Starting phenix.real_space_refine on Wed May 28 04:25:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydy_33760/05_2025/7ydy_33760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydy_33760/05_2025/7ydy_33760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ydy_33760/05_2025/7ydy_33760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydy_33760/05_2025/7ydy_33760.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydy_33760/05_2025/7ydy_33760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydy_33760/05_2025/7ydy_33760.cif" } resolution = 4.75 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1499 atoms to isotropic. 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 127 5.16 5 C 18280 2.51 5 N 4756 2.21 5 O 5597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28760 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "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: "G" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.29, per 1000 atoms: 0.57 Number of scatterers: 28760 At special positions: 0 Unit cell: (179.52, 161.92, 197.12, 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 127 16.00 O 5597 8.00 N 4756 7.00 C 18280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 4.1 seconds 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6788 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 65 sheets defined 16.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.618A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.110A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.804A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 748 through 754 removed outlier: 3.881A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.663A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.241A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.042A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.503A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.955A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.652A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.555A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.554A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 949 through 966 removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.075A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1032 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.667A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.744A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.924A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.695A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.719A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 946 through 966 removed outlier: 4.178A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.892A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1030 Processing helix chain 'H' and resid 196 through 200 removed outlier: 3.543A pdb=" N SER H 199 " --> pdb=" O PRO H 196 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 200' Processing helix chain 'L' and resid 129 through 133 removed outlier: 3.704A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.069A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.785A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.683A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.480A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.319A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.044A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.537A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.525A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.706A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.545A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.666A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.557A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.408A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 3.697A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.589A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.602A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.507A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.458A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.177A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.626A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.791A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.698A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.531A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 160 removed outlier: 5.302A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.997A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 597 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.581A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 355 through 358 removed outlier: 6.266A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.531A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.726A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.545A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.436A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.669A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.507A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.755A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.755A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 735 removed outlier: 4.194A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.665A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.801A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.583A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 152 through 158 removed outlier: 6.765A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.983A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.694A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 355 through 358 removed outlier: 5.604A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.668A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.381A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.510A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 721 removed outlier: 3.753A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 724 through 727 removed outlier: 3.504A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C1062 " --> pdb=" O GLU C 725 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.527A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.648A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.167A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.845A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.845A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.526A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 163 through 165 removed outlier: 4.191A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 209 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 218 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 216 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 17 through 23 removed outlier: 4.202A pdb=" N CYS L 22 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA L 73 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.833A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER L 92 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 101 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.833A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR L 106 " --> pdb=" O TYR L 88 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.121A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AH1, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.767A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.767A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL L 211 " --> pdb=" O TYR L 196 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2183 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: 13.99 Time building geometry restraints manager: 8.06 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: 9215 1.34 - 1.46: 7154 1.46 - 1.58: 12897 1.58 - 1.70: 0 1.70 - 1.82: 159 Bond restraints: 29425 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C3 NAG B1301 " pdb=" O3 NAG B1301 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 29420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 39171 1.40 - 2.80: 776 2.80 - 4.20: 92 4.20 - 5.60: 17 5.60 - 7.00: 7 Bond angle restraints: 40063 Sorted by residual: angle pdb=" C ILE C 896 " pdb=" N PRO C 897 " pdb=" CA PRO C 897 " ideal model delta sigma weight residual 120.03 116.11 3.92 9.90e-01 1.02e+00 1.57e+01 angle pdb=" N VAL B 524 " pdb=" CA VAL B 524 " pdb=" C VAL B 524 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" CA GLY B 431 " pdb=" C GLY B 431 " pdb=" O GLY B 431 " ideal model delta sigma weight residual 122.45 119.94 2.51 7.20e-01 1.93e+00 1.21e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" O GLY C 431 " ideal model delta sigma weight residual 122.52 119.95 2.57 7.90e-01 1.60e+00 1.06e+01 angle pdb=" CA PHE B 898 " pdb=" C PHE B 898 " pdb=" N PRO B 899 " ideal model delta sigma weight residual 120.79 117.77 3.02 9.70e-01 1.06e+00 9.71e+00 ... (remaining 40058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 17016 17.63 - 35.26: 833 35.26 - 52.89: 141 52.89 - 70.52: 38 70.52 - 88.16: 9 Dihedral angle restraints: 18037 sinusoidal: 7466 harmonic: 10571 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.97 82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 17.99 75.01 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 27.08 65.92 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 18034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3944 0.055 - 0.111: 632 0.111 - 0.166: 54 0.166 - 0.222: 3 0.222 - 0.277: 3 Chirality restraints: 4636 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4633 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG B1301 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG A1301 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " -0.014 2.00e-02 2.50e+03 1.63e-02 3.31e+00 pdb=" CG ASN A 282 " 0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.020 2.00e-02 2.50e+03 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6355 2.78 - 3.31: 24677 3.31 - 3.84: 45813 3.84 - 4.37: 51009 4.37 - 4.90: 90536 Nonbonded interactions: 218390 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.253 3.040 nonbonded pdb=" OG SER L 21 " pdb=" O ALA L 73 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.308 3.040 ... (remaining 218385 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 67.000 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 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 : 0.002 0.038 29508 Z= 0.124 Angle : 0.465 8.599 40265 Z= 0.251 Chirality : 0.042 0.277 4636 Planarity : 0.003 0.036 5150 Dihedral : 10.394 88.155 11108 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.89 % Rotamer: Outliers : 0.44 % Allowed : 2.02 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.11), residues: 3600 helix: -2.22 (0.14), residues: 570 sheet: -1.64 (0.18), residues: 677 loop : -3.18 (0.10), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 436 HIS 0.001 0.000 HIS B1064 PHE 0.010 0.000 PHE B 486 TYR 0.006 0.000 TYR A 495 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 30) link_NAG-ASN : angle 2.15686 ( 90) link_BETA1-4 : bond 0.00275 ( 6) link_BETA1-4 : angle 0.81917 ( 18) hydrogen bonds : bond 0.26190 ( 783) hydrogen bonds : angle 9.03761 ( 2183) SS BOND : bond 0.00166 ( 47) SS BOND : angle 0.57964 ( 94) covalent geometry : bond 0.00233 (29425) covalent geometry : angle 0.45394 (40063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 573 time to evaluate : 3.262 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8435 (t80) cc_final: 0.8193 (t80) REVERT: A 117 LEU cc_start: 0.8102 (tt) cc_final: 0.7824 (mt) REVERT: A 157 PHE cc_start: 0.6348 (t80) cc_final: 0.6022 (t80) REVERT: A 177 MET cc_start: -0.0082 (mmt) cc_final: -0.3511 (ttt) REVERT: A 238 PHE cc_start: 0.5773 (p90) cc_final: 0.5558 (p90) REVERT: A 242 LEU cc_start: 0.7813 (tp) cc_final: 0.7400 (tp) REVERT: A 244 LEU cc_start: 0.4697 (pt) cc_final: 0.4204 (mp) REVERT: A 321 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8348 (mp10) REVERT: A 697 MET cc_start: 0.6710 (ptm) cc_final: 0.6307 (mpp) REVERT: A 736 VAL cc_start: 0.8852 (t) cc_final: 0.8601 (m) REVERT: A 742 ILE cc_start: 0.7839 (mt) cc_final: 0.7487 (mp) REVERT: A 773 GLU cc_start: 0.8173 (tt0) cc_final: 0.7711 (mt-10) REVERT: A 859 THR cc_start: 0.7032 (p) cc_final: 0.6165 (p) REVERT: A 867 ASP cc_start: 0.9076 (m-30) cc_final: 0.8768 (t0) REVERT: A 878 LEU cc_start: 0.8080 (mt) cc_final: 0.7820 (mt) REVERT: A 896 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4952 (tp) REVERT: A 1018 ILE cc_start: 0.7449 (mm) cc_final: 0.7143 (mm) REVERT: A 1033 VAL cc_start: 0.6904 (t) cc_final: 0.6112 (t) REVERT: A 1118 ASP cc_start: 0.8625 (m-30) cc_final: 0.8355 (p0) REVERT: B 133 PHE cc_start: 0.6725 (m-80) cc_final: 0.6370 (m-80) REVERT: B 153 MET cc_start: 0.7346 (mmm) cc_final: 0.7115 (ppp) REVERT: B 177 MET cc_start: -0.1667 (mmt) cc_final: -0.3703 (ttt) REVERT: B 235 ILE cc_start: 0.5145 (mt) cc_final: 0.3807 (mm) REVERT: B 297 SER cc_start: 0.7358 (p) cc_final: 0.7091 (t) REVERT: B 380 TYR cc_start: 0.7581 (m-80) cc_final: 0.7223 (m-80) REVERT: B 421 TYR cc_start: 0.8495 (m-80) cc_final: 0.7906 (m-10) REVERT: B 578 ASP cc_start: 0.8326 (t0) cc_final: 0.7892 (m-30) REVERT: B 599 THR cc_start: 0.6959 (t) cc_final: 0.5953 (p) REVERT: B 697 MET cc_start: 0.7282 (ptm) cc_final: 0.7078 (tpt) REVERT: B 702 GLU cc_start: 0.7631 (tp30) cc_final: 0.7165 (mp0) REVERT: B 740 MET cc_start: 0.6733 (ttm) cc_final: 0.5935 (tpp) REVERT: B 762 GLN cc_start: 0.8370 (mt0) cc_final: 0.7915 (mp10) REVERT: B 788 ILE cc_start: 0.7445 (mm) cc_final: 0.7183 (mt) REVERT: B 866 THR cc_start: 0.6961 (p) cc_final: 0.6522 (t) REVERT: B 882 ILE cc_start: 0.8230 (pt) cc_final: 0.7530 (pt) REVERT: B 921 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8430 (mmmt) REVERT: B 953 ASN cc_start: 0.6788 (m-40) cc_final: 0.6482 (m-40) REVERT: B 993 ILE cc_start: 0.8812 (mt) cc_final: 0.8435 (mm) REVERT: B 996 LEU cc_start: 0.7783 (mt) cc_final: 0.7442 (tp) REVERT: B 997 ILE cc_start: 0.8678 (mt) cc_final: 0.7945 (mm) REVERT: B 1001 LEU cc_start: 0.8438 (tp) cc_final: 0.8236 (mm) REVERT: B 1005 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7511 (mt0) REVERT: B 1018 ILE cc_start: 0.8170 (mm) cc_final: 0.7964 (pt) REVERT: B 1019 ARG cc_start: 0.7893 (tpt-90) cc_final: 0.7586 (tpt170) REVERT: B 1033 VAL cc_start: 0.3815 (t) cc_final: 0.1747 (t) REVERT: B 1077 THR cc_start: 0.6976 (t) cc_final: 0.6534 (t) REVERT: C 48 LEU cc_start: 0.7000 (mt) cc_final: 0.6475 (tp) REVERT: C 177 MET cc_start: 0.1146 (mmt) cc_final: 0.0342 (ttp) REVERT: C 321 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7668 (mm-40) REVERT: C 408 ARG cc_start: 0.7301 (ppt170) cc_final: 0.7041 (tmm-80) REVERT: C 654 GLU cc_start: 0.8275 (pt0) cc_final: 0.7735 (mp0) REVERT: C 740 MET cc_start: 0.6416 (ttm) cc_final: 0.5789 (tpt) REVERT: C 762 GLN cc_start: 0.8196 (mt0) cc_final: 0.7619 (tp40) REVERT: C 794 ILE cc_start: 0.6904 (mt) cc_final: 0.6658 (tp) REVERT: C 814 LYS cc_start: 0.8093 (tptt) cc_final: 0.7860 (mmmt) REVERT: C 882 ILE cc_start: 0.8407 (pt) cc_final: 0.7829 (pt) REVERT: C 960 ASN cc_start: 0.7496 (m-40) cc_final: 0.6582 (t0) REVERT: C 980 ILE cc_start: 0.7572 (pt) cc_final: 0.7294 (pt) REVERT: C 992 GLN cc_start: 0.6535 (mm110) cc_final: 0.6099 (tt0) REVERT: C 1008 VAL cc_start: 0.7107 (t) cc_final: 0.6896 (t) REVERT: C 1029 MET cc_start: 0.7257 (tpp) cc_final: 0.6984 (tpp) REVERT: C 1033 VAL cc_start: 0.5616 (t) cc_final: 0.3192 (t) REVERT: C 1034 LEU cc_start: 0.5029 (mt) cc_final: 0.4695 (mt) REVERT: H 105 TYR cc_start: 0.7089 (m-80) cc_final: 0.6707 (t80) REVERT: H 225 LYS cc_start: 0.3447 (mptt) cc_final: 0.2138 (mttt) REVERT: L 29 ILE cc_start: 0.6933 (tt) cc_final: 0.6597 (pt) REVERT: L 36 HIS cc_start: 0.2416 (m-70) cc_final: 0.1026 (m-70) outliers start: 13 outliers final: 1 residues processed: 583 average time/residue: 0.4519 time to fit residues: 408.8142 Evaluate side-chains 275 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 172 optimal weight: 0.4980 chunk 210 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 HIS A 149 ASN A 183 GLN A 196 ASN A 218 GLN A 271 GLN A 360 ASN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 474 GLN A 493 GLN A 580 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 675 GLN A 774 GLN A 926 GLN A 935 GLN A 949 GLN A 953 ASN A 992 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1088 HIS B 69 HIS B 99 ASN B 146 HIS B 165 ASN B 183 GLN B 196 ASN B 207 HIS B 218 GLN B 271 GLN B 448 ASN B 493 GLN B 498 GLN B 544 ASN B 613 GLN B 675 GLN B 762 GLN B 926 GLN B 935 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 66 HIS C 183 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN C 271 GLN C 314 GLN C 448 ASN C 487 ASN C 493 GLN C 536 ASN C 542 ASN C 751 ASN C 762 GLN C 804 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 935 GLN C 957 GLN C1064 HIS H 166 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.094033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.071405 restraints weight = 285819.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.073273 restraints weight = 183072.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.074149 restraints weight = 104852.693| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29508 Z= 0.203 Angle : 0.695 12.844 40265 Z= 0.349 Chirality : 0.048 0.388 4636 Planarity : 0.005 0.055 5150 Dihedral : 5.074 59.647 4656 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.63 (0.12), residues: 3600 helix: 0.48 (0.21), residues: 579 sheet: -1.08 (0.18), residues: 782 loop : -2.78 (0.11), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 114 HIS 0.008 0.001 HIS C 146 PHE 0.030 0.002 PHE C 157 TYR 0.028 0.002 TYR C 170 ARG 0.010 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 30) link_NAG-ASN : angle 2.36391 ( 90) link_BETA1-4 : bond 0.00470 ( 6) link_BETA1-4 : angle 1.42840 ( 18) hydrogen bonds : bond 0.04297 ( 783) hydrogen bonds : angle 6.12753 ( 2183) SS BOND : bond 0.00512 ( 47) SS BOND : angle 1.51303 ( 94) covalent geometry : bond 0.00442 (29425) covalent geometry : angle 0.68348 (40063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 2.911 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: symmetry clash REVERT: A 117 LEU cc_start: 0.8605 (tt) cc_final: 0.8087 (mt) REVERT: A 157 PHE cc_start: 0.6519 (t80) cc_final: 0.6232 (t80) REVERT: A 177 MET cc_start: 0.0736 (mmt) cc_final: -0.3146 (ttt) REVERT: A 200 TYR cc_start: 0.5244 (m-80) cc_final: 0.4713 (m-10) REVERT: A 204 TYR cc_start: 0.7303 (m-80) cc_final: 0.6414 (m-80) REVERT: A 902 MET cc_start: 0.8503 (mmm) cc_final: 0.7682 (tpp) REVERT: A 1041 ASP cc_start: 0.7681 (t0) cc_final: 0.7467 (t0) REVERT: B 153 MET cc_start: 0.7473 (mmm) cc_final: 0.6820 (ppp) REVERT: B 177 MET cc_start: -0.2639 (mmt) cc_final: -0.4874 (ttt) REVERT: B 204 TYR cc_start: 0.7480 (m-80) cc_final: 0.6544 (m-10) REVERT: B 214 ARG cc_start: 0.7469 (ptt-90) cc_final: 0.7251 (mpt180) REVERT: B 224 GLU cc_start: 0.8859 (pm20) cc_final: 0.8323 (pm20) REVERT: B 421 TYR cc_start: 0.8312 (m-80) cc_final: 0.7168 (m-10) REVERT: B 740 MET cc_start: 0.6827 (ttm) cc_final: 0.5999 (tpp) REVERT: B 762 GLN cc_start: 0.8689 (mt0) cc_final: 0.8400 (mt0) REVERT: B 788 ILE cc_start: 0.7682 (mm) cc_final: 0.7443 (mp) REVERT: B 901 GLN cc_start: 0.5554 (tm-30) cc_final: 0.5203 (tm-30) REVERT: B 921 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8567 (mmmt) REVERT: B 1041 ASP cc_start: 0.7767 (t0) cc_final: 0.7478 (t0) REVERT: C 141 LEU cc_start: 0.7765 (mp) cc_final: 0.7316 (tt) REVERT: C 177 MET cc_start: -0.1448 (mmt) cc_final: -0.2003 (ttt) REVERT: C 245 HIS cc_start: 0.2444 (m-70) cc_final: 0.2108 (m-70) REVERT: C 266 TYR cc_start: 0.4136 (m-80) cc_final: 0.3649 (m-80) REVERT: C 529 LYS cc_start: 0.2892 (tttt) cc_final: 0.2664 (mttp) REVERT: C 614 ASP cc_start: 0.3107 (t0) cc_final: 0.2851 (t0) REVERT: C 731 MET cc_start: 0.8149 (ptt) cc_final: 0.7908 (ptm) REVERT: C 740 MET cc_start: 0.5943 (ttm) cc_final: 0.5340 (tpt) REVERT: C 773 GLU cc_start: 0.8214 (pt0) cc_final: 0.7990 (mm-30) REVERT: C 898 PHE cc_start: 0.7796 (t80) cc_final: 0.7247 (t80) REVERT: C 902 MET cc_start: 0.6270 (mmm) cc_final: 0.4900 (mmm) REVERT: C 960 ASN cc_start: 0.7388 (m-40) cc_final: 0.6584 (t0) REVERT: C 1005 GLN cc_start: 0.7388 (tp-100) cc_final: 0.7161 (mm-40) REVERT: C 1008 VAL cc_start: 0.8038 (t) cc_final: 0.7795 (p) REVERT: C 1029 MET cc_start: 0.7551 (tpp) cc_final: 0.7125 (tpp) REVERT: C 1031 GLU cc_start: 0.5857 (mt-10) cc_final: 0.5409 (mt-10) REVERT: C 1041 ASP cc_start: 0.7227 (t0) cc_final: 0.6996 (t0) REVERT: H 105 TYR cc_start: 0.6567 (m-80) cc_final: 0.6046 (t80) REVERT: H 220 LYS cc_start: 0.4459 (tttp) cc_final: 0.4047 (pttp) REVERT: H 225 LYS cc_start: 0.0219 (mptt) cc_final: -0.1434 (mttt) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.4189 time to fit residues: 213.8562 Evaluate side-chains 176 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 155 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 613 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1125 ASN B 87 ASN B 146 HIS B 207 HIS B 437 ASN B 501 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 992 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 437 ASN C 644 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1083 HIS C1088 HIS ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN H 182 GLN L 36 HIS L 189 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.086518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063616 restraints weight = 219181.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065463 restraints weight = 137503.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.066368 restraints weight = 81109.728| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 29508 Z= 0.281 Angle : 0.810 11.205 40265 Z= 0.414 Chirality : 0.051 0.450 4636 Planarity : 0.006 0.123 5150 Dihedral : 5.883 58.667 4656 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.62 (0.13), residues: 3600 helix: 0.26 (0.21), residues: 590 sheet: -1.30 (0.17), residues: 797 loop : -2.63 (0.11), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP H 114 HIS 0.014 0.002 HIS A 66 PHE 0.039 0.003 PHE C 823 TYR 0.038 0.003 TYR B 313 ARG 0.026 0.002 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00868 ( 30) link_NAG-ASN : angle 2.89503 ( 90) link_BETA1-4 : bond 0.00921 ( 6) link_BETA1-4 : angle 1.55055 ( 18) hydrogen bonds : bond 0.05333 ( 783) hydrogen bonds : angle 6.29844 ( 2183) SS BOND : bond 0.00741 ( 47) SS BOND : angle 1.84916 ( 94) covalent geometry : bond 0.00614 (29425) covalent geometry : angle 0.79458 (40063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9213 (tt) cc_final: 0.8897 (mt) REVERT: A 177 MET cc_start: -0.1310 (mmt) cc_final: -0.1553 (mmt) REVERT: A 200 TYR cc_start: 0.6304 (m-80) cc_final: 0.6058 (m-10) REVERT: A 357 ARG cc_start: 0.6772 (mtp180) cc_final: 0.6329 (mtm110) REVERT: A 380 TYR cc_start: 0.6401 (t80) cc_final: 0.6171 (t80) REVERT: A 428 ASP cc_start: 0.6270 (p0) cc_final: 0.5527 (m-30) REVERT: A 697 MET cc_start: 0.8035 (tpt) cc_final: 0.7636 (tpp) REVERT: A 1029 MET cc_start: 0.7773 (tpp) cc_final: 0.7480 (tpp) REVERT: A 1050 MET cc_start: 0.8209 (pmm) cc_final: 0.6996 (pmm) REVERT: B 153 MET cc_start: 0.6583 (mmm) cc_final: 0.5817 (ppp) REVERT: B 177 MET cc_start: -0.3744 (mmt) cc_final: -0.4377 (mtp) REVERT: B 224 GLU cc_start: 0.9033 (pm20) cc_final: 0.8667 (pm20) REVERT: B 421 TYR cc_start: 0.8348 (m-80) cc_final: 0.8047 (m-10) REVERT: B 650 LEU cc_start: 0.9221 (tp) cc_final: 0.8875 (tt) REVERT: B 740 MET cc_start: 0.7195 (ttm) cc_final: 0.6721 (tpp) REVERT: B 788 ILE cc_start: 0.8219 (mm) cc_final: 0.7992 (mp) REVERT: B 898 PHE cc_start: 0.8219 (t80) cc_final: 0.7749 (t80) REVERT: B 900 MET cc_start: 0.8274 (mtp) cc_final: 0.7802 (mtp) REVERT: B 1029 MET cc_start: 0.7496 (ttm) cc_final: 0.7250 (ttm) REVERT: C 141 LEU cc_start: 0.8063 (mp) cc_final: 0.7661 (tt) REVERT: C 177 MET cc_start: -0.1444 (mmt) cc_final: -0.2291 (ttm) REVERT: C 240 THR cc_start: 0.7656 (t) cc_final: 0.7419 (m) REVERT: C 245 HIS cc_start: 0.3365 (m-70) cc_final: 0.2939 (m-70) REVERT: C 390 LEU cc_start: 0.6488 (mt) cc_final: 0.5960 (mt) REVERT: C 529 LYS cc_start: 0.3855 (tttt) cc_final: 0.3575 (mttp) REVERT: C 898 PHE cc_start: 0.7451 (t80) cc_final: 0.6735 (t80) REVERT: C 900 MET cc_start: 0.8755 (mpp) cc_final: 0.8487 (mpp) REVERT: C 902 MET cc_start: 0.7165 (mmm) cc_final: 0.6832 (mmm) REVERT: C 960 ASN cc_start: 0.7513 (m-40) cc_final: 0.6831 (t0) REVERT: C 988 GLU cc_start: 0.8052 (tt0) cc_final: 0.7706 (tm-30) REVERT: C 1029 MET cc_start: 0.7537 (tpp) cc_final: 0.6463 (tpp) REVERT: H 105 TYR cc_start: 0.7131 (m-80) cc_final: 0.6004 (t80) REVERT: H 225 LYS cc_start: 0.0455 (mptt) cc_final: -0.1151 (mttt) outliers start: 4 outliers final: 4 residues processed: 210 average time/residue: 0.3960 time to fit residues: 134.8962 Evaluate side-chains 132 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 133 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 563 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1010 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 146 HIS C 196 ASN C 388 ASN C 519 HIS C 540 ASN C 856 ASN C1005 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.087594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065149 restraints weight = 202038.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066227 restraints weight = 131411.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066624 restraints weight = 100150.840| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29508 Z= 0.135 Angle : 0.577 9.614 40265 Z= 0.289 Chirality : 0.045 0.388 4636 Planarity : 0.004 0.080 5150 Dihedral : 5.169 56.585 4656 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.16 % Allowed : 2.34 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.21 (0.13), residues: 3600 helix: 1.12 (0.22), residues: 582 sheet: -1.14 (0.17), residues: 810 loop : -2.46 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.007 0.001 HIS A1048 PHE 0.026 0.002 PHE B 194 TYR 0.015 0.001 TYR B 313 ARG 0.007 0.001 ARG C1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 30) link_NAG-ASN : angle 2.53100 ( 90) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 1.20263 ( 18) hydrogen bonds : bond 0.03583 ( 783) hydrogen bonds : angle 5.57344 ( 2183) SS BOND : bond 0.00412 ( 47) SS BOND : angle 1.34560 ( 94) covalent geometry : bond 0.00299 (29425) covalent geometry : angle 0.56182 (40063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7759 (t80) cc_final: 0.7288 (t80) REVERT: A 117 LEU cc_start: 0.9237 (tt) cc_final: 0.8831 (mt) REVERT: A 200 TYR cc_start: 0.6413 (m-80) cc_final: 0.5911 (m-10) REVERT: A 315 THR cc_start: 0.6915 (p) cc_final: 0.6591 (p) REVERT: A 357 ARG cc_start: 0.7054 (mtp180) cc_final: 0.6658 (mtm110) REVERT: A 380 TYR cc_start: 0.6432 (t80) cc_final: 0.6165 (t80) REVERT: A 428 ASP cc_start: 0.5359 (p0) cc_final: 0.4971 (m-30) REVERT: A 697 MET cc_start: 0.8314 (tpt) cc_final: 0.8071 (tpp) REVERT: A 1050 MET cc_start: 0.7714 (pmm) cc_final: 0.7448 (pmm) REVERT: B 153 MET cc_start: 0.6563 (mmm) cc_final: 0.5769 (ppp) REVERT: B 177 MET cc_start: -0.1213 (mmt) cc_final: -0.2158 (mtp) REVERT: B 224 GLU cc_start: 0.8944 (pm20) cc_final: 0.8582 (pm20) REVERT: B 421 TYR cc_start: 0.8314 (m-80) cc_final: 0.8067 (m-10) REVERT: B 740 MET cc_start: 0.7130 (ttm) cc_final: 0.6662 (tpp) REVERT: B 896 ILE cc_start: 0.7903 (mp) cc_final: 0.7360 (pt) REVERT: B 898 PHE cc_start: 0.8199 (t80) cc_final: 0.7520 (t80) REVERT: B 900 MET cc_start: 0.8217 (mtp) cc_final: 0.7981 (mtp) REVERT: B 909 ILE cc_start: 0.7144 (pt) cc_final: 0.6426 (tp) REVERT: C 124 THR cc_start: 0.6497 (p) cc_final: 0.6186 (t) REVERT: C 141 LEU cc_start: 0.8090 (mp) cc_final: 0.7702 (tt) REVERT: C 177 MET cc_start: -0.1421 (mmt) cc_final: -0.2105 (ttm) REVERT: C 245 HIS cc_start: 0.3667 (m-70) cc_final: 0.3160 (m-70) REVERT: C 266 TYR cc_start: 0.5019 (m-80) cc_final: 0.4330 (m-80) REVERT: C 286 THR cc_start: 0.6947 (p) cc_final: 0.6340 (p) REVERT: C 529 LYS cc_start: 0.3675 (tttt) cc_final: 0.3451 (mttp) REVERT: C 614 ASP cc_start: 0.3961 (t0) cc_final: 0.3693 (t0) REVERT: C 731 MET cc_start: 0.8090 (ptt) cc_final: 0.7881 (ptm) REVERT: C 896 ILE cc_start: 0.8272 (pt) cc_final: 0.7825 (tp) REVERT: C 900 MET cc_start: 0.8518 (mpp) cc_final: 0.8160 (mmm) REVERT: C 960 ASN cc_start: 0.7338 (m-40) cc_final: 0.6812 (t0) REVERT: C 1029 MET cc_start: 0.7461 (tpp) cc_final: 0.6879 (tpp) REVERT: C 1033 VAL cc_start: 0.7888 (t) cc_final: 0.6060 (t) REVERT: H 105 TYR cc_start: 0.6857 (m-80) cc_final: 0.6047 (t80) REVERT: H 225 LYS cc_start: 0.0681 (mptt) cc_final: -0.1076 (mttt) outliers start: 4 outliers final: 0 residues processed: 196 average time/residue: 0.4134 time to fit residues: 132.2521 Evaluate side-chains 129 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 159 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 448 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 613 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.083365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059385 restraints weight = 214487.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060653 restraints weight = 131151.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061679 restraints weight = 89145.229| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29508 Z= 0.230 Angle : 0.738 16.257 40265 Z= 0.370 Chirality : 0.048 0.402 4636 Planarity : 0.005 0.069 5150 Dihedral : 5.796 47.878 4656 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.33 (0.13), residues: 3600 helix: 0.70 (0.21), residues: 594 sheet: -1.26 (0.17), residues: 812 loop : -2.44 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 886 HIS 0.012 0.002 HIS A 245 PHE 0.035 0.002 PHE B 275 TYR 0.025 0.002 TYR A 200 ARG 0.009 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00857 ( 30) link_NAG-ASN : angle 3.02875 ( 90) link_BETA1-4 : bond 0.00441 ( 6) link_BETA1-4 : angle 1.68266 ( 18) hydrogen bonds : bond 0.04441 ( 783) hydrogen bonds : angle 5.87572 ( 2183) SS BOND : bond 0.00734 ( 47) SS BOND : angle 2.06521 ( 94) covalent geometry : bond 0.00508 (29425) covalent geometry : angle 0.71840 (40063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7748 (t80) cc_final: 0.7246 (t80) REVERT: A 117 LEU cc_start: 0.9358 (tt) cc_final: 0.8835 (mt) REVERT: A 141 LEU cc_start: 0.6259 (mt) cc_final: 0.5877 (mt) REVERT: A 200 TYR cc_start: 0.6069 (m-80) cc_final: 0.5466 (m-10) REVERT: A 315 THR cc_start: 0.7086 (p) cc_final: 0.6720 (p) REVERT: A 357 ARG cc_start: 0.6949 (mtp180) cc_final: 0.6644 (mtp-110) REVERT: A 380 TYR cc_start: 0.6354 (t80) cc_final: 0.6065 (t80) REVERT: A 428 ASP cc_start: 0.5935 (p0) cc_final: 0.5327 (m-30) REVERT: A 731 MET cc_start: 0.7270 (ptm) cc_final: 0.7042 (ptm) REVERT: B 151 SER cc_start: 0.6682 (p) cc_final: 0.5723 (t) REVERT: B 153 MET cc_start: 0.6877 (mmm) cc_final: 0.6032 (ppp) REVERT: B 177 MET cc_start: -0.2580 (mmt) cc_final: -0.3202 (mtp) REVERT: B 214 ARG cc_start: 0.6157 (pmt-80) cc_final: 0.5022 (tpt90) REVERT: B 224 GLU cc_start: 0.8956 (pm20) cc_final: 0.8548 (pm20) REVERT: B 650 LEU cc_start: 0.9304 (tp) cc_final: 0.8646 (pp) REVERT: B 740 MET cc_start: 0.7422 (ttm) cc_final: 0.7085 (tpp) REVERT: B 900 MET cc_start: 0.8570 (mtp) cc_final: 0.8289 (mtp) REVERT: B 1029 MET cc_start: 0.7680 (ttm) cc_final: 0.7366 (ttm) REVERT: B 1050 MET cc_start: 0.8477 (pmm) cc_final: 0.8186 (pmm) REVERT: B 1130 ILE cc_start: 0.7737 (pt) cc_final: 0.7533 (mt) REVERT: C 141 LEU cc_start: 0.8126 (mp) cc_final: 0.7802 (tt) REVERT: C 177 MET cc_start: -0.1959 (mmt) cc_final: -0.3323 (ttt) REVERT: C 245 HIS cc_start: 0.3540 (m-70) cc_final: 0.3338 (m-70) REVERT: C 786 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8020 (mmmt) REVERT: C 960 ASN cc_start: 0.8029 (m-40) cc_final: 0.6977 (t0) REVERT: C 1029 MET cc_start: 0.8093 (tpp) cc_final: 0.7462 (tpp) REVERT: H 81 MET cc_start: 0.5210 (tmm) cc_final: 0.4895 (tmm) REVERT: H 105 TYR cc_start: 0.6698 (m-80) cc_final: 0.5726 (t80) REVERT: H 225 LYS cc_start: 0.5057 (mptt) cc_final: 0.4025 (mttt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.3960 time to fit residues: 112.6240 Evaluate side-chains 115 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 27 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 335 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A1048 HIS B 66 HIS B 540 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 544 ASN C1011 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.080330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057857 restraints weight = 188162.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059050 restraints weight = 127821.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.060043 restraints weight = 80746.882| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.8750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 29508 Z= 0.271 Angle : 0.822 16.012 40265 Z= 0.411 Chirality : 0.052 0.454 4636 Planarity : 0.006 0.113 5150 Dihedral : 6.667 54.662 4656 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.52 (0.13), residues: 3600 helix: 0.35 (0.21), residues: 593 sheet: -1.39 (0.17), residues: 785 loop : -2.49 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 886 HIS 0.016 0.002 HIS A 245 PHE 0.049 0.003 PHE C 759 TYR 0.031 0.003 TYR A 873 ARG 0.010 0.001 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 30) link_NAG-ASN : angle 3.77304 ( 90) link_BETA1-4 : bond 0.00778 ( 6) link_BETA1-4 : angle 1.84496 ( 18) hydrogen bonds : bond 0.04575 ( 783) hydrogen bonds : angle 6.28720 ( 2183) SS BOND : bond 0.00476 ( 47) SS BOND : angle 2.43080 ( 94) covalent geometry : bond 0.00598 (29425) covalent geometry : angle 0.79466 (40063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7850 (t80) cc_final: 0.7458 (t80) REVERT: A 117 LEU cc_start: 0.9204 (tt) cc_final: 0.8598 (mt) REVERT: A 177 MET cc_start: -0.1009 (mmt) cc_final: -0.1210 (mmt) REVERT: A 200 TYR cc_start: 0.6403 (m-80) cc_final: 0.5844 (m-10) REVERT: A 278 LYS cc_start: 0.7392 (tttm) cc_final: 0.6859 (tptm) REVERT: A 315 THR cc_start: 0.7099 (p) cc_final: 0.6890 (p) REVERT: A 428 ASP cc_start: 0.5346 (p0) cc_final: 0.4647 (m-30) REVERT: A 584 ILE cc_start: 0.7599 (mm) cc_final: 0.7087 (mm) REVERT: A 697 MET cc_start: 0.8570 (tpp) cc_final: 0.7924 (tpt) REVERT: A 731 MET cc_start: 0.7435 (ptm) cc_final: 0.6551 (ppp) REVERT: A 869 MET cc_start: 0.7901 (mpp) cc_final: 0.7683 (mpp) REVERT: B 151 SER cc_start: 0.6650 (p) cc_final: 0.5875 (t) REVERT: B 153 MET cc_start: 0.6924 (mmm) cc_final: 0.6196 (ppp) REVERT: B 177 MET cc_start: -0.0532 (mmt) cc_final: -0.1392 (mtp) REVERT: B 214 ARG cc_start: 0.6614 (pmt-80) cc_final: 0.5089 (ttp80) REVERT: B 224 GLU cc_start: 0.9006 (pm20) cc_final: 0.8668 (pm20) REVERT: B 523 THR cc_start: 0.5686 (p) cc_final: 0.5397 (t) REVERT: B 650 LEU cc_start: 0.8898 (tp) cc_final: 0.8285 (pp) REVERT: B 740 MET cc_start: 0.7337 (ttm) cc_final: 0.7066 (tpp) REVERT: C 141 LEU cc_start: 0.8424 (mp) cc_final: 0.8208 (tt) REVERT: C 177 MET cc_start: -0.1143 (mmt) cc_final: -0.1710 (ttm) REVERT: C 214 ARG cc_start: 0.7345 (ptt-90) cc_final: 0.6866 (mmm160) REVERT: C 449 TYR cc_start: 0.5493 (m-10) cc_final: 0.5248 (m-80) REVERT: C 1029 MET cc_start: 0.7802 (tpp) cc_final: 0.7346 (tpp) REVERT: H 105 TYR cc_start: 0.6886 (m-80) cc_final: 0.5601 (t80) REVERT: H 225 LYS cc_start: 0.1378 (mptt) cc_final: -0.0617 (mttm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4044 time to fit residues: 105.3301 Evaluate side-chains 106 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 332 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 66 HIS ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 949 GLN C 978 ASN C1011 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.082389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062231 restraints weight = 224804.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061614 restraints weight = 171140.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061836 restraints weight = 136713.158| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.8848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29508 Z= 0.156 Angle : 0.645 15.959 40265 Z= 0.320 Chirality : 0.047 0.371 4636 Planarity : 0.005 0.078 5150 Dihedral : 5.950 51.722 4656 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.06 % Allowed : 1.42 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.22 (0.13), residues: 3600 helix: 0.92 (0.21), residues: 584 sheet: -1.19 (0.17), residues: 793 loop : -2.39 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 886 HIS 0.010 0.001 HIS A 245 PHE 0.022 0.002 PHE B 275 TYR 0.017 0.002 TYR B 756 ARG 0.007 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 30) link_NAG-ASN : angle 3.15464 ( 90) link_BETA1-4 : bond 0.00627 ( 6) link_BETA1-4 : angle 1.46417 ( 18) hydrogen bonds : bond 0.03858 ( 783) hydrogen bonds : angle 5.80008 ( 2183) SS BOND : bond 0.00379 ( 47) SS BOND : angle 1.55824 ( 94) covalent geometry : bond 0.00351 (29425) covalent geometry : angle 0.62395 (40063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7740 (t80) cc_final: 0.7414 (t80) REVERT: A 117 LEU cc_start: 0.9148 (tt) cc_final: 0.8453 (mt) REVERT: A 200 TYR cc_start: 0.6389 (m-80) cc_final: 0.5869 (m-10) REVERT: A 315 THR cc_start: 0.7253 (p) cc_final: 0.6878 (p) REVERT: A 428 ASP cc_start: 0.5114 (p0) cc_final: 0.4521 (m-30) REVERT: A 584 ILE cc_start: 0.7707 (mm) cc_final: 0.7201 (mm) REVERT: A 697 MET cc_start: 0.8474 (tpp) cc_final: 0.8015 (tpt) REVERT: A 756 TYR cc_start: 0.6623 (m-80) cc_final: 0.6291 (m-10) REVERT: B 153 MET cc_start: 0.6872 (mmm) cc_final: 0.6187 (ppp) REVERT: B 177 MET cc_start: -0.0710 (mmt) cc_final: -0.1551 (mtp) REVERT: B 214 ARG cc_start: 0.6894 (pmt-80) cc_final: 0.5554 (ttp80) REVERT: B 224 GLU cc_start: 0.9048 (pm20) cc_final: 0.8745 (pm20) REVERT: B 523 THR cc_start: 0.5816 (p) cc_final: 0.5576 (t) REVERT: B 650 LEU cc_start: 0.8999 (tp) cc_final: 0.8091 (pp) REVERT: B 740 MET cc_start: 0.7366 (ttm) cc_final: 0.7133 (tpp) REVERT: B 1005 GLN cc_start: 0.6171 (mt0) cc_final: 0.5951 (mt0) REVERT: C 141 LEU cc_start: 0.8506 (mp) cc_final: 0.8273 (tt) REVERT: C 177 MET cc_start: -0.1042 (mmt) cc_final: -0.2367 (ttt) REVERT: C 214 ARG cc_start: 0.7513 (ptt-90) cc_final: 0.6995 (mmm160) REVERT: C 408 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.8282 (tmm-80) REVERT: C 473 TYR cc_start: 0.6091 (t80) cc_final: 0.5389 (t80) REVERT: C 1029 MET cc_start: 0.8024 (tpp) cc_final: 0.7517 (tpp) REVERT: H 105 TYR cc_start: 0.6792 (m-80) cc_final: 0.5589 (t80) REVERT: L 68 LYS cc_start: 0.8026 (tptt) cc_final: 0.6729 (mttm) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.4280 time to fit residues: 107.0577 Evaluate side-chains 106 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 229 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 347 optimal weight: 50.0000 chunk 307 optimal weight: 10.0000 chunk 48 optimal weight: 40.0000 chunk 68 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 978 ASN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.078903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057365 restraints weight = 270395.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056945 restraints weight = 183991.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057603 restraints weight = 130680.344| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.9712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 29508 Z= 0.254 Angle : 0.792 16.382 40265 Z= 0.396 Chirality : 0.050 0.404 4636 Planarity : 0.006 0.073 5150 Dihedral : 6.749 58.512 4656 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.32 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.44 (0.13), residues: 3600 helix: 0.44 (0.21), residues: 590 sheet: -1.31 (0.17), residues: 790 loop : -2.45 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 886 HIS 0.015 0.002 HIS A 245 PHE 0.034 0.003 PHE B 906 TYR 0.027 0.002 TYR A 873 ARG 0.023 0.001 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 30) link_NAG-ASN : angle 3.44281 ( 90) link_BETA1-4 : bond 0.00820 ( 6) link_BETA1-4 : angle 1.86040 ( 18) hydrogen bonds : bond 0.04473 ( 783) hydrogen bonds : angle 6.22272 ( 2183) SS BOND : bond 0.00583 ( 47) SS BOND : angle 2.04688 ( 94) covalent geometry : bond 0.00571 (29425) covalent geometry : angle 0.76983 (40063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7813 (t80) cc_final: 0.7489 (t80) REVERT: A 200 TYR cc_start: 0.6578 (m-80) cc_final: 0.6274 (m-10) REVERT: A 315 THR cc_start: 0.7283 (p) cc_final: 0.7048 (p) REVERT: A 428 ASP cc_start: 0.5277 (p0) cc_final: 0.4647 (m-30) REVERT: A 615 VAL cc_start: 0.7300 (t) cc_final: 0.7095 (t) REVERT: A 697 MET cc_start: 0.8226 (tpt) cc_final: 0.7507 (tpt) REVERT: A 731 MET cc_start: 0.7294 (ptm) cc_final: 0.6994 (ppp) REVERT: A 869 MET cc_start: 0.7991 (mpp) cc_final: 0.7670 (mpp) REVERT: A 913 GLN cc_start: 0.8188 (pp30) cc_final: 0.7897 (pp30) REVERT: A 1041 ASP cc_start: 0.8451 (t0) cc_final: 0.7891 (t0) REVERT: B 153 MET cc_start: 0.6967 (mmm) cc_final: 0.6167 (ppp) REVERT: B 214 ARG cc_start: 0.6968 (pmt-80) cc_final: 0.5739 (ttp80) REVERT: B 650 LEU cc_start: 0.9008 (tp) cc_final: 0.8433 (pp) REVERT: B 909 ILE cc_start: 0.8680 (pt) cc_final: 0.8360 (mm) REVERT: B 1005 GLN cc_start: 0.6356 (mt0) cc_final: 0.6075 (mt0) REVERT: C 141 LEU cc_start: 0.8702 (mp) cc_final: 0.8494 (tt) REVERT: C 169 GLU cc_start: 0.5829 (tm-30) cc_final: 0.5496 (mp0) REVERT: C 177 MET cc_start: -0.0842 (mmt) cc_final: -0.2473 (mmm) REVERT: C 214 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.6829 (mmm160) REVERT: C 408 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.8219 (tmm-80) REVERT: C 740 MET cc_start: 0.6288 (tpt) cc_final: 0.5680 (tmm) REVERT: C 1029 MET cc_start: 0.8062 (tpp) cc_final: 0.7519 (tpp) REVERT: H 81 MET cc_start: 0.5002 (tmm) cc_final: 0.4745 (tmm) REVERT: H 105 TYR cc_start: 0.6426 (m-80) cc_final: 0.5280 (t80) REVERT: H 116 ARG cc_start: 0.7781 (tpm170) cc_final: 0.7539 (tpm170) REVERT: H 158 PRO cc_start: 0.1429 (Cg_endo) cc_final: 0.1156 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4008 time to fit residues: 96.3796 Evaluate side-chains 109 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 102 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.080068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.058062 restraints weight = 200125.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.058211 restraints weight = 132792.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058801 restraints weight = 108095.167| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.9747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29508 Z= 0.149 Angle : 0.651 16.309 40265 Z= 0.323 Chirality : 0.047 0.372 4636 Planarity : 0.005 0.070 5150 Dihedral : 6.107 52.146 4656 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.18 (0.13), residues: 3600 helix: 0.87 (0.21), residues: 586 sheet: -1.12 (0.18), residues: 791 loop : -2.35 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.009 0.001 HIS A 245 PHE 0.023 0.002 PHE B 275 TYR 0.027 0.002 TYR A 380 ARG 0.008 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 30) link_NAG-ASN : angle 3.05062 ( 90) link_BETA1-4 : bond 0.00689 ( 6) link_BETA1-4 : angle 1.37915 ( 18) hydrogen bonds : bond 0.03791 ( 783) hydrogen bonds : angle 5.80997 ( 2183) SS BOND : bond 0.00421 ( 47) SS BOND : angle 1.76914 ( 94) covalent geometry : bond 0.00338 (29425) covalent geometry : angle 0.62963 (40063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7694 (t80) cc_final: 0.7457 (t80) REVERT: A 117 LEU cc_start: 0.9062 (tp) cc_final: 0.8840 (tp) REVERT: A 177 MET cc_start: -0.1254 (mmt) cc_final: -0.1459 (mmt) REVERT: A 224 GLU cc_start: 0.7816 (mp0) cc_final: 0.7611 (pm20) REVERT: A 242 LEU cc_start: 0.7468 (mm) cc_final: 0.7125 (tp) REVERT: A 315 THR cc_start: 0.7326 (p) cc_final: 0.6930 (p) REVERT: A 428 ASP cc_start: 0.5549 (p0) cc_final: 0.4916 (m-30) REVERT: A 697 MET cc_start: 0.8158 (tpt) cc_final: 0.7380 (tpt) REVERT: A 731 MET cc_start: 0.7365 (ptm) cc_final: 0.7058 (ppp) REVERT: A 756 TYR cc_start: 0.6805 (m-80) cc_final: 0.6490 (m-10) REVERT: A 869 MET cc_start: 0.7719 (mpp) cc_final: 0.7313 (mpp) REVERT: A 913 GLN cc_start: 0.8146 (pp30) cc_final: 0.7804 (pp30) REVERT: A 1041 ASP cc_start: 0.8205 (t0) cc_final: 0.7811 (t0) REVERT: B 214 ARG cc_start: 0.6979 (pmt-80) cc_final: 0.5766 (ttp80) REVERT: B 650 LEU cc_start: 0.9052 (tp) cc_final: 0.8335 (pp) REVERT: B 909 ILE cc_start: 0.8515 (pt) cc_final: 0.8098 (mm) REVERT: B 919 ASN cc_start: 0.6914 (p0) cc_final: 0.6175 (m-40) REVERT: C 141 LEU cc_start: 0.8547 (mp) cc_final: 0.8277 (tt) REVERT: C 169 GLU cc_start: 0.6203 (tm-30) cc_final: 0.5821 (mp0) REVERT: C 177 MET cc_start: -0.0729 (mmt) cc_final: -0.2229 (ttt) REVERT: C 214 ARG cc_start: 0.7611 (ptt-90) cc_final: 0.6930 (mmm160) REVERT: C 449 TYR cc_start: 0.6915 (m-80) cc_final: 0.6614 (m-80) REVERT: C 740 MET cc_start: 0.6243 (tpt) cc_final: 0.5590 (tmm) REVERT: C 861 LEU cc_start: 0.9326 (tp) cc_final: 0.9088 (tt) REVERT: C 1029 MET cc_start: 0.7939 (tpp) cc_final: 0.7553 (tpp) REVERT: C 1033 VAL cc_start: 0.8437 (t) cc_final: 0.7509 (t) REVERT: H 105 TYR cc_start: 0.6685 (m-80) cc_final: 0.5680 (t80) REVERT: H 158 PRO cc_start: 0.1528 (Cg_endo) cc_final: 0.1262 (Cg_exo) REVERT: L 68 LYS cc_start: 0.7676 (tppt) cc_final: 0.6878 (mmtp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3951 time to fit residues: 94.0903 Evaluate side-chains 109 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 25 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.078168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056717 restraints weight = 242537.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056366 restraints weight = 173835.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056760 restraints weight = 121424.251| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 1.0347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29508 Z= 0.233 Angle : 0.759 14.272 40265 Z= 0.380 Chirality : 0.050 0.390 4636 Planarity : 0.005 0.061 5150 Dihedral : 6.460 49.422 4656 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -2.38 (0.13), residues: 3600 helix: 0.54 (0.21), residues: 589 sheet: -1.29 (0.17), residues: 830 loop : -2.43 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 886 HIS 0.013 0.002 HIS A 245 PHE 0.035 0.002 PHE C 759 TYR 0.028 0.002 TYR C 873 ARG 0.007 0.001 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 30) link_NAG-ASN : angle 3.26026 ( 90) link_BETA1-4 : bond 0.00738 ( 6) link_BETA1-4 : angle 1.67666 ( 18) hydrogen bonds : bond 0.04326 ( 783) hydrogen bonds : angle 6.18201 ( 2183) SS BOND : bond 0.00538 ( 47) SS BOND : angle 1.77808 ( 94) covalent geometry : bond 0.00527 (29425) covalent geometry : angle 0.73886 (40063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7710 (t80) cc_final: 0.7407 (t80) REVERT: A 117 LEU cc_start: 0.8885 (tp) cc_final: 0.8561 (tp) REVERT: A 128 ILE cc_start: 0.7749 (mt) cc_final: 0.7520 (mt) REVERT: A 200 TYR cc_start: 0.6643 (m-80) cc_final: 0.6435 (m-10) REVERT: A 224 GLU cc_start: 0.8102 (mp0) cc_final: 0.7870 (pm20) REVERT: A 315 THR cc_start: 0.7456 (p) cc_final: 0.7094 (p) REVERT: A 428 ASP cc_start: 0.5954 (p0) cc_final: 0.5322 (m-30) REVERT: A 697 MET cc_start: 0.8243 (tpt) cc_final: 0.7542 (tpt) REVERT: A 731 MET cc_start: 0.7263 (ptm) cc_final: 0.7006 (ppp) REVERT: A 869 MET cc_start: 0.8099 (mpp) cc_final: 0.7742 (mpp) REVERT: A 913 GLN cc_start: 0.8179 (pp30) cc_final: 0.7884 (pp30) REVERT: B 214 ARG cc_start: 0.7077 (pmt-80) cc_final: 0.5892 (ttp80) REVERT: B 919 ASN cc_start: 0.6881 (p0) cc_final: 0.6072 (m-40) REVERT: B 1005 GLN cc_start: 0.6286 (mt0) cc_final: 0.6078 (mt0) REVERT: B 1050 MET cc_start: 0.8225 (pmm) cc_final: 0.7988 (pmm) REVERT: C 169 GLU cc_start: 0.5980 (tm-30) cc_final: 0.5696 (mp0) REVERT: C 177 MET cc_start: -0.1625 (mmt) cc_final: -0.2771 (mmt) REVERT: C 214 ARG cc_start: 0.7848 (ptt-90) cc_final: 0.6783 (ttp80) REVERT: C 449 TYR cc_start: 0.6709 (m-80) cc_final: 0.6469 (m-80) REVERT: C 740 MET cc_start: 0.6084 (tpt) cc_final: 0.5191 (tmm) REVERT: C 1029 MET cc_start: 0.8039 (tpp) cc_final: 0.7498 (tpp) REVERT: C 1033 VAL cc_start: 0.8577 (t) cc_final: 0.7664 (t) REVERT: H 81 MET cc_start: 0.5091 (tmm) cc_final: 0.4801 (tmm) REVERT: H 105 TYR cc_start: 0.6293 (m-80) cc_final: 0.5246 (t80) REVERT: H 116 ARG cc_start: 0.7677 (tpm170) cc_final: 0.6287 (ttt-90) REVERT: H 158 PRO cc_start: 0.1643 (Cg_endo) cc_final: 0.1321 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3627 time to fit residues: 82.2278 Evaluate side-chains 111 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 258 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 308 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.078702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056817 restraints weight = 240945.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056661 restraints weight = 168165.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057697 restraints weight = 120406.453| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 1.0514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29508 Z= 0.180 Angle : 0.676 15.378 40265 Z= 0.338 Chirality : 0.047 0.372 4636 Planarity : 0.005 0.067 5150 Dihedral : 6.228 48.758 4656 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.22 (0.13), residues: 3600 helix: 0.77 (0.21), residues: 594 sheet: -1.08 (0.17), residues: 807 loop : -2.41 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.011 0.001 HIS A 245 PHE 0.021 0.002 PHE C 759 TYR 0.037 0.002 TYR B 495 ARG 0.012 0.001 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 30) link_NAG-ASN : angle 3.06683 ( 90) link_BETA1-4 : bond 0.00742 ( 6) link_BETA1-4 : angle 1.29487 ( 18) hydrogen bonds : bond 0.03923 ( 783) hydrogen bonds : angle 5.92076 ( 2183) SS BOND : bond 0.00384 ( 47) SS BOND : angle 1.76930 ( 94) covalent geometry : bond 0.00407 (29425) covalent geometry : angle 0.65608 (40063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9050.30 seconds wall clock time: 159 minutes 52.70 seconds (9592.70 seconds total)