.4878 (mmt) cc_final: 0.3080 (ppp) REVERT: B 377 LYS cc_start: 0.8442 (tppp) cc_final: 0.8158 (tppp) REVERT: B 450 TYR cc_start: 0.7083 (m-80) cc_final: 0.6307 (m-10) REVERT: B 569 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8133 (t0) REVERT: B 644 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8117 (mtm180) REVERT: B 981 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7997 (ptp90) REVERT: B 986 GLU cc_start: 0.8340 (mp0) cc_final: 0.8111 (mp0) REVERT: G 121 ASN cc_start: 0.7422 (m-40) cc_final: 0.6779 (t0) REVERT: G 140 PHE cc_start: 0.8091 (p90) cc_final: 0.7632 (p90) REVERT: G 346 PHE cc_start: 0.7720 (m-80) cc_final: 0.7044 (m-80) REVERT: G 450 TYR cc_start: 0.7126 (m-80) cc_final: 0.6296 (m-10) REVERT: G 623 HIS cc_start: 0.8038 (m-70) cc_final: 0.7808 (m-70) outliers start: 33 outliers final: 23 residues processed: 181 average time/residue: 0.9807 time to fit residues: 217.8819 Evaluate side-chains 175 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 569 ASP 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 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 569 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 981 ARG Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 11 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 0.2980 chunk 189 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 G 538 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076179 restraints weight = 43725.185| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.97 r_work: 0.2885 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25872 Z= 0.161 Angle : 0.649 14.425 35310 Z= 0.331 Chirality : 0.048 0.354 4116 Planarity : 0.004 0.044 4452 Dihedral : 7.547 84.856 4410 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.28 % Allowed : 11.34 % Favored : 87.38 % 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: -0.18 (0.15), residues: 3078 helix: 1.64 (0.20), residues: 708 sheet: 0.98 (0.19), residues: 759 loop : -1.58 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 631 HIS 0.006 0.001 HIS A1062 PHE 0.030 0.002 PHE B 937 TYR 0.018 0.001 TYR A1065 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 45) link_NAG-ASN : angle 2.81552 ( 135) link_BETA1-4 : bond 0.00346 ( 6) link_BETA1-4 : angle 1.01979 ( 18) hydrogen bonds : bond 0.06142 ( 999) hydrogen bonds : angle 5.01360 ( 2835) SS BOND : bond 0.00299 ( 39) SS BOND : angle 2.98830 ( 78) covalent geometry : bond 0.00386 (25773) covalent geometry : angle 0.61057 (35079) Misc. bond : bond 0.00177 ( 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 191 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7930 (m-40) cc_final: 0.7383 (t0) REVERT: A 140 PHE cc_start: 0.8185 (p90) cc_final: 0.7397 (p90) REVERT: A 177 MET cc_start: 0.4805 (mmt) cc_final: 0.3642 (ppp) REVERT: A 215 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: A 346 PHE cc_start: 0.8038 (m-80) cc_final: 0.7618 (m-80) REVERT: A 359 ASN cc_start: 0.8870 (m-40) cc_final: 0.8620 (m-40) REVERT: A 626 GLN cc_start: 0.8222 (mt0) cc_final: 0.7958 (mt0) REVERT: A 644 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8174 (mtm180) REVERT: A 866 GLU cc_start: 0.8476 (mp0) cc_final: 0.8164 (mp0) REVERT: B 121 ASN cc_start: 0.7737 (m-40) cc_final: 0.7108 (t0) REVERT: B 135 PHE cc_start: 0.7835 (m-80) cc_final: 0.7545 (m-80) REVERT: B 140 PHE cc_start: 0.8068 (p90) cc_final: 0.7720 (p90) REVERT: B 171 VAL cc_start: 0.8705 (p) cc_final: 0.8409 (t) REVERT: B 177 MET cc_start: 0.4906 (mmt) cc_final: 0.3220 (ppp) REVERT: B 377 LYS cc_start: 0.8471 (tppp) cc_final: 0.8190 (tppp) REVERT: B 450 TYR cc_start: 0.7103 (m-80) cc_final: 0.6290 (m-10) REVERT: B 644 ARG cc_start: 0.8630 (mtp-110) cc_final: 0.8112 (mtm180) REVERT: B 981 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8063 (ptp90) REVERT: B 986 GLU cc_start: 0.8371 (mp0) cc_final: 0.8127 (mp0) REVERT: G 121 ASN cc_start: 0.7366 (m-40) cc_final: 0.6757 (t0) REVERT: G 140 PHE cc_start: 0.8114 (p90) cc_final: 0.7681 (p90) REVERT: G 177 MET cc_start: 0.4677 (mmt) cc_final: 0.3122 (ppp) REVERT: G 450 TYR cc_start: 0.7164 (m-80) cc_final: 0.6331 (m-10) REVERT: G 623 HIS cc_start: 0.8062 (m-70) cc_final: 0.7845 (m-70) outliers start: 35 outliers final: 27 residues processed: 182 average time/residue: 1.3929 time to fit residues: 316.5824 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 : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 738 MET Chi-restraints excluded: chain A residue 914 LEU 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 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 574 VAL 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 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: 9.9990 chunk 131 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 199 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 0.0470 chunk 193 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.129773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078010 restraints weight = 44046.215| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.98 r_work: 0.2932 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25872 Z= 0.117 Angle : 0.605 11.330 35310 Z= 0.307 Chirality : 0.046 0.342 4116 Planarity : 0.004 0.047 4452 Dihedral : 7.117 77.791 4410 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.10 % Allowed : 11.78 % Favored : 87.12 % 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: 1.76 (0.20), residues: 708 sheet: 1.07 (0.19), residues: 762 loop : -1.51 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 631 HIS 0.004 0.001 HIS G1062 PHE 0.032 0.001 PHE G 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 0.00340 ( 45) link_NAG-ASN : angle 2.74136 ( 135) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 0.86999 ( 18) hydrogen bonds : bond 0.05109 ( 999) hydrogen bonds : angle 4.83523 ( 2835) SS BOND : bond 0.00254 ( 39) SS BOND : angle 2.40242 ( 78) covalent geometry : bond 0.00258 (25773) covalent geometry : angle 0.57169 (35079) Misc. bond : bond 0.00154 ( 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 195 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7918 (m-40) cc_final: 0.7479 (t0) REVERT: A 140 PHE cc_start: 0.8174 (p90) cc_final: 0.7385 (p90) REVERT: A 177 MET cc_start: 0.4951 (mmt) cc_final: 0.3933 (ppp) REVERT: A 346 PHE cc_start: 0.8023 (m-80) cc_final: 0.7513 (m-80) REVERT: A 359 ASN cc_start: 0.8907 (m-40) cc_final: 0.8639 (m-40) REVERT: A 439 LYS cc_start: 0.9311 (tmmt) cc_final: 0.8808 (mmpt) REVERT: A 452 TYR cc_start: 0.6990 (p90) cc_final: 0.6682 (p90) REVERT: A 644 ARG cc_start: 0.8741 (mtp-110) cc_final: 0.8172 (mtm180) REVERT: A 866 GLU cc_start: 0.8457 (mp0) cc_final: 0.8166 (mp0) REVERT: B 121 ASN cc_start: 0.7737 (m-40) cc_final: 0.7171 (t0) REVERT: B 135 PHE cc_start: 0.7810 (m-80) cc_final: 0.7508 (m-80) REVERT: B 140 PHE cc_start: 0.8064 (p90) cc_final: 0.7683 (p90) REVERT: B 171 VAL cc_start: 0.8667 (p) cc_final: 0.8370 (t) REVERT: B 177 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.3195 (ppp) REVERT: B 377 LYS cc_start: 0.8470 (tppp) cc_final: 0.8189 (tppp) REVERT: B 450 TYR cc_start: 0.7105 (m-80) cc_final: 0.6182 (m-10) REVERT: B 569 ASP cc_start: 0.8370 (m-30) cc_final: 0.8120 (OUTLIER) REVERT: B 644 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8091 (mtm180) REVERT: B 981 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (ptp90) REVERT: B 986 GLU cc_start: 0.8400 (mp0) cc_final: 0.7642 (mp0) REVERT: G 121 ASN cc_start: 0.7479 (m-40) cc_final: 0.6866 (t0) REVERT: G 140 PHE cc_start: 0.8100 (p90) cc_final: 0.7668 (p90) REVERT: G 177 MET cc_start: 0.4820 (mmt) cc_final: 0.3533 (ppp) REVERT: G 346 PHE cc_start: 0.7840 (m-80) cc_final: 0.7139 (m-80) REVERT: G 450 TYR cc_start: 0.7197 (m-80) cc_final: 0.6333 (m-10) REVERT: G 569 ASP cc_start: 0.8443 (m-30) cc_final: 0.8138 (t0) REVERT: G 623 HIS cc_start: 0.8035 (m-70) cc_final: 0.7812 (m-70) outliers start: 30 outliers final: 23 residues processed: 188 average time/residue: 0.9577 time to fit residues: 221.6166 Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 914 LEU 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 G residue 127 PHE 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 736 CYS Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 854 ASN Chi-restraints excluded: chain G residue 958 ASN Chi-restraints excluded: chain G residue 1090 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 286 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 40 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.129379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077519 restraints weight = 43659.996| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.96 r_work: 0.2897 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25872 Z= 0.130 Angle : 0.616 11.358 35310 Z= 0.312 Chirality : 0.046 0.338 4116 Planarity : 0.004 0.047 4452 Dihedral : 6.767 68.194 4410 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.91 % Allowed : 12.37 % 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: 1.76 (0.20), residues: 708 sheet: 1.07 (0.19), residues: 762 loop : -1.53 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 631 HIS 0.005 0.001 HIS G1062 PHE 0.033 0.001 PHE G 937 TYR 0.017 0.001 TYR G1065 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 45) link_NAG-ASN : angle 2.81891 ( 135) link_BETA1-4 : bond 0.00354 ( 6) link_BETA1-4 : angle 0.93574 ( 18) hydrogen bonds : bond 0.05474 ( 999) hydrogen bonds : angle 4.86042 ( 2835) SS BOND : bond 0.00278 ( 39) SS BOND : angle 2.37396 ( 78) covalent geometry : bond 0.00301 (25773) covalent geometry : angle 0.58151 (35079) Misc. bond : bond 0.00156 ( 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 184 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7905 (m-40) cc_final: 0.7448 (t0) REVERT: A 140 PHE cc_start: 0.8176 (p90) cc_final: 0.7389 (p90) REVERT: A 177 MET cc_start: 0.4961 (mmt) cc_final: 0.3994 (ppp) REVERT: A 346 PHE cc_start: 0.7945 (m-80) cc_final: 0.7459 (m-80) REVERT: A 359 ASN cc_start: 0.8961 (m-40) cc_final: 0.8699 (m-40) REVERT: A 452 TYR cc_start: 0.7012 (p90) cc_final: 0.6653 (p90) REVERT: A 626 GLN cc_start: 0.8208 (mt0) cc_final: 0.8000 (mt0) REVERT: A 644 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8143 (mtm180) REVERT: A 866 GLU cc_start: 0.8467 (mp0) cc_final: 0.8159 (mp0) REVERT: B 121 ASN cc_start: 0.7721 (m-40) cc_final: 0.7145 (t0) REVERT: B 135 PHE cc_start: 0.7835 (m-80) cc_final: 0.7528 (m-80) REVERT: B 140 PHE cc_start: 0.8053 (p90) cc_final: 0.7666 (p90) REVERT: B 171 VAL cc_start: 0.8661 (p) cc_final: 0.8361 (t) REVERT: B 177 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.3236 (ppp) REVERT: B 377 LYS cc_start: 0.8443 (tppp) cc_final: 0.8158 (tppp) REVERT: B 450 TYR cc_start: 0.7174 (m-80) cc_final: 0.6405 (m-10) REVERT: B 644 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8072 (mtm180) REVERT: B 981 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8022 (ptp90) REVERT: B 986 GLU cc_start: 0.8384 (mp0) cc_final: 0.7648 (mp0) REVERT: G 121 ASN cc_start: 0.7456 (m-40) cc_final: 0.6843 (t0) REVERT: G 140 PHE cc_start: 0.8102 (p90) cc_final: 0.7667 (p90) REVERT: G 177 MET cc_start: 0.4816 (mmt) cc_final: 0.3584 (ppp) REVERT: G 346 PHE cc_start: 0.7871 (m-80) cc_final: 0.7132 (m-80) REVERT: G 450 TYR cc_start: 0.7200 (m-80) cc_final: 0.6279 (m-10) REVERT: G 569 ASP cc_start: 0.8425 (m-30) cc_final: 0.8148 (t0) REVERT: G 623 HIS cc_start: 0.8037 (m-70) cc_final: 0.7810 (m-70) outliers start: 25 outliers final: 24 residues processed: 178 average time/residue: 1.5423 time to fit residues: 336.8975 Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 6.008 ------------------------------------------------------------------------------- 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 569 ASP 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 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 G residue 127 PHE 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 275 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 252 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.128344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076145 restraints weight = 43758.412| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.97 r_work: 0.2899 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25872 Z= 0.172 Angle : 0.644 11.384 35310 Z= 0.328 Chirality : 0.047 0.351 4116 Planarity : 0.004 0.047 4452 Dihedral : 6.686 61.455 4410 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.10 % Allowed : 12.22 % Favored : 86.68 % 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: -0.13 (0.15), residues: 3078 helix: 1.70 (0.20), residues: 708 sheet: 1.12 (0.19), residues: 753 loop : -1.61 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 631 HIS 0.006 0.001 HIS A1062 PHE 0.032 0.002 PHE G 937 TYR 0.018 0.001 TYR A1065 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 45) link_NAG-ASN : angle 2.95981 ( 135) link_BETA1-4 : bond 0.00300 ( 6) link_BETA1-4 : angle 1.00434 ( 18) hydrogen bonds : bond 0.06150 ( 999) hydrogen bonds : angle 4.96067 ( 2835) SS BOND : bond 0.00282 ( 39) SS BOND : angle 2.50427 ( 78) covalent geometry : bond 0.00419 (25773) covalent geometry : angle 0.60741 (35079) Misc. bond : bond 0.00158 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25954.28 seconds wall clock time: 456 minutes 41.77 seconds (27401.77 seconds total)