Starting phenix.real_space_refine on Sun Jun 22 02:52:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlo_27508/06_2025/8dlo_27508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlo_27508/06_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_27508/06_2025/8dlo_27508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlo_27508/06_2025/8dlo_27508.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlo_27508/06_2025/8dlo_27508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlo_27508/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.78, per 1000 atoms: 0.70 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: 7.07 Conformation dependent library (CDL) restraints added in 3.9 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: 4.54 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: 14.54 Time building geometry restraints manager: 8.40 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: 0.10 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: 37.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 72.060 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.370 ------------------------------------------------------------------------------- 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 : 2.751 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: 1.1173 time to fit residues: 297.8742 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 : 2.618 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.171274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.104668 restraints weight = 41371.763| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.68 r_work: 0.3267 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 0.00467 ( 42) link_NAG-ASN : angle 2.25103 ( 126) link_BETA1-4 : bond 0.00380 ( 18) link_BETA1-4 : angle 1.26652 ( 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 : 2.787 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 314 GLN cc_start: 0.9108 (tt0) cc_final: 0.8819 (tt0) REVERT: A 964 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8737 (mtpt) REVERT: A 1050 MET cc_start: 0.9090 (ptm) cc_final: 0.8874 (ptm) REVERT: A 1141 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 169 GLU cc_start: 0.7126 (tt0) cc_final: 0.6529 (mp0) REVERT: B 191 GLU cc_start: 0.7538 (mp0) cc_final: 0.6807 (mp0) REVERT: B 314 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: B 353 TRP cc_start: 0.5005 (p-90) cc_final: 0.4576 (p-90) REVERT: B 990 GLU cc_start: 0.8516 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 1010 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: C 351 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.5952 (p90) REVERT: C 360 ASN cc_start: 0.7698 (m-40) cc_final: 0.7061 (t0) REVERT: C 403 ARG cc_start: 0.5471 (mtp180) cc_final: 0.5028 (mtp-110) REVERT: C 452 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6911 (pp) REVERT: C 512 VAL cc_start: 0.7708 (t) cc_final: 0.7480 (p) REVERT: C 515 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: C 565 PHE cc_start: 0.8301 (p90) cc_final: 0.8080 (OUTLIER) outliers start: 22 outliers final: 6 residues processed: 163 average time/residue: 1.2305 time to fit residues: 239.1929 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 : 2.675 ------------------------------------------------------------------------------- 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: 1.9990 chunk 163 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 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: 0.8980 chunk 281 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.104281 restraints weight = 41357.514| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.58 r_work: 0.3254 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1382 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= 0.145 Angle : 0.534 9.902 35424 Z= 0.271 Chirality : 0.045 0.268 4155 Planarity : 0.004 0.061 4473 Dihedral : 6.036 54.690 4608 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.80 % Allowed : 8.27 % Favored : 90.93 % 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: 0.00 (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 0.003 0.001 HIS A 66 PHE 0.030 0.001 PHE C 565 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 42) link_NAG-ASN : angle 2.12165 ( 126) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.23644 ( 54) hydrogen bonds : bond 0.04319 ( 970) hydrogen bonds : angle 6.38573 ( 2838) SS BOND : bond 0.00115 ( 42) SS BOND : angle 0.61030 ( 84) covalent geometry : bond 0.00329 (25830) covalent geometry : angle 0.51769 (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 146 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 2.788 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 314 GLN cc_start: 0.9120 (tt0) cc_final: 0.8857 (tt0) REVERT: A 964 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8747 (mtpt) REVERT: A 1050 MET cc_start: 0.9075 (ptm) cc_final: 0.8737 (ptm) REVERT: B 169 GLU cc_start: 0.7105 (tt0) cc_final: 0.6591 (mp0) REVERT: B 191 GLU cc_start: 0.7603 (mp0) cc_final: 0.6786 (mp0) REVERT: B 353 TRP cc_start: 0.5170 (p-90) cc_final: 0.4711 (p-90) REVERT: B 990 GLU cc_start: 0.8569 (tt0) cc_final: 0.7901 (tm-30) REVERT: C 351 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6013 (p90) REVERT: C 360 ASN cc_start: 0.7729 (m-40) cc_final: 0.7046 (t0) REVERT: C 403 ARG cc_start: 0.5512 (mtp180) cc_final: 0.4645 (mmm160) REVERT: C 452 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6946 (pp) REVERT: C 512 VAL cc_start: 0.7747 (t) cc_final: 0.7520 (p) outliers start: 22 outliers final: 6 residues processed: 139 average time/residue: 1.0921 time to fit residues: 184.7108 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 : 2.661 ------------------------------------------------------------------------------- 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: 1.9990 chunk 164 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 227 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.170384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103716 restraints weight = 41559.570| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.69 r_work: 0.3261 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25932 Z= 0.130 Angle : 0.517 11.009 35424 Z= 0.260 Chirality : 0.044 0.264 4155 Planarity : 0.004 0.056 4473 Dihedral : 5.504 56.115 4608 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.84 % Allowed : 9.18 % Favored : 89.97 % 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: 0.09 (0.15), residues: 3072 helix: 2.02 (0.20), residues: 700 sheet: -0.27 (0.19), residues: 662 loop : -0.62 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 104 HIS 0.003 0.001 HIS A 66 PHE 0.027 0.001 PHE C 565 TYR 0.026 0.001 TYR C 453 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 42) link_NAG-ASN : angle 2.01419 ( 126) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 1.18852 ( 54) hydrogen bonds : bond 0.04017 ( 970) hydrogen bonds : angle 6.06702 ( 2838) SS BOND : bond 0.00109 ( 42) SS BOND : angle 0.58040 ( 84) covalent geometry : bond 0.00293 (25830) covalent geometry : angle 0.50180 (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 153 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 314 GLN cc_start: 0.9110 (tt0) cc_final: 0.8865 (tt0) REVERT: A 964 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8729 (mtpt) REVERT: A 1050 MET cc_start: 0.9063 (ptm) cc_final: 0.8636 (ptm) REVERT: B 191 GLU cc_start: 0.7627 (mp0) cc_final: 0.6845 (mp0) REVERT: B 353 TRP cc_start: 0.4836 (p-90) cc_final: 0.4531 (p-90) REVERT: B 990 GLU cc_start: 0.8541 (tt0) cc_final: 0.7870 (tm-30) REVERT: C 238 PHE cc_start: 0.5906 (p90) cc_final: 0.5701 (p90) REVERT: C 275 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7072 (t80) REVERT: C 351 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6089 (p90) REVERT: C 403 ARG cc_start: 0.5412 (mtp180) cc_final: 0.4570 (mmm160) REVERT: C 452 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6885 (pp) REVERT: C 512 VAL cc_start: 0.7712 (t) cc_final: 0.7509 (m) outliers start: 23 outliers final: 8 residues processed: 144 average time/residue: 1.5754 time to fit residues: 274.5553 Evaluate side-chains 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 3.326 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 302 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.167901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099666 restraints weight = 41523.622| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.76 r_work: 0.3197 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 25932 Z= 0.249 Angle : 0.595 9.840 35424 Z= 0.298 Chirality : 0.047 0.267 4155 Planarity : 0.004 0.062 4473 Dihedral : 5.781 59.612 4608 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.13 % Allowed : 10.46 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3072 helix: 1.86 (0.20), residues: 692 sheet: -0.35 (0.19), residues: 669 loop : -0.75 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS A1048 PHE 0.027 0.002 PHE C 565 TYR 0.025 0.002 TYR B1067 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 42) link_NAG-ASN : angle 2.21443 ( 126) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.41268 ( 54) hydrogen bonds : bond 0.04723 ( 970) hydrogen bonds : angle 6.23556 ( 2838) SS BOND : bond 0.00175 ( 42) SS BOND : angle 0.67342 ( 84) covalent geometry : bond 0.00583 (25830) covalent geometry : angle 0.57844 (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 159 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 2.751 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8399 (tm-30) REVERT: A 235 ILE cc_start: 0.6232 (mt) cc_final: 0.5872 (mp) REVERT: A 1050 MET cc_start: 0.9147 (ptm) cc_final: 0.8760 (ptm) REVERT: B 169 GLU cc_start: 0.7216 (tt0) cc_final: 0.6623 (mp0) REVERT: B 191 GLU cc_start: 0.7649 (mp0) cc_final: 0.6752 (mp0) REVERT: B 269 TYR cc_start: 0.7831 (m-80) cc_final: 0.7596 (m-80) REVERT: B 314 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8433 (tm-30) REVERT: B 353 TRP cc_start: 0.4756 (p-90) cc_final: 0.4403 (p-90) REVERT: B 987 PRO cc_start: 0.8421 (Cg_exo) cc_final: 0.8163 (Cg_endo) REVERT: B 990 GLU cc_start: 0.8600 (tt0) cc_final: 0.7954 (tm-30) REVERT: C 266 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: C 275 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7569 (t80) REVERT: C 347 PHE cc_start: 0.3597 (OUTLIER) cc_final: 0.2895 (m-10) REVERT: C 351 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6339 (p90) REVERT: C 403 ARG cc_start: 0.5443 (mtp180) cc_final: 0.4573 (mmm160) REVERT: C 509 ARG cc_start: 0.5281 (OUTLIER) cc_final: 0.4743 (ttp-170) REVERT: C 512 VAL cc_start: 0.7701 (t) cc_final: 0.7472 (m) outliers start: 31 outliers final: 13 residues processed: 148 average time/residue: 1.1005 time to fit residues: 197.2218 Evaluate side-chains 138 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 2.642 ------------------------------------------------------------------------------- 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 314 GLN 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 118 LEU 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 400 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 509 ARG 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: 3.9990 chunk 185 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 chunk 253 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.168881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102882 restraints weight = 41137.659| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.61 r_work: 0.3205 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1846 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= 0.165 Angle : 0.549 9.574 35424 Z= 0.275 Chirality : 0.045 0.261 4155 Planarity : 0.004 0.057 4473 Dihedral : 5.579 58.693 4608 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.10 % Allowed : 10.87 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3072 helix: 1.93 (0.20), residues: 693 sheet: -0.37 (0.19), residues: 674 loop : -0.71 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.031 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 0.00417 ( 42) link_NAG-ASN : angle 2.06611 ( 126) link_BETA1-4 : bond 0.00257 ( 18) link_BETA1-4 : angle 1.25364 ( 54) hydrogen bonds : bond 0.04252 ( 970) hydrogen bonds : angle 6.06289 ( 2838) SS BOND : bond 0.00117 ( 42) SS BOND : angle 0.59011 ( 84) covalent geometry : bond 0.00377 (25830) covalent geometry : angle 0.53393 (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 155 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 235 ILE cc_start: 0.6252 (mt) cc_final: 0.5899 (mp) REVERT: A 314 GLN cc_start: 0.9135 (tt0) cc_final: 0.8888 (tt0) REVERT: A 964 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8674 (mtmt) REVERT: A 1050 MET cc_start: 0.9128 (ptm) cc_final: 0.8720 (ptm) REVERT: B 191 GLU cc_start: 0.7694 (mp0) cc_final: 0.6732 (mp0) REVERT: B 269 TYR cc_start: 0.7849 (m-80) cc_final: 0.7583 (m-80) REVERT: B 353 TRP cc_start: 0.4624 (p-90) cc_final: 0.4338 (p-90) REVERT: B 987 PRO cc_start: 0.8463 (Cg_exo) cc_final: 0.8263 (Cg_endo) REVERT: B 990 GLU cc_start: 0.8574 (tt0) cc_final: 0.7871 (tm-30) REVERT: C 266 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: C 275 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7820 (t80) REVERT: C 347 PHE cc_start: 0.3571 (OUTLIER) cc_final: 0.3081 (m-10) REVERT: C 351 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6422 (p90) REVERT: C 403 ARG cc_start: 0.5294 (mtp180) cc_final: 0.4436 (mmm160) outliers start: 30 outliers final: 13 residues processed: 146 average time/residue: 1.0159 time to fit residues: 182.2255 Evaluate side-chains 135 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 51 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 239 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 280 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 217 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 606 ASN B1002 GLN B1010 GLN C 360 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 = 0.4384 r_free = 0.4384 target = 0.169013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101120 restraints weight = 41318.451| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.81 r_work: 0.3227 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25932 Z= 0.145 Angle : 0.537 9.415 35424 Z= 0.269 Chirality : 0.045 0.256 4155 Planarity : 0.004 0.056 4473 Dihedral : 5.398 56.275 4608 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.10 % Allowed : 11.09 % 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: 0.01 (0.15), residues: 3072 helix: 2.04 (0.20), residues: 687 sheet: -0.37 (0.19), residues: 684 loop : -0.66 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.033 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 0.00401 ( 42) link_NAG-ASN : angle 2.00518 ( 126) link_BETA1-4 : bond 0.00317 ( 18) link_BETA1-4 : angle 1.24019 ( 54) hydrogen bonds : bond 0.04091 ( 970) hydrogen bonds : angle 5.95288 ( 2838) SS BOND : bond 0.00101 ( 42) SS BOND : angle 0.57668 ( 84) covalent geometry : bond 0.00332 (25830) covalent geometry : angle 0.52256 (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 159 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.6380 (mt) cc_final: 0.6165 (mp) REVERT: A 314 GLN cc_start: 0.9142 (tt0) cc_final: 0.8935 (tt0) REVERT: A 964 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8819 (mtpt) REVERT: A 1050 MET cc_start: 0.9087 (ptm) cc_final: 0.8662 (ptm) REVERT: B 191 GLU cc_start: 0.7579 (mp0) cc_final: 0.6596 (mp0) REVERT: B 269 TYR cc_start: 0.7775 (m-80) cc_final: 0.7561 (m-80) REVERT: B 353 TRP cc_start: 0.4739 (p-90) cc_final: 0.4434 (p-90) REVERT: B 900 MET cc_start: 0.9003 (mtp) cc_final: 0.8789 (mtp) REVERT: B 990 GLU cc_start: 0.8535 (tt0) cc_final: 0.7905 (tm-30) REVERT: C 266 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: C 275 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7826 (t80) REVERT: C 347 PHE cc_start: 0.3644 (OUTLIER) cc_final: 0.2720 (m-10) REVERT: C 351 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6506 (p90) REVERT: C 403 ARG cc_start: 0.5413 (mtp180) cc_final: 0.4488 (mmm160) REVERT: C 509 ARG cc_start: 0.5275 (OUTLIER) cc_final: 0.4814 (mtp85) outliers start: 30 outliers final: 14 residues processed: 153 average time/residue: 1.0237 time to fit residues: 190.6348 Evaluate side-chains 137 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 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 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 509 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 0.0030 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.168488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100686 restraints weight = 41074.092| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.69 r_work: 0.3212 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25932 Z= 0.182 Angle : 0.563 9.392 35424 Z= 0.283 Chirality : 0.046 0.254 4155 Planarity : 0.004 0.050 4473 Dihedral : 5.397 52.370 4608 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.13 % Allowed : 11.38 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3072 helix: 1.99 (0.20), residues: 687 sheet: -0.40 (0.19), residues: 679 loop : -0.70 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.034 0.001 PHE A 168 TYR 0.022 0.001 TYR B1067 ARG 0.008 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 42) link_NAG-ASN : angle 2.04398 ( 126) link_BETA1-4 : bond 0.00252 ( 18) link_BETA1-4 : angle 1.28860 ( 54) hydrogen bonds : bond 0.04277 ( 970) hydrogen bonds : angle 5.97066 ( 2838) SS BOND : bond 0.00118 ( 42) SS BOND : angle 0.60521 ( 84) covalent geometry : bond 0.00420 (25830) covalent geometry : angle 0.54817 (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 153 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6415 (m-80) cc_final: 0.5939 (m-10) REVERT: A 235 ILE cc_start: 0.6368 (mt) cc_final: 0.6161 (mp) REVERT: A 314 GLN cc_start: 0.9154 (tt0) cc_final: 0.8931 (tt0) REVERT: A 964 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8819 (mtpt) REVERT: A 1050 MET cc_start: 0.9118 (ptm) cc_final: 0.8699 (ptm) REVERT: B 191 GLU cc_start: 0.7573 (mp0) cc_final: 0.6573 (mp0) REVERT: B 269 TYR cc_start: 0.7769 (m-80) cc_final: 0.7564 (m-80) REVERT: B 353 TRP cc_start: 0.4934 (p-90) cc_final: 0.4580 (p-90) REVERT: B 900 MET cc_start: 0.9043 (mtp) cc_final: 0.8806 (mtp) REVERT: B 988 GLU cc_start: 0.8584 (mp0) cc_final: 0.8361 (pm20) REVERT: B 990 GLU cc_start: 0.8619 (tt0) cc_final: 0.7975 (tm-30) REVERT: C 266 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.6153 (m-80) REVERT: C 275 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7683 (t80) REVERT: C 347 PHE cc_start: 0.3677 (OUTLIER) cc_final: 0.2848 (m-10) REVERT: C 403 ARG cc_start: 0.5414 (mtp180) cc_final: 0.4481 (mmm160) REVERT: C 509 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.4833 (mtp85) outliers start: 31 outliers final: 17 residues processed: 145 average time/residue: 1.0653 time to fit residues: 190.7127 Evaluate side-chains 138 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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 51 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 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 509 ARG 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: 6.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 308 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 B1002 GLN B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.168637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.101095 restraints weight = 41415.469| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.79 r_work: 0.3220 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25932 Z= 0.158 Angle : 0.548 9.377 35424 Z= 0.276 Chirality : 0.045 0.253 4155 Planarity : 0.004 0.050 4473 Dihedral : 5.268 52.352 4608 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.17 % Allowed : 11.38 % Favored : 87.45 % 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: -0.01 (0.15), residues: 3072 helix: 1.97 (0.20), residues: 695 sheet: -0.39 (0.19), residues: 671 loop : -0.66 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 104 HIS 0.003 0.001 HIS A1048 PHE 0.034 0.001 PHE A 168 TYR 0.027 0.001 TYR C 453 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 42) link_NAG-ASN : angle 1.98789 ( 126) link_BETA1-4 : bond 0.00266 ( 18) link_BETA1-4 : angle 1.23459 ( 54) hydrogen bonds : bond 0.04107 ( 970) hydrogen bonds : angle 5.88456 ( 2838) SS BOND : bond 0.00106 ( 42) SS BOND : angle 0.60177 ( 84) covalent geometry : bond 0.00365 (25830) covalent geometry : angle 0.53424 (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 159 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6423 (m-80) cc_final: 0.5951 (m-10) REVERT: A 314 GLN cc_start: 0.9142 (tt0) cc_final: 0.8929 (tt0) REVERT: A 1050 MET cc_start: 0.9106 (ptm) cc_final: 0.8687 (ptm) REVERT: B 191 GLU cc_start: 0.7682 (mp0) cc_final: 0.6719 (mp0) REVERT: B 900 MET cc_start: 0.9039 (mtp) cc_final: 0.8791 (mtp) REVERT: B 990 GLU cc_start: 0.8542 (tt0) cc_final: 0.7888 (tm-30) REVERT: C 266 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: C 275 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 347 PHE cc_start: 0.3626 (OUTLIER) cc_final: 0.2988 (m-10) REVERT: C 403 ARG cc_start: 0.5306 (mtp180) cc_final: 0.4430 (mmm160) REVERT: C 509 ARG cc_start: 0.5256 (OUTLIER) cc_final: 0.4793 (mtp85) outliers start: 32 outliers final: 18 residues processed: 152 average time/residue: 1.0318 time to fit residues: 192.3760 Evaluate side-chains 140 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 2.622 ------------------------------------------------------------------------------- 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 565 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 323 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 347 PHE 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 509 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 95 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 202 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.169694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101973 restraints weight = 41302.020| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.82 r_work: 0.3244 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25932 Z= 0.115 Angle : 0.532 10.601 35424 Z= 0.266 Chirality : 0.044 0.253 4155 Planarity : 0.004 0.050 4473 Dihedral : 5.000 52.363 4608 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.99 % Allowed : 11.82 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3072 helix: 2.03 (0.20), residues: 704 sheet: -0.32 (0.19), residues: 671 loop : -0.59 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 PHE 0.035 0.001 PHE A 168 TYR 0.022 0.001 TYR B 396 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 42) link_NAG-ASN : angle 1.87877 ( 126) link_BETA1-4 : bond 0.00305 ( 18) link_BETA1-4 : angle 1.15972 ( 54) hydrogen bonds : bond 0.03799 ( 970) hydrogen bonds : angle 5.72002 ( 2838) SS BOND : bond 0.00116 ( 42) SS BOND : angle 0.58293 ( 84) covalent geometry : bond 0.00260 (25830) covalent geometry : angle 0.51878 (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 158 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 4.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6332 (m-80) cc_final: 0.5784 (m-10) REVERT: A 964 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8758 (mtmt) REVERT: A 1050 MET cc_start: 0.9033 (ptm) cc_final: 0.8695 (ptm) REVERT: B 191 GLU cc_start: 0.7535 (mp0) cc_final: 0.6555 (mp0) REVERT: B 269 TYR cc_start: 0.7737 (m-80) cc_final: 0.7429 (m-80) REVERT: B 353 TRP cc_start: 0.4485 (p-90) cc_final: 0.4220 (p-90) REVERT: B 900 MET cc_start: 0.9001 (mtp) cc_final: 0.8748 (mtp) REVERT: B 990 GLU cc_start: 0.8551 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 192 PHE cc_start: 0.6722 (m-80) cc_final: 0.6514 (m-10) REVERT: C 266 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: C 275 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7409 (t80) REVERT: C 403 ARG cc_start: 0.5395 (mtp180) cc_final: 0.4924 (mtp-110) outliers start: 27 outliers final: 17 residues processed: 150 average time/residue: 1.4553 time to fit residues: 264.6378 Evaluate side-chains 139 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 6.362 ------------------------------------------------------------------------------- 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 323 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 82 optimal weight: 0.6980 chunk 212 optimal weight: 7.9990 chunk 218 optimal weight: 0.5980 chunk 175 optimal weight: 0.0030 chunk 237 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 279 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.170011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103934 restraints weight = 41067.130| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.63 r_work: 0.3252 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25932 Z= 0.110 Angle : 0.526 10.791 35424 Z= 0.263 Chirality : 0.044 0.254 4155 Planarity : 0.004 0.062 4473 Dihedral : 4.751 52.586 4608 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.84 % Allowed : 12.15 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3072 helix: 2.12 (0.20), residues: 704 sheet: -0.23 (0.19), residues: 692 loop : -0.53 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 PHE 0.034 0.001 PHE A 168 TYR 0.027 0.001 TYR C 453 ARG 0.016 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 42) link_NAG-ASN : angle 1.82434 ( 126) link_BETA1-4 : bond 0.00306 ( 18) link_BETA1-4 : angle 1.14867 ( 54) hydrogen bonds : bond 0.03706 ( 970) hydrogen bonds : angle 5.60767 ( 2838) SS BOND : bond 0.00105 ( 42) SS BOND : angle 0.57648 ( 84) covalent geometry : bond 0.00247 (25830) covalent geometry : angle 0.51334 (35160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43166.80 seconds wall clock time: 743 minutes 7.31 seconds (44587.31 seconds total)