Starting phenix.real_space_refine on Tue Feb 20 04:51:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlm_27506/02_2024/8dlm_27506.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlm_27506/02_2024/8dlm_27506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlm_27506/02_2024/8dlm_27506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlm_27506/02_2024/8dlm_27506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlm_27506/02_2024/8dlm_27506.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlm_27506/02_2024/8dlm_27506.pdb" } resolution = 2.89 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= -0.001 sd= 0.038 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 124 5.16 5 C 17102 2.51 5 N 4380 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26852 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6523 Classifications: {'peptide': 837} Link IDs: {'PTRANS': 45, 'TRANS': 791} Chain breaks: 8 Chain: "B" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 6514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6514 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 45, 'TRANS': 790} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "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: "V" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 13.40, per 1000 atoms: 0.50 Number of scatterers: 26852 At special positions: 0 Unit cell: (140, 158, 237, 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 124 16.00 O 5246 8.00 N 4380 7.00 C 17102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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 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=2.03 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 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 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 V 1 " - " NAG V 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 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 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 10.36 Conformation dependent library (CDL) restraints added in 5.0 seconds 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 43 sheets defined 34.2% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.099A 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: 3.619A 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: 3.919A 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 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.337A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.096A 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: 3.608A 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 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.895A 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 1032 removed outlier: 4.078A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.087A 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: 3.611A 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: 3.921A 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 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 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.051A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.671A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.716A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.771A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.123A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.693A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.798A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.835A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.526A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.565A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.676A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.170A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.581A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.327A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.654A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.519A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.804A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.536A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 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: 8.130A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.052A 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: 4.079A 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: 3.824A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.684A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.917A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.072A 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: 6.337A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.800A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS B 790 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.296A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.700A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.065A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.822A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.348A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.728A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.054A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.138A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.777A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS C 790 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.984A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.658A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.682A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.910A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.118A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.379A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.85 Time building geometry restraints manager: 11.17 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: 8446 1.34 - 1.47: 6919 1.47 - 1.59: 11928 1.59 - 1.72: 0 1.72 - 1.84: 172 Bond restraints: 27465 Sorted by residual: bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.87e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27460 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.60: 670 105.60 - 112.99: 14800 112.99 - 120.38: 10442 120.38 - 127.76: 11234 127.76 - 135.15: 221 Bond angle restraints: 37367 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 122.21 -8.31 1.80e+00 3.09e-01 2.13e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.04 -5.34 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.03 -5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.20 -5.84 1.42e+00 4.96e-01 1.69e+01 ... (remaining 37362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 15762 17.73 - 35.46: 1089 35.46 - 53.19: 208 53.19 - 70.92: 67 70.92 - 88.65: 35 Dihedral angle restraints: 17161 sinusoidal: 7548 harmonic: 9613 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.93 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 17.75 61.25 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" CB GLU C1111 " pdb=" CG GLU C1111 " pdb=" CD GLU C1111 " pdb=" OE1 GLU C1111 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 17158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3540 0.070 - 0.140: 773 0.140 - 0.210: 67 0.210 - 0.280: 6 0.280 - 0.350: 3 Chirality restraints: 4389 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+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 Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4386 not shown) Planarity restraints: 4795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO E 590 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 499 " -0.041 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO E 500 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 500 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 500 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.027 2.00e-02 2.50e+03 1.71e-02 5.86e+00 pdb=" CG TYR B 495 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.004 2.00e-02 2.50e+03 ... (remaining 4792 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7389 2.81 - 3.34: 23115 3.34 - 3.86: 45975 3.86 - 4.38: 52166 4.38 - 4.90: 90280 Nonbonded interactions: 218925 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.293 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.303 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.313 2.440 ... (remaining 218920 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' and (resid 14 through 528 or resid 530 through 1147 or resid 1301 thr \ ough 1306)) selection = chain 'C' } ncs_group { reference = chain 'D' 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' selection = chain 'V' } 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: 2.990 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: 0.010 Extract box with map and model: 14.620 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 70.470 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.055 27465 Z= 0.313 Angle : 0.794 10.148 37367 Z= 0.435 Chirality : 0.056 0.350 4389 Planarity : 0.006 0.061 4751 Dihedral : 13.167 88.650 10853 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 3249 helix: 1.48 (0.14), residues: 994 sheet: 0.94 (0.20), residues: 586 loop : -0.73 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 69 HIS 0.008 0.001 HIS E 34 PHE 0.024 0.002 PHE A 275 TYR 0.040 0.002 TYR B 495 ARG 0.008 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8590 (m-80) cc_final: 0.8197 (m-10) REVERT: A 90 VAL cc_start: 0.7311 (t) cc_final: 0.7056 (p) REVERT: A 106 PHE cc_start: 0.8677 (m-80) cc_final: 0.8123 (m-10) REVERT: A 168 PHE cc_start: 0.8028 (t80) cc_final: 0.7768 (t80) REVERT: A 194 PHE cc_start: 0.8753 (m-80) cc_final: 0.7757 (m-80) REVERT: A 284 THR cc_start: 0.8875 (m) cc_final: 0.8625 (p) REVERT: A 740 MET cc_start: 0.8104 (ttt) cc_final: 0.7800 (ttp) REVERT: B 337 PRO cc_start: 0.8811 (Cg_exo) cc_final: 0.8536 (Cg_endo) REVERT: B 532 ASN cc_start: 0.8495 (m-40) cc_final: 0.8278 (p0) REVERT: C 170 TYR cc_start: 0.8356 (t80) cc_final: 0.8150 (t80) REVERT: C 197 ILE cc_start: 0.8196 (mp) cc_final: 0.7903 (mm) REVERT: C 238 PHE cc_start: 0.7716 (p90) cc_final: 0.7078 (p90) REVERT: C 269 TYR cc_start: 0.6714 (m-80) cc_final: 0.6412 (m-80) REVERT: E 82 MET cc_start: 0.7868 (mtp) cc_final: 0.7635 (mpt) REVERT: E 134 ASN cc_start: 0.7235 (t0) cc_final: 0.6859 (p0) REVERT: E 292 ASP cc_start: 0.5134 (t70) cc_final: 0.4031 (m-30) REVERT: E 323 MET cc_start: 0.6582 (mmp) cc_final: 0.6113 (mpm) REVERT: E 474 MET cc_start: -0.0590 (mmt) cc_final: -0.1007 (mmt) REVERT: E 564 GLU cc_start: 0.3784 (mm-30) cc_final: 0.2991 (pm20) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 1.4167 time to fit residues: 519.2828 Evaluate side-chains 130 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 762 GLN C 907 ASN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27465 Z= 0.217 Angle : 0.584 10.170 37367 Z= 0.297 Chirality : 0.045 0.506 4389 Planarity : 0.005 0.058 4751 Dihedral : 6.327 59.608 4824 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.52 % Allowed : 8.10 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3249 helix: 2.35 (0.16), residues: 991 sheet: 0.97 (0.20), residues: 579 loop : -0.58 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS E 34 PHE 0.017 0.001 PHE C 86 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 149 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7165 (t) cc_final: 0.6939 (p) REVERT: A 104 TRP cc_start: 0.7977 (m-90) cc_final: 0.7563 (m-10) REVERT: A 106 PHE cc_start: 0.8805 (m-80) cc_final: 0.8342 (m-10) REVERT: A 168 PHE cc_start: 0.8095 (t80) cc_final: 0.7824 (t80) REVERT: A 194 PHE cc_start: 0.8322 (m-80) cc_final: 0.7656 (m-80) REVERT: A 284 THR cc_start: 0.8923 (m) cc_final: 0.8679 (p) REVERT: A 740 MET cc_start: 0.8237 (ttt) cc_final: 0.7951 (ttp) REVERT: A 780 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: B 380 TYR cc_start: 0.7483 (m-80) cc_final: 0.7202 (m-80) REVERT: C 170 TYR cc_start: 0.8595 (t80) cc_final: 0.7794 (t80) REVERT: C 197 ILE cc_start: 0.8135 (mp) cc_final: 0.7838 (mm) REVERT: C 238 PHE cc_start: 0.7358 (p90) cc_final: 0.6871 (p90) REVERT: E 62 MET cc_start: 0.7840 (ttp) cc_final: 0.7454 (tpp) REVERT: E 134 ASN cc_start: 0.7075 (t0) cc_final: 0.6650 (p0) REVERT: E 270 MET cc_start: 0.1427 (tpp) cc_final: 0.0817 (tpp) REVERT: E 323 MET cc_start: 0.6165 (mmp) cc_final: 0.4946 (mmt) REVERT: E 564 GLU cc_start: 0.3638 (mm-30) cc_final: 0.2968 (pm20) outliers start: 44 outliers final: 12 residues processed: 178 average time/residue: 1.1272 time to fit residues: 243.6736 Evaluate side-chains 136 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 chunk 322 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 239 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 926 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27465 Z= 0.216 Angle : 0.544 8.831 37367 Z= 0.277 Chirality : 0.044 0.278 4389 Planarity : 0.004 0.074 4751 Dihedral : 5.683 59.294 4820 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.72 % Allowed : 9.45 % Favored : 88.83 % 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: 0.98 (0.14), residues: 3249 helix: 2.50 (0.16), residues: 1003 sheet: 0.71 (0.21), residues: 552 loop : -0.52 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 104 HIS 0.004 0.001 HIS E 34 PHE 0.024 0.001 PHE C 106 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8186 (m-90) cc_final: 0.7882 (m-10) REVERT: A 106 PHE cc_start: 0.8637 (m-80) cc_final: 0.7923 (m-10) REVERT: A 168 PHE cc_start: 0.8121 (t80) cc_final: 0.7840 (t80) REVERT: A 194 PHE cc_start: 0.8413 (m-80) cc_final: 0.7754 (m-80) REVERT: A 195 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8181 (ttpp) REVERT: A 902 MET cc_start: 0.8745 (tpp) cc_final: 0.8375 (tpt) REVERT: B 153 MET cc_start: 0.2035 (ptt) cc_final: 0.1670 (tmm) REVERT: B 408 ARG cc_start: 0.7493 (ppt170) cc_final: 0.7149 (pmt-80) REVERT: C 170 TYR cc_start: 0.8641 (t80) cc_final: 0.7871 (t80) REVERT: C 197 ILE cc_start: 0.8170 (mp) cc_final: 0.7883 (mm) REVERT: C 238 PHE cc_start: 0.7495 (p90) cc_final: 0.6923 (p90) REVERT: C 269 TYR cc_start: 0.6650 (m-80) cc_final: 0.6422 (m-80) REVERT: E 62 MET cc_start: 0.7779 (ttp) cc_final: 0.7330 (tpp) REVERT: E 134 ASN cc_start: 0.7085 (t0) cc_final: 0.6618 (p0) REVERT: E 564 GLU cc_start: 0.3713 (mm-30) cc_final: 0.3043 (pm20) outliers start: 50 outliers final: 21 residues processed: 162 average time/residue: 1.1563 time to fit residues: 225.8638 Evaluate side-chains 137 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 128 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 20.0000 chunk 224 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 142 optimal weight: 0.0170 chunk 200 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 283 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 856 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 804 GLN C 824 ASN C 907 ASN C 926 GLN C 935 GLN C 978 ASN C1005 GLN E 96 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27465 Z= 0.321 Angle : 0.575 9.322 37367 Z= 0.292 Chirality : 0.044 0.293 4389 Planarity : 0.004 0.074 4751 Dihedral : 5.512 59.928 4820 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.14 % Allowed : 9.45 % Favored : 88.41 % 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: 0.94 (0.14), residues: 3249 helix: 2.49 (0.16), residues: 1008 sheet: 0.55 (0.21), residues: 551 loop : -0.51 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 104 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.001 PHE C 106 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 123 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8049 (m-90) cc_final: 0.7808 (m-10) REVERT: A 106 PHE cc_start: 0.8529 (m-80) cc_final: 0.8094 (m-10) REVERT: A 168 PHE cc_start: 0.8146 (t80) cc_final: 0.7860 (t80) REVERT: A 194 PHE cc_start: 0.8415 (m-80) cc_final: 0.7785 (m-80) REVERT: A 740 MET cc_start: 0.8055 (ttp) cc_final: 0.7800 (ttp) REVERT: A 900 MET cc_start: 0.8258 (mtp) cc_final: 0.8053 (mtm) REVERT: B 153 MET cc_start: 0.2352 (ptt) cc_final: 0.1803 (tmm) REVERT: B 408 ARG cc_start: 0.7435 (ppt170) cc_final: 0.7036 (pmt-80) REVERT: C 170 TYR cc_start: 0.8629 (t80) cc_final: 0.8142 (t80) REVERT: C 197 ILE cc_start: 0.8262 (mp) cc_final: 0.8002 (mm) REVERT: C 762 GLN cc_start: 0.8471 (mt0) cc_final: 0.8207 (mt0) REVERT: C 987 PRO cc_start: 0.8954 (OUTLIER) cc_final: 0.8711 (Cg_endo) REVERT: E 62 MET cc_start: 0.7778 (ttp) cc_final: 0.7309 (tpp) REVERT: E 134 ASN cc_start: 0.7063 (t0) cc_final: 0.6558 (p0) REVERT: E 332 MET cc_start: 0.4447 (ptp) cc_final: 0.4090 (pmm) outliers start: 62 outliers final: 26 residues processed: 169 average time/residue: 1.1896 time to fit residues: 241.9554 Evaluate side-chains 135 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 130 optimal weight: 0.0980 chunk 270 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 284 optimal weight: 30.0000 chunk 80 optimal weight: 0.8980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 907 ASN A1005 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 804 GLN C 907 ASN C 926 GLN C 935 GLN C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27465 Z= 0.174 Angle : 0.523 8.471 37367 Z= 0.266 Chirality : 0.043 0.277 4389 Planarity : 0.004 0.072 4751 Dihedral : 5.129 58.947 4820 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.07 % Allowed : 10.10 % Favored : 87.83 % 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: 1.04 (0.14), residues: 3249 helix: 2.64 (0.16), residues: 1001 sheet: 0.49 (0.21), residues: 563 loop : -0.45 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 104 HIS 0.003 0.001 HIS E 34 PHE 0.024 0.001 PHE C 541 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 118 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7817 (m-90) cc_final: 0.7581 (m-10) REVERT: A 106 PHE cc_start: 0.8498 (m-80) cc_final: 0.8021 (m-10) REVERT: A 168 PHE cc_start: 0.8126 (t80) cc_final: 0.7833 (t80) REVERT: A 194 PHE cc_start: 0.8456 (m-80) cc_final: 0.7754 (m-80) REVERT: A 740 MET cc_start: 0.7985 (ttp) cc_final: 0.7777 (ttp) REVERT: A 900 MET cc_start: 0.8165 (mtp) cc_final: 0.7941 (mtm) REVERT: B 408 ARG cc_start: 0.7450 (ppt170) cc_final: 0.7223 (pmt-80) REVERT: C 197 ILE cc_start: 0.8292 (mp) cc_final: 0.8031 (mm) REVERT: E 62 MET cc_start: 0.7781 (ttp) cc_final: 0.7319 (tpp) REVERT: E 134 ASN cc_start: 0.7258 (t0) cc_final: 0.6783 (p0) REVERT: E 270 MET cc_start: 0.1371 (tmm) cc_final: 0.1099 (ttp) REVERT: E 332 MET cc_start: 0.4649 (ptp) cc_final: 0.4391 (pmm) REVERT: E 557 MET cc_start: 0.5674 (tmm) cc_final: 0.5300 (tmt) outliers start: 60 outliers final: 24 residues processed: 158 average time/residue: 1.1734 time to fit residues: 224.7415 Evaluate side-chains 131 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 78 optimal weight: 0.1980 chunk 317 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 907 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 334 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 804 GLN C 926 GLN C 935 GLN C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27465 Z= 0.353 Angle : 0.592 10.861 37367 Z= 0.301 Chirality : 0.045 0.304 4389 Planarity : 0.004 0.075 4751 Dihedral : 5.471 59.487 4820 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.76 % Allowed : 11.03 % Favored : 87.21 % 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: 0.90 (0.14), residues: 3249 helix: 2.45 (0.16), residues: 1013 sheet: 0.48 (0.20), residues: 575 loop : -0.53 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.004 0.001 HIS E 34 PHE 0.019 0.002 PHE C 106 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7159 (t) cc_final: 0.6713 (m) REVERT: A 104 TRP cc_start: 0.7926 (m-90) cc_final: 0.7679 (m-10) REVERT: A 106 PHE cc_start: 0.8722 (m-80) cc_final: 0.8457 (m-80) REVERT: A 168 PHE cc_start: 0.8108 (t80) cc_final: 0.7818 (t80) REVERT: A 194 PHE cc_start: 0.8461 (m-80) cc_final: 0.7859 (m-80) REVERT: A 740 MET cc_start: 0.7988 (ttp) cc_final: 0.7760 (ttp) REVERT: A 900 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: B 408 ARG cc_start: 0.7322 (ppt170) cc_final: 0.7089 (pmt-80) REVERT: C 197 ILE cc_start: 0.8314 (mp) cc_final: 0.8084 (mm) REVERT: C 987 PRO cc_start: 0.8878 (OUTLIER) cc_final: 0.8614 (Cg_endo) REVERT: E 62 MET cc_start: 0.7781 (ttp) cc_final: 0.7503 (mtp) REVERT: E 134 ASN cc_start: 0.7140 (t0) cc_final: 0.6618 (p0) REVERT: E 332 MET cc_start: 0.4694 (ptp) cc_final: 0.4391 (pmm) REVERT: E 557 MET cc_start: 0.6035 (tmm) cc_final: 0.5643 (tmt) outliers start: 51 outliers final: 26 residues processed: 150 average time/residue: 1.2054 time to fit residues: 220.4179 Evaluate side-chains 131 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 987 PRO Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 231 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 267 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 316 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 192 optimal weight: 0.1980 chunk 145 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 872 GLN C 804 GLN C 926 GLN C 935 GLN C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27465 Z= 0.151 Angle : 0.520 9.342 37367 Z= 0.265 Chirality : 0.043 0.282 4389 Planarity : 0.004 0.072 4751 Dihedral : 5.104 58.720 4820 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.55 % Allowed : 11.55 % Favored : 86.90 % 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: 1.10 (0.14), residues: 3249 helix: 2.64 (0.16), residues: 1000 sheet: 0.63 (0.20), residues: 579 loop : -0.41 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.003 0.001 HIS E 34 PHE 0.023 0.001 PHE A 135 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8694 (m-80) cc_final: 0.8347 (m-10) REVERT: A 168 PHE cc_start: 0.8191 (t80) cc_final: 0.7940 (t80) REVERT: A 194 PHE cc_start: 0.8473 (m-80) cc_final: 0.7823 (m-80) REVERT: A 900 MET cc_start: 0.8149 (mtp) cc_final: 0.7903 (mtm) REVERT: A 983 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8159 (tpm170) REVERT: A 1029 MET cc_start: 0.8772 (tpp) cc_final: 0.8518 (ttm) REVERT: B 408 ARG cc_start: 0.7328 (ppt170) cc_final: 0.7108 (pmt-80) REVERT: C 197 ILE cc_start: 0.8330 (mp) cc_final: 0.8105 (mm) REVERT: E 62 MET cc_start: 0.7779 (ttp) cc_final: 0.7325 (tpp) REVERT: E 134 ASN cc_start: 0.7172 (t0) cc_final: 0.6709 (p0) REVERT: E 332 MET cc_start: 0.5008 (OUTLIER) cc_final: 0.4662 (pmm) REVERT: E 366 MET cc_start: 0.2291 (tpp) cc_final: 0.1917 (mpp) REVERT: E 557 MET cc_start: 0.6102 (tmm) cc_final: 0.5773 (tmt) outliers start: 45 outliers final: 20 residues processed: 147 average time/residue: 1.1829 time to fit residues: 210.3317 Evaluate side-chains 126 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 188 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 215 optimal weight: 0.0060 chunk 156 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 248 optimal weight: 0.0070 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27465 Z= 0.161 Angle : 0.518 9.821 37367 Z= 0.263 Chirality : 0.043 0.290 4389 Planarity : 0.004 0.072 4751 Dihedral : 4.862 59.136 4820 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.28 % Allowed : 12.28 % Favored : 86.45 % 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: 1.16 (0.14), residues: 3249 helix: 2.64 (0.16), residues: 1007 sheet: 0.69 (0.21), residues: 544 loop : -0.34 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.003 0.001 HIS E 34 PHE 0.015 0.001 PHE C 541 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8027 (m-10) cc_final: 0.7705 (m-10) REVERT: A 106 PHE cc_start: 0.8656 (m-80) cc_final: 0.8320 (m-10) REVERT: A 168 PHE cc_start: 0.8065 (t80) cc_final: 0.7844 (t80) REVERT: A 194 PHE cc_start: 0.8286 (m-80) cc_final: 0.7879 (m-80) REVERT: A 900 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7924 (mtm) REVERT: A 983 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8142 (tpm170) REVERT: A 1029 MET cc_start: 0.8775 (tpp) cc_final: 0.8560 (ttm) REVERT: B 408 ARG cc_start: 0.7320 (ppt170) cc_final: 0.7101 (pmt-80) REVERT: C 197 ILE cc_start: 0.8375 (mp) cc_final: 0.8158 (mm) REVERT: E 62 MET cc_start: 0.7778 (ttp) cc_final: 0.7309 (tpp) REVERT: E 134 ASN cc_start: 0.7183 (t0) cc_final: 0.6712 (p0) REVERT: E 332 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.4762 (pmm) REVERT: E 557 MET cc_start: 0.6096 (tmm) cc_final: 0.5766 (tmt) outliers start: 37 outliers final: 15 residues processed: 140 average time/residue: 1.1909 time to fit residues: 202.6852 Evaluate side-chains 123 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 20.0000 chunk 302 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 278 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 804 GLN C 935 GLN C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 27465 Z= 0.404 Angle : 0.649 12.513 37367 Z= 0.328 Chirality : 0.046 0.312 4389 Planarity : 0.004 0.074 4751 Dihedral : 5.479 58.593 4820 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.38 % Allowed : 12.14 % Favored : 86.48 % 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: 0.80 (0.14), residues: 3249 helix: 2.33 (0.16), residues: 1009 sheet: 0.37 (0.20), residues: 573 loop : -0.53 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 104 HIS 0.006 0.001 HIS E 493 PHE 0.019 0.002 PHE C 201 TYR 0.025 0.002 TYR E 237 ARG 0.006 0.001 ARG E 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 108 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8296 (m-10) cc_final: 0.7987 (m-10) REVERT: A 168 PHE cc_start: 0.7968 (t80) cc_final: 0.7720 (t80) REVERT: A 194 PHE cc_start: 0.8373 (m-80) cc_final: 0.7992 (m-80) REVERT: A 902 MET cc_start: 0.8890 (tpp) cc_final: 0.8573 (tpt) REVERT: A 983 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8209 (tpm170) REVERT: B 408 ARG cc_start: 0.7290 (ppt170) cc_final: 0.7074 (pmt-80) REVERT: C 133 PHE cc_start: 0.7338 (m-80) cc_final: 0.6970 (m-80) REVERT: C 197 ILE cc_start: 0.8463 (mp) cc_final: 0.8252 (mm) REVERT: C 314 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: E 62 MET cc_start: 0.7792 (ttp) cc_final: 0.7504 (mtp) REVERT: E 134 ASN cc_start: 0.6893 (t0) cc_final: 0.6432 (p0) REVERT: E 332 MET cc_start: 0.5257 (ptp) cc_final: 0.3959 (tmm) REVERT: E 408 MET cc_start: 0.6891 (mpp) cc_final: 0.6678 (mmt) REVERT: E 557 MET cc_start: 0.6230 (tmm) cc_final: 0.5945 (tmt) outliers start: 40 outliers final: 20 residues processed: 136 average time/residue: 1.2975 time to fit residues: 210.4811 Evaluate side-chains 123 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 260 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27465 Z= 0.160 Angle : 0.553 12.328 37367 Z= 0.279 Chirality : 0.043 0.287 4389 Planarity : 0.004 0.074 4751 Dihedral : 5.070 58.641 4820 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.83 % Allowed : 13.07 % Favored : 86.10 % 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: 1.02 (0.14), residues: 3249 helix: 2.47 (0.16), residues: 999 sheet: 0.56 (0.20), residues: 576 loop : -0.38 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 104 HIS 0.004 0.001 HIS E 535 PHE 0.015 0.001 PHE C 541 TYR 0.021 0.001 TYR A1067 ARG 0.008 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8060 (m-10) cc_final: 0.7683 (m-10) REVERT: A 106 PHE cc_start: 0.8677 (m-80) cc_final: 0.8279 (m-10) REVERT: A 168 PHE cc_start: 0.8037 (t80) cc_final: 0.7826 (t80) REVERT: A 194 PHE cc_start: 0.8391 (m-80) cc_final: 0.7902 (m-80) REVERT: A 983 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8192 (tpm170) REVERT: A 1029 MET cc_start: 0.8778 (tpp) cc_final: 0.8506 (ttm) REVERT: B 408 ARG cc_start: 0.7317 (ppt170) cc_final: 0.7091 (pmt-80) REVERT: C 133 PHE cc_start: 0.7259 (m-80) cc_final: 0.6868 (m-80) REVERT: C 197 ILE cc_start: 0.8511 (mp) cc_final: 0.8287 (mm) REVERT: C 314 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: E 62 MET cc_start: 0.7786 (ttp) cc_final: 0.7323 (tpp) REVERT: E 134 ASN cc_start: 0.7195 (t0) cc_final: 0.6743 (p0) REVERT: E 332 MET cc_start: 0.5455 (ptp) cc_final: 0.4186 (tmm) REVERT: E 376 MET cc_start: 0.7677 (ttt) cc_final: 0.7423 (ttm) REVERT: E 480 MET cc_start: 0.6783 (mtm) cc_final: 0.6554 (mtp) REVERT: E 557 MET cc_start: 0.6305 (tmm) cc_final: 0.6053 (tmt) outliers start: 24 outliers final: 20 residues processed: 125 average time/residue: 1.3850 time to fit residues: 206.2580 Evaluate side-chains 122 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 260 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C1005 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.099484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060289 restraints weight = 97855.338| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.71 r_work: 0.3069 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27465 Z= 0.290 Angle : 0.583 11.988 37367 Z= 0.295 Chirality : 0.044 0.303 4389 Planarity : 0.004 0.073 4751 Dihedral : 5.166 59.893 4820 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.00 % Allowed : 12.86 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3249 helix: 2.46 (0.16), residues: 999 sheet: 0.49 (0.21), residues: 564 loop : -0.44 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.004 0.001 HIS E 378 PHE 0.017 0.001 PHE E 327 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7211.62 seconds wall clock time: 130 minutes 54.66 seconds (7854.66 seconds total)