Starting phenix.real_space_refine (version: dev) on Sat Feb 25 11:23:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxt_25505/02_2023/7sxt_25505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxt_25505/02_2023/7sxt_25505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxt_25505/02_2023/7sxt_25505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxt_25505/02_2023/7sxt_25505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxt_25505/02_2023/7sxt_25505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxt_25505/02_2023/7sxt_25505.pdb" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.035 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 Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 13.78, per 1000 atoms: 0.55 Number of scatterers: 25248 At special positions: 0 Unit cell: (141, 145, 197, 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 4125 7.00 C 16074 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.91 Conformation dependent library (CDL) restraints added in 3.8 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: 63 helices and 51 sheets defined 24.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 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 364 through 371 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.682A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.461A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.104A 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: 3.680A 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 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.920A 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 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.030A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.562A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.002A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.674A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.910A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.978A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.633A 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 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.575A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.902A 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 removed outlier: 3.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 1032 removed outlier: 3.968A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.550A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.810A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.670A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.530A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.907A 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: 3.715A 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 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.964A 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 945 through 965 removed outlier: 3.601A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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: 3.508A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.266A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.599A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.976A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.789A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.982A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.993A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.559A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.829A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.206A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.685A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.341A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.623A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.078A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.192A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.677A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.823A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.645A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.636A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.228A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.190A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.190A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.951A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.704A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.154A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.723A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.743A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.254A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 1087 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.83 Time building geometry restraints manager: 11.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7333 1.34 - 1.46: 6169 1.46 - 1.58: 12178 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25818 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.51e-02 4.39e+03 1.22e+01 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.51e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.360 -0.024 1.36e-02 5.41e+03 3.15e+00 bond pdb=" CB PRO B 987 " pdb=" CG PRO B 987 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.75e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.23e+00 ... (remaining 25813 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.51: 449 104.51 - 111.88: 12255 111.88 - 119.26: 8693 119.26 - 126.63: 13459 126.63 - 134.00: 289 Bond angle restraints: 35145 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.08 -5.38 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.60 -4.67 1.20e+00 6.94e-01 1.52e+01 ... (remaining 35140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14114 17.98 - 35.97: 964 35.97 - 53.95: 115 53.95 - 71.93: 51 71.93 - 89.92: 29 Dihedral angle restraints: 15273 sinusoidal: 6192 harmonic: 9081 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 15270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3304 0.061 - 0.122: 734 0.122 - 0.183: 103 0.183 - 0.244: 14 0.244 - 0.306: 3 Chirality restraints: 4158 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 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLN C 920 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1029 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C MET A1029 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A1029 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A1030 " -0.017 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6828 2.81 - 3.33: 21059 3.33 - 3.85: 43297 3.85 - 4.38: 49762 4.38 - 4.90: 84966 Nonbonded interactions: 205912 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 2.440 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.311 2.440 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.329 2.440 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.334 2.440 ... (remaining 205907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16074 2.51 5 N 4125 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.700 Check model and map are aligned: 0.360 Process input model: 69.030 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.004 0.083 25818 Z= 0.271 Angle : 0.742 9.953 35145 Z= 0.406 Chirality : 0.052 0.306 4158 Planarity : 0.007 0.065 4476 Dihedral : 12.871 89.918 9303 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3072 helix: 0.10 (0.18), residues: 650 sheet: 0.11 (0.18), residues: 687 loop : -0.86 (0.13), residues: 1735 *********************** 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 307 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 1.3614 time to fit residues: 485.3428 Evaluate side-chains 163 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3435 time to fit residues: 4.4170 ------------------------------------------------------------------------------- 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: 4.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A1010 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 779 GLN C 957 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 25818 Z= 0.208 Angle : 0.549 12.078 35145 Z= 0.288 Chirality : 0.045 0.576 4158 Planarity : 0.004 0.065 4476 Dihedral : 4.939 24.607 3705 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3072 helix: 1.46 (0.20), residues: 672 sheet: 0.37 (0.19), residues: 687 loop : -0.66 (0.14), residues: 1713 *********************** 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 207 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 196 average time/residue: 1.3803 time to fit residues: 318.0085 Evaluate side-chains 161 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 3.209 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.6850 time to fit residues: 7.9530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 281 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 487 ASN A 755 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 901 GLN B1011 GLN C 121 ASN C 207 HIS C 856 ASN C 955 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 25818 Z= 0.250 Angle : 0.533 10.026 35145 Z= 0.278 Chirality : 0.045 0.364 4158 Planarity : 0.004 0.058 4476 Dihedral : 4.811 22.136 3705 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.76 % 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: 0.37 (0.15), residues: 3072 helix: 2.01 (0.21), residues: 667 sheet: 0.46 (0.20), residues: 670 loop : -0.54 (0.14), residues: 1735 *********************** 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 199 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 151 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 18 residues processed: 188 average time/residue: 1.3298 time to fit residues: 299.3419 Evaluate side-chains 155 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.5433 time to fit residues: 7.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN C 824 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 25818 Z= 0.295 Angle : 0.558 11.059 35145 Z= 0.289 Chirality : 0.046 0.244 4158 Planarity : 0.004 0.053 4476 Dihedral : 4.884 22.466 3705 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3072 helix: 2.11 (0.20), residues: 668 sheet: 0.29 (0.19), residues: 697 loop : -0.51 (0.14), residues: 1707 *********************** 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 196 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 22 residues processed: 181 average time/residue: 1.2853 time to fit residues: 276.0074 Evaluate side-chains 154 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 3.026 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 5 average time/residue: 0.4919 time to fit residues: 7.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 121 ASN B 755 GLN C 856 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 25818 Z= 0.272 Angle : 0.544 12.362 35145 Z= 0.280 Chirality : 0.045 0.250 4158 Planarity : 0.004 0.051 4476 Dihedral : 4.792 21.614 3705 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3072 helix: 2.20 (0.20), residues: 668 sheet: 0.33 (0.19), residues: 685 loop : -0.46 (0.14), residues: 1719 *********************** 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 188 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 176 average time/residue: 1.2997 time to fit residues: 271.6045 Evaluate side-chains 146 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 3.034 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 4 average time/residue: 0.3406 time to fit residues: 6.1069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 856 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 25818 Z= 0.221 Angle : 0.529 12.239 35145 Z= 0.272 Chirality : 0.044 0.258 4158 Planarity : 0.004 0.052 4476 Dihedral : 4.735 21.533 3705 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.43 % 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: 0.51 (0.15), residues: 3072 helix: 2.31 (0.20), residues: 668 sheet: 0.33 (0.20), residues: 667 loop : -0.42 (0.14), residues: 1737 *********************** 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 175 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 167 average time/residue: 1.2762 time to fit residues: 254.1225 Evaluate side-chains 148 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 3.059 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.3487 time to fit residues: 6.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0570 chunk 34 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25818 Z= 0.222 Angle : 0.533 12.398 35145 Z= 0.272 Chirality : 0.044 0.258 4158 Planarity : 0.004 0.088 4476 Dihedral : 4.700 22.503 3705 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.17 % 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: 0.53 (0.15), residues: 3072 helix: 2.32 (0.20), residues: 670 sheet: 0.33 (0.19), residues: 667 loop : -0.40 (0.14), residues: 1735 *********************** 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 170 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 162 average time/residue: 1.2336 time to fit residues: 240.1568 Evaluate side-chains 142 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 2.903 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 1 average time/residue: 0.4992 time to fit residues: 4.7417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 0.0020 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN C 856 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25818 Z= 0.173 Angle : 0.527 12.733 35145 Z= 0.268 Chirality : 0.044 0.260 4158 Planarity : 0.003 0.038 4476 Dihedral : 4.660 26.678 3705 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.21 % 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: 0.60 (0.15), residues: 3072 helix: 2.41 (0.20), residues: 669 sheet: 0.36 (0.19), residues: 667 loop : -0.37 (0.14), residues: 1736 *********************** 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 161 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 156 average time/residue: 1.2535 time to fit residues: 235.5868 Evaluate side-chains 142 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 0.8454 time to fit residues: 7.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 220 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 20.0000 chunk 265 optimal weight: 0.7980 chunk 279 optimal weight: 0.0170 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 856 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25818 Z= 0.191 Angle : 0.528 12.746 35145 Z= 0.268 Chirality : 0.044 0.256 4158 Planarity : 0.003 0.039 4476 Dihedral : 4.663 25.017 3705 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.88 % 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: 0.61 (0.15), residues: 3072 helix: 2.40 (0.20), residues: 677 sheet: 0.34 (0.19), residues: 668 loop : -0.35 (0.14), residues: 1727 *********************** 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 fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 155 average time/residue: 1.3668 time to fit residues: 253.2300 Evaluate side-chains 146 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 2 average time/residue: 0.4177 time to fit residues: 5.3620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 0.0980 chunk 286 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 755 GLN C 856 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25818 Z= 0.186 Angle : 0.531 12.896 35145 Z= 0.269 Chirality : 0.044 0.254 4158 Planarity : 0.003 0.040 4476 Dihedral : 4.661 23.949 3705 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.80 % 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: 0.65 (0.15), residues: 3072 helix: 2.48 (0.20), residues: 671 sheet: 0.32 (0.19), residues: 665 loop : -0.31 (0.14), residues: 1736 ********************** 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 154 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 151 average time/residue: 1.3119 time to fit residues: 236.7258 Evaluate side-chains 142 residues out of total 2733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 2 average time/residue: 1.0471 time to fit residues: 6.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 856 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075668 restraints weight = 54411.500| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.05 r_work: 0.2985 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 25818 Z= 0.270 Angle : 0.550 12.877 35145 Z= 0.281 Chirality : 0.045 0.247 4158 Planarity : 0.004 0.040 4476 Dihedral : 4.758 23.224 3705 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.80 % 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: 0.60 (0.15), residues: 3072 helix: 2.40 (0.20), residues: 675 sheet: 0.33 (0.19), residues: 673 loop : -0.36 (0.14), residues: 1724 =============================================================================== Job complete usr+sys time: 7991.66 seconds wall clock time: 144 minutes 42.93 seconds (8682.93 seconds total)