Starting phenix.real_space_refine on Sat May 24 12:42:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlo_27508/05_2025/8dlo_27508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlo_27508/05_2025/8dlo_27508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlo_27508/05_2025/8dlo_27508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlo_27508/05_2025/8dlo_27508.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlo_27508/05_2025/8dlo_27508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlo_27508/05_2025/8dlo_27508.cif" } resolution = 2.25 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16095 2.51 5 N 4113 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25257 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: 15.35, per 1000 atoms: 0.61 Number of scatterers: 25257 At special positions: 0 Unit cell: (141, 146, 198, 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 111 16.00 O 4938 8.00 N 4113 7.00 C 16095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.04 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=2.03 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=2.04 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 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 3.3 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 44 sheets defined 25.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.760A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.718A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.797A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.567A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.070A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.515A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.574A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.901A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.060A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.618A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.222A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.836A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.189A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.674A pdb=" N TYR B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.511A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.885A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.627A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.016A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.087A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.841A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.594A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.765A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.605A pdb=" N TYR C 421 " --> pdb=" O THR C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.730A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.619A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.054A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.563A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.024A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.221A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.596A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.617A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 172 removed outlier: 5.440A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL A 159 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 172 removed outlier: 5.440A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL A 159 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.106A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.311A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.576A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.853A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.266A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.889A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.864A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 68 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.864A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 94 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.520A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.731A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.234A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.558A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.513A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.126A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.671A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.671A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.321A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.398A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 67 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.781A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 7.016A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N TYR C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 159 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.166A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.596A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.046A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.164A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1026 hydrogen bonds defined for protein. 2838 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: 11.13 Time building geometry restraints manager: 7.97 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: 7958 1.34 - 1.47: 6519 1.47 - 1.59: 11215 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25830 Sorted by residual: bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.45e+01 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.334 1.412 -0.078 2.34e-02 1.83e+03 1.11e+01 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.04e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.73e+00 ... (remaining 25825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 34257 2.18 - 4.35: 817 4.35 - 6.53: 65 6.53 - 8.71: 19 8.71 - 10.89: 2 Bond angle restraints: 35160 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.56 -5.86 1.22e+00 6.72e-01 2.30e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.43 -5.73 1.22e+00 6.72e-01 2.21e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.98 -5.28 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 122.20 -4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CA TYR C1067 " pdb=" CB TYR C1067 " pdb=" CG TYR C1067 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 ... (remaining 35155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14657 17.96 - 35.93: 1216 35.93 - 53.89: 211 53.89 - 71.85: 44 71.85 - 89.81: 33 Dihedral angle restraints: 16161 sinusoidal: 7074 harmonic: 9087 Sorted by residual: dihedral pdb=" CA PHE C 392 " pdb=" C PHE C 392 " pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 56.90 36.10 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 16158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3575 0.085 - 0.170: 554 0.170 - 0.255: 21 0.255 - 0.340: 3 0.340 - 0.425: 2 Chirality restraints: 4155 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CG LEU C 517 " pdb=" CB LEU C 517 " pdb=" CD1 LEU C 517 " pdb=" CD2 LEU C 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB THR C 430 " pdb=" CA THR C 430 " pdb=" OG1 THR C 430 " pdb=" CG2 THR C 430 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4152 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO C 986 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO B 986 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 896 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C ILE B 896 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE B 896 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 897 " -0.014 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6232 2.80 - 3.33: 21704 3.33 - 3.85: 42701 3.85 - 4.38: 48601 4.38 - 4.90: 84271 Nonbonded interactions: 203509 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.285 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.295 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.309 3.040 ... (remaining 203504 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: 0.08 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 58.920 Find NCS groups from input model: 1.190 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 25932 Z= 0.247 Angle : 0.801 15.094 35424 Z= 0.417 Chirality : 0.056 0.425 4155 Planarity : 0.005 0.064 4473 Dihedral : 13.689 89.813 10191 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3072 helix: 1.89 (0.20), residues: 684 sheet: -0.47 (0.21), residues: 620 loop : -0.80 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.012 0.001 HIS A1048 PHE 0.041 0.002 PHE C 565 TYR 0.030 0.002 TYR B 204 ARG 0.013 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 42) link_NAG-ASN : angle 2.77357 ( 126) link_BETA1-4 : bond 0.00701 ( 18) link_BETA1-4 : angle 1.58016 ( 54) hydrogen bonds : bond 0.19322 ( 970) hydrogen bonds : angle 9.36911 ( 2838) SS BOND : bond 0.00260 ( 42) SS BOND : angle 1.17392 ( 84) covalent geometry : bond 0.00535 (25830) covalent geometry : angle 0.78206 (35160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 2.737 Fit side-chains REVERT: A 567 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7932 (mtt180) REVERT: B 130 VAL cc_start: 0.6545 (t) cc_final: 0.6328 (t) REVERT: B 153 MET cc_start: 0.5090 (ptp) cc_final: 0.3034 (tpt) REVERT: B 169 GLU cc_start: 0.7320 (tt0) cc_final: 0.6864 (mp0) REVERT: B 191 GLU cc_start: 0.7655 (mp0) cc_final: 0.7239 (mp0) REVERT: B 267 VAL cc_start: 0.7138 (t) cc_final: 0.6852 (t) REVERT: B 353 TRP cc_start: 0.5881 (p-90) cc_final: 0.5122 (p-90) REVERT: B 542 ASN cc_start: 0.7679 (t0) cc_final: 0.7464 (t0) REVERT: B 990 GLU cc_start: 0.8047 (tt0) cc_final: 0.7837 (tm-30) REVERT: C 54 LEU cc_start: 0.8390 (mm) cc_final: 0.8113 (mm) REVERT: C 360 ASN cc_start: 0.7467 (m-40) cc_final: 0.6983 (t0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 1.0999 time to fit residues: 294.0301 Evaluate side-chains 141 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 271 GLN B1002 GLN B1010 GLN B1135 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 532 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.170641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.104265 restraints weight = 41462.994| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.74 r_work: 0.3266 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25932 Z= 0.142 Angle : 0.556 10.484 35424 Z= 0.285 Chirality : 0.045 0.276 4155 Planarity : 0.004 0.056 4473 Dihedral : 6.616 54.218 4608 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.80 % Allowed : 5.74 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3072 helix: 1.90 (0.20), residues: 693 sheet: -0.38 (0.20), residues: 630 loop : -0.72 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.038 0.001 PHE C 565 TYR 0.037 0.001 TYR B 265 ARG 0.007 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 42) link_NAG-ASN : angle 2.25103 ( 126) link_BETA1-4 : bond 0.00380 ( 18) link_BETA1-4 : angle 1.26654 ( 54) hydrogen bonds : bond 0.04537 ( 970) hydrogen bonds : angle 6.83122 ( 2838) SS BOND : bond 0.00116 ( 42) SS BOND : angle 0.66355 ( 84) covalent geometry : bond 0.00316 (25830) covalent geometry : angle 0.53866 (35160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 2.526 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 314 GLN cc_start: 0.9111 (tt0) cc_final: 0.8823 (tt0) REVERT: A 964 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8741 (mtpt) REVERT: A 1050 MET cc_start: 0.9090 (ptm) cc_final: 0.8874 (ptm) REVERT: A 1141 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 169 GLU cc_start: 0.7111 (tt0) cc_final: 0.6516 (mp0) REVERT: B 191 GLU cc_start: 0.7532 (mp0) cc_final: 0.6798 (mp0) REVERT: B 314 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: B 353 TRP cc_start: 0.5039 (p-90) cc_final: 0.4599 (p-90) REVERT: B 990 GLU cc_start: 0.8521 (tt0) cc_final: 0.7898 (tm-30) REVERT: B 1010 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: C 351 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.5955 (p90) REVERT: C 360 ASN cc_start: 0.7697 (m-40) cc_final: 0.7060 (t0) REVERT: C 403 ARG cc_start: 0.5477 (mtp180) cc_final: 0.5034 (mtp-110) REVERT: C 452 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6911 (pp) REVERT: C 512 VAL cc_start: 0.7704 (t) cc_final: 0.7475 (p) REVERT: C 515 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: C 565 PHE cc_start: 0.8306 (p90) cc_final: 0.8084 (OUTLIER) outliers start: 22 outliers final: 6 residues processed: 163 average time/residue: 1.1248 time to fit residues: 219.5606 Evaluate side-chains 131 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 175 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 150 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 40.0000 chunk 272 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 955 ASN A 957 GLN A1002 GLN B 271 GLN B1002 GLN B1010 GLN C 49 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.170701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104118 restraints weight = 41355.894| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.66 r_work: 0.3257 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25932 Z= 0.144 Angle : 0.533 9.873 35424 Z= 0.271 Chirality : 0.045 0.268 4155 Planarity : 0.004 0.061 4473 Dihedral : 6.031 54.557 4608 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.77 % Allowed : 8.27 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3072 helix: 1.94 (0.20), residues: 699 sheet: -0.34 (0.20), residues: 657 loop : -0.66 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.004 0.001 HIS A 66 PHE 0.030 0.001 PHE C 565 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 42) link_NAG-ASN : angle 2.11783 ( 126) link_BETA1-4 : bond 0.00262 ( 18) link_BETA1-4 : angle 1.23096 ( 54) hydrogen bonds : bond 0.04310 ( 970) hydrogen bonds : angle 6.36769 ( 2838) SS BOND : bond 0.00116 ( 42) SS BOND : angle 0.61431 ( 84) covalent geometry : bond 0.00326 (25830) covalent geometry : angle 0.51709 (35160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.544 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8378 (tm-30) REVERT: A 314 GLN cc_start: 0.9117 (tt0) cc_final: 0.8860 (tt0) REVERT: A 964 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8743 (mtpt) REVERT: A 1050 MET cc_start: 0.9098 (ptm) cc_final: 0.8759 (ptm) REVERT: B 169 GLU cc_start: 0.7130 (tt0) cc_final: 0.6623 (mp0) REVERT: B 191 GLU cc_start: 0.7601 (mp0) cc_final: 0.6772 (mp0) REVERT: B 353 TRP cc_start: 0.5033 (p-90) cc_final: 0.4607 (p-90) REVERT: B 990 GLU cc_start: 0.8535 (tt0) cc_final: 0.7881 (tm-30) REVERT: C 351 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6018 (p90) REVERT: C 360 ASN cc_start: 0.7724 (m-40) cc_final: 0.7047 (t0) REVERT: C 403 ARG cc_start: 0.5485 (mtp180) cc_final: 0.4638 (mmm160) REVERT: C 452 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6941 (pp) REVERT: C 512 VAL cc_start: 0.7739 (t) cc_final: 0.7484 (m) REVERT: C 565 PHE cc_start: 0.8417 (p90) cc_final: 0.8205 (p90) outliers start: 21 outliers final: 6 residues processed: 138 average time/residue: 0.9942 time to fit residues: 168.3190 Evaluate side-chains 124 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 266 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 267 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 957 GLN A1002 GLN B 271 GLN B 751 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.170863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.104394 restraints weight = 41452.662| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.77 r_work: 0.3258 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25932 Z= 0.115 Angle : 0.506 11.513 35424 Z= 0.255 Chirality : 0.044 0.263 4155 Planarity : 0.004 0.062 4473 Dihedral : 5.417 54.709 4608 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.80 % Allowed : 8.93 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3072 helix: 2.06 (0.20), residues: 700 sheet: -0.24 (0.19), residues: 659 loop : -0.59 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.003 0.001 HIS B 66 PHE 0.021 0.001 PHE C 565 TYR 0.027 0.001 TYR C 453 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 42) link_NAG-ASN : angle 1.97488 ( 126) link_BETA1-4 : bond 0.00292 ( 18) link_BETA1-4 : angle 1.16092 ( 54) hydrogen bonds : bond 0.03881 ( 970) hydrogen bonds : angle 6.00400 ( 2838) SS BOND : bond 0.00106 ( 42) SS BOND : angle 0.57223 ( 84) covalent geometry : bond 0.00256 (25830) covalent geometry : angle 0.49119 (35160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 314 GLN cc_start: 0.9112 (tt0) cc_final: 0.8888 (tt0) REVERT: A 964 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8768 (mtpt) REVERT: A 1050 MET cc_start: 0.9061 (ptm) cc_final: 0.8728 (ptm) REVERT: B 191 GLU cc_start: 0.7630 (mp0) cc_final: 0.6854 (mp0) REVERT: B 353 TRP cc_start: 0.4615 (p-90) cc_final: 0.4372 (p-90) REVERT: B 990 GLU cc_start: 0.8551 (tt0) cc_final: 0.7883 (tm-30) REVERT: C 238 PHE cc_start: 0.5858 (p90) cc_final: 0.5653 (p90) REVERT: C 275 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7069 (t80) REVERT: C 351 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6077 (p90) REVERT: C 403 ARG cc_start: 0.5293 (mtp180) cc_final: 0.4528 (mmm160) REVERT: C 452 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6813 (pp) REVERT: C 565 PHE cc_start: 0.8442 (p90) cc_final: 0.8198 (p90) REVERT: C 780 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8778 (mt-10) outliers start: 22 outliers final: 9 residues processed: 143 average time/residue: 1.0911 time to fit residues: 188.7499 Evaluate side-chains 132 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 92 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 252 optimal weight: 0.2980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1002 GLN B 271 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.168916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.102262 restraints weight = 41430.521| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.62 r_work: 0.3221 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25932 Z= 0.188 Angle : 0.554 9.498 35424 Z= 0.277 Chirality : 0.046 0.259 4155 Planarity : 0.004 0.063 4473 Dihedral : 5.450 58.671 4608 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.95 % Allowed : 10.14 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3072 helix: 1.96 (0.20), residues: 699 sheet: -0.30 (0.19), residues: 672 loop : -0.65 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.023 0.001 PHE C 565 TYR 0.023 0.001 TYR B1067 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 42) link_NAG-ASN : angle 2.10250 ( 126) link_BETA1-4 : bond 0.00257 ( 18) link_BETA1-4 : angle 1.31346 ( 54) hydrogen bonds : bond 0.04387 ( 970) hydrogen bonds : angle 6.06936 ( 2838) SS BOND : bond 0.00131 ( 42) SS BOND : angle 0.61473 ( 84) covalent geometry : bond 0.00435 (25830) covalent geometry : angle 0.53798 (35160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 314 GLN cc_start: 0.9130 (tt0) cc_final: 0.8899 (tt0) REVERT: A 1010 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8730 (mp10) REVERT: A 1050 MET cc_start: 0.9128 (ptm) cc_final: 0.8717 (ptm) REVERT: B 191 GLU cc_start: 0.7706 (mp0) cc_final: 0.6837 (mp0) REVERT: B 269 TYR cc_start: 0.7862 (m-80) cc_final: 0.7619 (m-80) REVERT: B 314 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: B 353 TRP cc_start: 0.4929 (p-90) cc_final: 0.4499 (p-90) REVERT: B 900 MET cc_start: 0.9116 (mtp) cc_final: 0.8875 (mtp) REVERT: B 985 ASP cc_start: 0.7888 (p0) cc_final: 0.7673 (p0) REVERT: B 990 GLU cc_start: 0.8574 (tt0) cc_final: 0.7898 (tm-30) REVERT: C 266 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6360 (m-80) REVERT: C 275 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7437 (t80) REVERT: C 351 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6261 (p90) REVERT: C 403 ARG cc_start: 0.5406 (mtp180) cc_final: 0.4548 (mmm160) REVERT: C 565 PHE cc_start: 0.8459 (p90) cc_final: 0.8059 (p90) outliers start: 26 outliers final: 10 residues processed: 148 average time/residue: 1.0148 time to fit residues: 182.6681 Evaluate side-chains 133 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 4.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 55 optimal weight: 0.3980 chunk 185 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 271 GLN B1002 GLN B1010 GLN C 121 ASN C 532 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.170017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.102427 restraints weight = 41213.362| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.72 r_work: 0.3244 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25932 Z= 0.119 Angle : 0.516 9.149 35424 Z= 0.259 Chirality : 0.044 0.257 4155 Planarity : 0.004 0.059 4473 Dihedral : 5.175 57.836 4608 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.13 % Allowed : 10.54 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3072 helix: 2.03 (0.20), residues: 702 sheet: -0.25 (0.19), residues: 680 loop : -0.59 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.028 0.001 PHE A 168 TYR 0.028 0.001 TYR C 453 ARG 0.003 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 42) link_NAG-ASN : angle 1.94409 ( 126) link_BETA1-4 : bond 0.00320 ( 18) link_BETA1-4 : angle 1.16351 ( 54) hydrogen bonds : bond 0.03884 ( 970) hydrogen bonds : angle 5.84808 ( 2838) SS BOND : bond 0.00096 ( 42) SS BOND : angle 0.55456 ( 84) covalent geometry : bond 0.00267 (25830) covalent geometry : angle 0.50182 (35160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.9145 (tt0) cc_final: 0.8939 (tt0) REVERT: A 964 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8663 (mtmt) REVERT: A 1050 MET cc_start: 0.9052 (ptm) cc_final: 0.8718 (ptm) REVERT: B 191 GLU cc_start: 0.7663 (mp0) cc_final: 0.6705 (mp0) REVERT: B 353 TRP cc_start: 0.4854 (p-90) cc_final: 0.4536 (p-90) REVERT: B 900 MET cc_start: 0.9097 (mtp) cc_final: 0.8866 (mtp) REVERT: B 987 PRO cc_start: 0.8431 (Cg_exo) cc_final: 0.8169 (Cg_endo) REVERT: B 990 GLU cc_start: 0.8566 (tt0) cc_final: 0.7901 (tm-30) REVERT: C 266 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: C 275 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7391 (t80) REVERT: C 347 PHE cc_start: 0.3591 (OUTLIER) cc_final: 0.3206 (m-10) REVERT: C 351 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6204 (p90) REVERT: C 403 ARG cc_start: 0.5428 (mtp180) cc_final: 0.4495 (mmm160) REVERT: C 565 PHE cc_start: 0.8446 (p90) cc_final: 0.8029 (p90) outliers start: 31 outliers final: 12 residues processed: 147 average time/residue: 1.0354 time to fit residues: 186.4672 Evaluate side-chains 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 239 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 280 optimal weight: 0.1980 chunk 71 optimal weight: 0.0970 chunk 207 optimal weight: 0.5980 chunk 143 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 957 GLN A1002 GLN B 271 GLN B 606 ASN B1002 GLN B1010 GLN C 532 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.169668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102214 restraints weight = 41479.738| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.66 r_work: 0.3242 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25932 Z= 0.128 Angle : 0.521 9.882 35424 Z= 0.261 Chirality : 0.044 0.254 4155 Planarity : 0.004 0.057 4473 Dihedral : 5.088 58.013 4608 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.24 % Allowed : 10.76 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3072 helix: 2.05 (0.20), residues: 702 sheet: -0.26 (0.19), residues: 685 loop : -0.56 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.032 0.001 PHE A 168 TYR 0.023 0.001 TYR B 170 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 42) link_NAG-ASN : angle 1.93316 ( 126) link_BETA1-4 : bond 0.00287 ( 18) link_BETA1-4 : angle 1.17924 ( 54) hydrogen bonds : bond 0.03903 ( 970) hydrogen bonds : angle 5.79555 ( 2838) SS BOND : bond 0.00092 ( 42) SS BOND : angle 0.55539 ( 84) covalent geometry : bond 0.00290 (25830) covalent geometry : angle 0.50714 (35160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6380 (m-80) cc_final: 0.5900 (m-10) REVERT: A 314 GLN cc_start: 0.9141 (tt0) cc_final: 0.8940 (tt0) REVERT: A 964 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8787 (mtpt) REVERT: A 1050 MET cc_start: 0.9041 (ptm) cc_final: 0.8699 (ptm) REVERT: B 128 ILE cc_start: 0.6307 (mp) cc_final: 0.5814 (tt) REVERT: B 170 TYR cc_start: 0.5739 (t80) cc_final: 0.5480 (t80) REVERT: B 191 GLU cc_start: 0.7616 (mp0) cc_final: 0.6640 (mp0) REVERT: B 269 TYR cc_start: 0.7815 (m-80) cc_final: 0.7539 (m-80) REVERT: B 353 TRP cc_start: 0.4818 (p-90) cc_final: 0.4518 (p-90) REVERT: B 990 GLU cc_start: 0.8528 (tt0) cc_final: 0.7885 (tm-30) REVERT: C 266 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: C 275 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7408 (t80) REVERT: C 347 PHE cc_start: 0.3649 (OUTLIER) cc_final: 0.3235 (m-10) REVERT: C 351 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6395 (p90) REVERT: C 403 ARG cc_start: 0.5444 (mtp180) cc_final: 0.4500 (mmm160) REVERT: C 565 PHE cc_start: 0.8528 (p90) cc_final: 0.8077 (p90) outliers start: 34 outliers final: 13 residues processed: 145 average time/residue: 1.0165 time to fit residues: 180.4310 Evaluate side-chains 132 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 30.0000 chunk 174 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 271 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN C 360 ASN C 532 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.168958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100883 restraints weight = 41155.144| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.82 r_work: 0.3223 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25932 Z= 0.171 Angle : 0.549 9.733 35424 Z= 0.275 Chirality : 0.045 0.254 4155 Planarity : 0.004 0.050 4473 Dihedral : 5.199 59.279 4608 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.17 % Allowed : 11.01 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3072 helix: 2.04 (0.20), residues: 693 sheet: -0.27 (0.19), residues: 681 loop : -0.58 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.032 0.001 PHE A 168 TYR 0.027 0.001 TYR C 453 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 42) link_NAG-ASN : angle 2.00529 ( 126) link_BETA1-4 : bond 0.00254 ( 18) link_BETA1-4 : angle 1.25503 ( 54) hydrogen bonds : bond 0.04177 ( 970) hydrogen bonds : angle 5.86660 ( 2838) SS BOND : bond 0.00112 ( 42) SS BOND : angle 0.58223 ( 84) covalent geometry : bond 0.00394 (25830) covalent geometry : angle 0.53477 (35160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6496 (m-80) cc_final: 0.5996 (m-10) REVERT: A 239 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 314 GLN cc_start: 0.9147 (tt0) cc_final: 0.8939 (tt0) REVERT: A 964 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8819 (mtpt) REVERT: A 1050 MET cc_start: 0.9100 (ptm) cc_final: 0.8772 (ptm) REVERT: B 191 GLU cc_start: 0.7659 (mp0) cc_final: 0.6669 (mp0) REVERT: B 269 TYR cc_start: 0.7887 (m-80) cc_final: 0.7635 (m-80) REVERT: B 314 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: B 353 TRP cc_start: 0.4676 (p-90) cc_final: 0.4370 (p-90) REVERT: B 990 GLU cc_start: 0.8619 (tt0) cc_final: 0.7969 (tm-30) REVERT: C 266 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: C 275 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7567 (t80) REVERT: C 347 PHE cc_start: 0.3685 (OUTLIER) cc_final: 0.3244 (m-10) REVERT: C 351 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6634 (p90) REVERT: C 403 ARG cc_start: 0.5402 (mtp180) cc_final: 0.4481 (mmm160) REVERT: C 565 PHE cc_start: 0.8474 (p90) cc_final: 0.8062 (p90) REVERT: C 1141 LEU cc_start: 0.8401 (tp) cc_final: 0.8183 (tm) outliers start: 32 outliers final: 18 residues processed: 152 average time/residue: 1.0611 time to fit residues: 196.0761 Evaluate side-chains 146 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 708 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 223 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 308 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 0.1980 chunk 178 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 271 GLN B1002 GLN B1010 GLN C 532 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.169641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102227 restraints weight = 41441.671| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.81 r_work: 0.3239 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25932 Z= 0.122 Angle : 0.528 9.418 35424 Z= 0.265 Chirality : 0.044 0.256 4155 Planarity : 0.004 0.050 4473 Dihedral : 5.075 59.035 4608 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.17 % Allowed : 11.20 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3072 helix: 2.03 (0.20), residues: 702 sheet: -0.29 (0.19), residues: 669 loop : -0.56 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.035 0.001 PHE A 168 TYR 0.021 0.001 TYR B 396 ARG 0.009 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 42) link_NAG-ASN : angle 1.91710 ( 126) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.17197 ( 54) hydrogen bonds : bond 0.03880 ( 970) hydrogen bonds : angle 5.75641 ( 2838) SS BOND : bond 0.00094 ( 42) SS BOND : angle 0.54838 ( 84) covalent geometry : bond 0.00277 (25830) covalent geometry : angle 0.51448 (35160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6476 (m-80) cc_final: 0.5950 (m-10) REVERT: A 314 GLN cc_start: 0.9138 (tt0) cc_final: 0.8934 (tt0) REVERT: A 780 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8929 (mt-10) REVERT: A 964 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8818 (mtpt) REVERT: A 1050 MET cc_start: 0.9043 (ptm) cc_final: 0.8705 (ptm) REVERT: B 191 GLU cc_start: 0.7661 (mp0) cc_final: 0.6671 (mp0) REVERT: B 269 TYR cc_start: 0.7878 (m-80) cc_final: 0.7629 (m-80) REVERT: B 353 TRP cc_start: 0.4816 (p-90) cc_final: 0.4495 (p-90) REVERT: B 990 GLU cc_start: 0.8560 (tt0) cc_final: 0.7931 (tm-30) REVERT: C 266 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: C 275 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7412 (t80) REVERT: C 351 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6679 (p90) REVERT: C 403 ARG cc_start: 0.5332 (mtp180) cc_final: 0.4871 (mtp-110) REVERT: C 565 PHE cc_start: 0.8552 (p90) cc_final: 0.8117 (p90) REVERT: C 1141 LEU cc_start: 0.8394 (tp) cc_final: 0.8188 (tm) outliers start: 32 outliers final: 16 residues processed: 143 average time/residue: 1.0130 time to fit residues: 176.9995 Evaluate side-chains 135 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 0.9980 chunk 208 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 182 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 72 optimal weight: 0.4980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 271 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN C 532 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.169173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101544 restraints weight = 41404.918| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.77 r_work: 0.3232 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25932 Z= 0.143 Angle : 0.538 10.154 35424 Z= 0.269 Chirality : 0.045 0.257 4155 Planarity : 0.004 0.049 4473 Dihedral : 5.070 59.907 4608 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.84 % Allowed : 11.31 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3072 helix: 2.05 (0.20), residues: 701 sheet: -0.32 (0.19), residues: 680 loop : -0.55 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.033 0.001 PHE A 168 TYR 0.030 0.001 TYR C 453 ARG 0.009 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 42) link_NAG-ASN : angle 1.93692 ( 126) link_BETA1-4 : bond 0.00280 ( 18) link_BETA1-4 : angle 1.20939 ( 54) hydrogen bonds : bond 0.03986 ( 970) hydrogen bonds : angle 5.75335 ( 2838) SS BOND : bond 0.00099 ( 42) SS BOND : angle 0.55761 ( 84) covalent geometry : bond 0.00326 (25830) covalent geometry : angle 0.52504 (35160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6480 (m-80) cc_final: 0.5969 (m-10) REVERT: A 780 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8915 (mt-10) REVERT: A 1050 MET cc_start: 0.9058 (ptm) cc_final: 0.8722 (ptm) REVERT: B 191 GLU cc_start: 0.7563 (mp0) cc_final: 0.6574 (mp0) REVERT: B 269 TYR cc_start: 0.7861 (m-80) cc_final: 0.7626 (m-80) REVERT: B 353 TRP cc_start: 0.4755 (p-90) cc_final: 0.4394 (p-90) REVERT: B 990 GLU cc_start: 0.8576 (tt0) cc_final: 0.7965 (tm-30) REVERT: C 266 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: C 403 ARG cc_start: 0.5385 (mtp180) cc_final: 0.4912 (mtp-110) REVERT: C 565 PHE cc_start: 0.8504 (p90) cc_final: 0.8098 (p90) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 1.0392 time to fit residues: 177.7373 Evaluate side-chains 135 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 82 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 279 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 271 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.169342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101392 restraints weight = 41109.301| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.79 r_work: 0.3234 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 25932 Z= 0.153 Angle : 0.678 61.586 35424 Z= 0.327 Chirality : 0.048 1.235 4155 Planarity : 0.004 0.090 4473 Dihedral : 5.075 59.919 4608 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.84 % Allowed : 11.60 % Favored : 87.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3072 helix: 2.06 (0.20), residues: 701 sheet: -0.31 (0.19), residues: 680 loop : -0.56 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 104 HIS 0.002 0.001 HIS A 207 PHE 0.032 0.001 PHE A 168 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 42) link_NAG-ASN : angle 1.93770 ( 126) link_BETA1-4 : bond 0.00247 ( 18) link_BETA1-4 : angle 1.21888 ( 54) hydrogen bonds : bond 0.03974 ( 970) hydrogen bonds : angle 5.75201 ( 2838) SS BOND : bond 0.00098 ( 42) SS BOND : angle 0.54901 ( 84) covalent geometry : bond 0.00341 (25830) covalent geometry : angle 0.66883 (35160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36570.34 seconds wall clock time: 625 minutes 50.65 seconds (37550.65 seconds total)