Starting phenix.real_space_refine on Mon Apr 15 15:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlu_27516/04_2024/8dlu_27516.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlu_27516/04_2024/8dlu_27516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlu_27516/04_2024/8dlu_27516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlu_27516/04_2024/8dlu_27516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlu_27516/04_2024/8dlu_27516.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlu_27516/04_2024/8dlu_27516.pdb" } resolution = 3.14 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= 0.034 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 169 5.16 5 C 22377 2.51 5 N 5759 2.21 5 O 6832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35137 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" 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: "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: "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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" 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: 17.51, per 1000 atoms: 0.50 Number of scatterers: 35137 At special positions: 0 Unit cell: (171, 155, 235, 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 169 16.00 O 6832 8.00 N 5759 7.00 C 22377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 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 W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " 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 17 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 17 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 11.74 Conformation dependent library (CDL) restraints added in 6.0 seconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 49 sheets defined 37.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.405A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.511A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.683A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.903A 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: 3.616A 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: 3.950A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.537A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.260A 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 365 through 370 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: 4.054A 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: 3.594A 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: 3.924A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.072A 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 337 through 343 removed outlier: 3.855A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.815A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.896A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.671A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.565A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' 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: 3.570A 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 886 through 891 removed outlier: 3.714A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.502A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.901A 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: 4.056A 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 'D' and resid 20 through 53 removed outlier: 4.119A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.811A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.151A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.683A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.732A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.843A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.555A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.706A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.161A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.562A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.397A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.718A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.490A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.836A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.056A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 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: 3.833A 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: 4.117A 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: 3.649A 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: 3.694A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.802A 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: 3.789A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.503A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.529A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.650A 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: 4.200A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.921A 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: 3.570A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.354A 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: 3.698A 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: 4.482A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.824A 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 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.346A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.934A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.094A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.923A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.468A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.183A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.019A 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: 5.114A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.278A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.203A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.574A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.951A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.321A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.928A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.268A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.129A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.819A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 156 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.745A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.228A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.181A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.839A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 4.002A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.327A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 5.957A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.106A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.545A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 154 through 172 current: chain 'C' and resid 259 through 260 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.705A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.975A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.836A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.667A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.987A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.890A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.050A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.347A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.829A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.017A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.336A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1471 hydrogen bonds defined for protein. 4152 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: 16.84 Time building geometry restraints manager: 13.00 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: 11138 1.34 - 1.47: 9129 1.47 - 1.59: 15473 1.59 - 1.72: 0 1.72 - 1.84: 238 Bond restraints: 35978 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 ... (remaining 35973 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.19: 812 105.19 - 112.41: 17919 112.41 - 119.63: 12138 119.63 - 126.85: 17591 126.85 - 134.07: 485 Bond angle restraints: 48945 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.29 -5.59 1.22e+00 6.72e-01 2.10e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.05 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.02 -5.32 1.22e+00 6.72e-01 1.90e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C SER A 359 " pdb=" N ASN A 360 " pdb=" CA ASN A 360 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 ... (remaining 48940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 20511 17.88 - 35.76: 1460 35.76 - 53.63: 241 53.63 - 71.51: 77 71.51 - 89.39: 44 Dihedral angle restraints: 22333 sinusoidal: 9753 harmonic: 12580 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 -49.39 -36.61 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 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=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 22330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4641 0.073 - 0.146: 903 0.146 - 0.218: 78 0.218 - 0.291: 8 0.291 - 0.364: 3 Chirality restraints: 5633 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 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 ... (remaining 5630 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 200 " -0.008 2.00e-02 2.50e+03 5.76e-02 6.63e+01 pdb=" CG TYR B 200 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 200 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 200 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 200 " -0.086 2.00e-02 2.50e+03 pdb=" CE2 TYR B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 200 " -0.076 2.00e-02 2.50e+03 pdb=" OH TYR B 200 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 36 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ALA E 36 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA E 36 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU E 37 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 36 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA D 36 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA D 36 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU D 37 " -0.019 2.00e-02 2.50e+03 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9634 2.81 - 3.33: 30461 3.33 - 3.86: 60356 3.86 - 4.38: 68717 4.38 - 4.90: 118534 Nonbonded interactions: 287702 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.288 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.292 2.440 nonbonded pdb=" ND2 ASN A 360 " pdb=" O GLU B 169 " model vdw 2.298 2.520 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.300 2.440 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.302 2.440 ... (remaining 287697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = 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' selection = chain 'W' } 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: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.510 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 92.010 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 0.069 35978 Z= 0.300 Angle : 0.798 8.905 48945 Z= 0.440 Chirality : 0.055 0.364 5633 Planarity : 0.006 0.062 6249 Dihedral : 13.062 89.389 14095 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 4260 helix: 1.05 (0.12), residues: 1437 sheet: 0.85 (0.19), residues: 701 loop : -0.76 (0.12), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 69 HIS 0.006 0.001 HIS D 378 PHE 0.030 0.002 PHE A 275 TYR 0.086 0.002 TYR B 200 ARG 0.008 0.001 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9262 (t80) cc_final: 0.8973 (t80) REVERT: A 229 LEU cc_start: 0.9294 (tp) cc_final: 0.9086 (tp) REVERT: A 981 LEU cc_start: 0.9492 (mm) cc_final: 0.9204 (pp) REVERT: A 1005 GLN cc_start: 0.8270 (mt0) cc_final: 0.7956 (tt0) REVERT: B 79 PHE cc_start: 0.6651 (t80) cc_final: 0.6001 (t80) REVERT: B 88 ASP cc_start: 0.8861 (m-30) cc_final: 0.8351 (p0) REVERT: B 365 TYR cc_start: 0.8521 (m-80) cc_final: 0.8123 (m-80) REVERT: C 135 PHE cc_start: 0.8016 (m-10) cc_final: 0.7737 (m-80) REVERT: C 197 ILE cc_start: 0.9373 (mm) cc_final: 0.9057 (mp) REVERT: C 238 PHE cc_start: 0.7693 (p90) cc_final: 0.7294 (p90) REVERT: C 1005 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8424 (mt0) REVERT: D 27 THR cc_start: 0.4517 (p) cc_final: 0.4268 (t) REVERT: D 31 LYS cc_start: -0.0929 (tptp) cc_final: -0.1292 (mmtt) REVERT: D 115 ARG cc_start: 0.5011 (tpt-90) cc_final: 0.4384 (mmm160) REVERT: D 290 ASN cc_start: 0.5875 (t0) cc_final: 0.5438 (p0) REVERT: D 306 ARG cc_start: 0.3820 (ttt-90) cc_final: 0.3314 (mtp180) REVERT: D 315 PHE cc_start: 0.0930 (m-80) cc_final: 0.0588 (m-80) REVERT: D 323 MET cc_start: 0.0017 (mmp) cc_final: -0.0832 (mmm) REVERT: D 383 MET cc_start: 0.4765 (mtp) cc_final: 0.3452 (tmm) REVERT: D 480 MET cc_start: 0.0210 (mtp) cc_final: -0.0189 (mtp) REVERT: D 508 ASN cc_start: 0.4634 (m-40) cc_final: 0.4336 (m110) REVERT: D 520 LEU cc_start: 0.6339 (mp) cc_final: 0.6114 (mp) REVERT: D 544 ILE cc_start: -0.0165 (pt) cc_final: -0.0747 (pt) REVERT: D 579 MET cc_start: -0.2557 (ptm) cc_final: -0.2835 (ttt) REVERT: E 152 MET cc_start: 0.2089 (mmm) cc_final: 0.1568 (mmm) REVERT: E 338 ASN cc_start: 0.8077 (t0) cc_final: 0.7774 (p0) REVERT: E 367 ASP cc_start: 0.9440 (m-30) cc_final: 0.9212 (p0) REVERT: E 462 MET cc_start: 0.7562 (mtp) cc_final: 0.7298 (ptp) REVERT: E 510 TYR cc_start: 0.8101 (m-80) cc_final: 0.7750 (m-10) outliers start: 3 outliers final: 0 residues processed: 412 average time/residue: 0.4925 time to fit residues: 320.8620 Evaluate side-chains 203 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 1.9990 chunk 325 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 219 optimal weight: 0.0170 chunk 174 optimal weight: 0.9980 chunk 337 optimal weight: 20.0000 chunk 130 optimal weight: 0.0980 chunk 204 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 390 optimal weight: 0.0570 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 96 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 472 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35978 Z= 0.148 Angle : 0.536 10.699 48945 Z= 0.275 Chirality : 0.042 0.243 5633 Planarity : 0.004 0.048 6249 Dihedral : 5.726 59.825 6139 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.87 % Allowed : 7.03 % Favored : 92.10 % 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: 0.71 (0.12), residues: 4260 helix: 1.84 (0.13), residues: 1425 sheet: 0.84 (0.19), residues: 691 loop : -0.59 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 275 HIS 0.010 0.001 HIS B 245 PHE 0.025 0.001 PHE C 565 TYR 0.016 0.001 TYR D 158 ARG 0.007 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 219 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9254 (t80) cc_final: 0.8958 (t80) REVERT: B 88 ASP cc_start: 0.8807 (m-30) cc_final: 0.8365 (p0) REVERT: B 365 TYR cc_start: 0.8767 (m-80) cc_final: 0.8189 (m-80) REVERT: C 101 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8587 (pt) REVERT: C 135 PHE cc_start: 0.7889 (m-10) cc_final: 0.7622 (m-80) REVERT: C 164 ASN cc_start: 0.8261 (m-40) cc_final: 0.7612 (t0) REVERT: C 238 PHE cc_start: 0.7409 (p90) cc_final: 0.6993 (p90) REVERT: C 1005 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8469 (mt0) REVERT: D 27 THR cc_start: 0.4771 (p) cc_final: 0.4360 (p) REVERT: D 41 TYR cc_start: 0.4023 (t80) cc_final: 0.3761 (t80) REVERT: D 62 MET cc_start: 0.3346 (tmm) cc_final: 0.2711 (ppp) REVERT: D 145 GLU cc_start: 0.1214 (tp30) cc_final: 0.0700 (pt0) REVERT: D 179 LEU cc_start: 0.2554 (tp) cc_final: 0.2229 (tp) REVERT: D 240 LEU cc_start: 0.0812 (tp) cc_final: 0.0508 (pp) REVERT: D 290 ASN cc_start: 0.6048 (t0) cc_final: 0.5140 (p0) REVERT: D 306 ARG cc_start: 0.3828 (ttt-90) cc_final: 0.3218 (mtp180) REVERT: D 383 MET cc_start: 0.4445 (mtp) cc_final: 0.3214 (tmm) REVERT: D 579 MET cc_start: -0.2800 (ptm) cc_final: -0.3011 (ttt) REVERT: E 367 ASP cc_start: 0.9424 (m-30) cc_final: 0.9179 (p0) REVERT: E 510 TYR cc_start: 0.8072 (m-80) cc_final: 0.7771 (m-10) REVERT: E 579 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.4900 (ppp) outliers start: 33 outliers final: 15 residues processed: 242 average time/residue: 0.4637 time to fit residues: 188.1179 Evaluate side-chains 195 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 217 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 391 optimal weight: 0.7980 chunk 422 optimal weight: 7.9990 chunk 348 optimal weight: 40.0000 chunk 387 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 313 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 245 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 872 GLN A 907 ASN A 926 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 824 ASN B 955 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 613 GLN C 824 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 442 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 35978 Z= 0.397 Angle : 0.640 11.365 48945 Z= 0.322 Chirality : 0.044 0.274 5633 Planarity : 0.004 0.067 6249 Dihedral : 5.679 59.075 6139 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.64 % Allowed : 7.77 % Favored : 90.59 % 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: 0.77 (0.12), residues: 4260 helix: 1.93 (0.14), residues: 1417 sheet: 0.53 (0.19), residues: 711 loop : -0.45 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 48 HIS 0.013 0.001 HIS D 378 PHE 0.023 0.002 PHE D 314 TYR 0.020 0.002 TYR B 380 ARG 0.029 0.001 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 182 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9713 (tp) cc_final: 0.9391 (mt) REVERT: B 88 ASP cc_start: 0.8933 (m-30) cc_final: 0.8539 (p0) REVERT: B 365 TYR cc_start: 0.8912 (m-80) cc_final: 0.8333 (m-80) REVERT: C 135 PHE cc_start: 0.8192 (m-10) cc_final: 0.7729 (m-80) REVERT: C 979 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8602 (t0) REVERT: D 41 TYR cc_start: 0.4021 (t80) cc_final: 0.3796 (t80) REVERT: D 62 MET cc_start: 0.3640 (tmm) cc_final: 0.3266 (ptm) REVERT: D 115 ARG cc_start: 0.4646 (tpt-90) cc_final: 0.3849 (mmm160) REVERT: D 145 GLU cc_start: 0.1317 (tp30) cc_final: 0.0853 (pt0) REVERT: D 240 LEU cc_start: 0.1004 (tp) cc_final: 0.0606 (pp) REVERT: D 290 ASN cc_start: 0.4746 (t0) cc_final: 0.3732 (p0) REVERT: D 306 ARG cc_start: 0.3855 (ttt-90) cc_final: 0.3177 (mtp180) REVERT: D 383 MET cc_start: 0.4929 (mtp) cc_final: 0.3631 (tmm) REVERT: D 510 TYR cc_start: 0.2799 (OUTLIER) cc_final: 0.2410 (m-80) REVERT: D 579 MET cc_start: -0.1739 (ptm) cc_final: -0.2213 (ptm) REVERT: E 270 MET cc_start: 0.4749 (tpp) cc_final: 0.4416 (tpp) REVERT: E 367 ASP cc_start: 0.9443 (m-30) cc_final: 0.9219 (p0) REVERT: E 510 TYR cc_start: 0.8333 (m-80) cc_final: 0.8059 (m-10) outliers start: 62 outliers final: 34 residues processed: 228 average time/residue: 0.3857 time to fit residues: 149.5935 Evaluate side-chains 194 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 341 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 386 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 chunk 262 optimal weight: 10.0000 chunk 392 optimal weight: 20.0000 chunk 415 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 580 GLN A 824 ASN A 856 ASN A 913 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 250 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 493 HIS ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35978 Z= 0.286 Angle : 0.558 12.642 48945 Z= 0.280 Chirality : 0.042 0.266 5633 Planarity : 0.003 0.042 6249 Dihedral : 5.449 57.637 6139 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.35 % Allowed : 9.17 % Favored : 89.48 % 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 (0.13), residues: 4260 helix: 1.95 (0.14), residues: 1429 sheet: 0.51 (0.19), residues: 683 loop : -0.41 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 461 HIS 0.010 0.001 HIS D 378 PHE 0.015 0.001 PHE A 486 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9697 (tp) cc_final: 0.9382 (mt) REVERT: A 779 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 88 ASP cc_start: 0.8970 (m-30) cc_final: 0.8599 (p0) REVERT: B 365 TYR cc_start: 0.8901 (m-80) cc_final: 0.8246 (m-80) REVERT: B 369 TYR cc_start: 0.9065 (t80) cc_final: 0.8779 (t80) REVERT: C 135 PHE cc_start: 0.8174 (m-10) cc_final: 0.7746 (m-80) REVERT: C 238 PHE cc_start: 0.7639 (p90) cc_final: 0.7160 (p90) REVERT: C 540 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8847 (p0) REVERT: D 41 TYR cc_start: 0.4107 (t80) cc_final: 0.3903 (t80) REVERT: D 62 MET cc_start: 0.3522 (tmm) cc_final: 0.3122 (ptm) REVERT: D 145 GLU cc_start: 0.1330 (tp30) cc_final: 0.0876 (pt0) REVERT: D 240 LEU cc_start: 0.1076 (tp) cc_final: 0.0571 (pp) REVERT: D 290 ASN cc_start: 0.4675 (t0) cc_final: 0.3570 (p0) REVERT: D 306 ARG cc_start: 0.3834 (ttt-90) cc_final: 0.3128 (mtp180) REVERT: D 383 MET cc_start: 0.5230 (mtp) cc_final: 0.3870 (tmm) REVERT: D 480 MET cc_start: -0.0276 (mpp) cc_final: -0.1223 (tpp) REVERT: D 510 TYR cc_start: 0.2891 (OUTLIER) cc_final: 0.2474 (m-80) REVERT: E 270 MET cc_start: 0.4732 (tpp) cc_final: 0.4404 (tpp) REVERT: E 323 MET cc_start: 0.9023 (mmp) cc_final: 0.8699 (mmm) REVERT: E 367 ASP cc_start: 0.9445 (m-30) cc_final: 0.9205 (p0) REVERT: E 510 TYR cc_start: 0.8365 (m-80) cc_final: 0.8093 (m-10) outliers start: 51 outliers final: 33 residues processed: 203 average time/residue: 0.4452 time to fit residues: 154.1695 Evaluate side-chains 199 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 346 optimal weight: 30.0000 chunk 235 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 287 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 373 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 134 GLN A 907 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 764 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 524 GLN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35978 Z= 0.207 Angle : 0.510 11.081 48945 Z= 0.256 Chirality : 0.042 0.269 5633 Planarity : 0.003 0.041 6249 Dihedral : 5.043 57.563 6139 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.45 % Allowed : 9.56 % Favored : 88.98 % 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: 0.85 (0.13), residues: 4260 helix: 2.00 (0.14), residues: 1421 sheet: 0.37 (0.19), residues: 679 loop : -0.32 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 461 HIS 0.011 0.001 HIS D 378 PHE 0.020 0.001 PHE B 175 TYR 0.012 0.001 TYR A1067 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 3.861 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 189 LEU cc_start: 0.9678 (tp) cc_final: 0.9315 (mt) REVERT: A 1002 GLN cc_start: 0.8830 (tp40) cc_final: 0.8612 (tp40) REVERT: B 88 ASP cc_start: 0.8991 (m-30) cc_final: 0.8593 (p0) REVERT: B 365 TYR cc_start: 0.8907 (m-80) cc_final: 0.8254 (m-80) REVERT: B 369 TYR cc_start: 0.9019 (t80) cc_final: 0.8699 (t80) REVERT: C 135 PHE cc_start: 0.8055 (m-10) cc_final: 0.7623 (m-80) REVERT: C 540 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8904 (p0) REVERT: D 41 TYR cc_start: 0.3998 (t80) cc_final: 0.3763 (t80) REVERT: D 62 MET cc_start: 0.3582 (tmm) cc_final: 0.3173 (ptm) REVERT: D 145 GLU cc_start: 0.1255 (tp30) cc_final: 0.0820 (pt0) REVERT: D 161 ARG cc_start: 0.1305 (mtp85) cc_final: 0.0723 (ptm160) REVERT: D 240 LEU cc_start: 0.1001 (tp) cc_final: 0.0576 (pp) REVERT: D 290 ASN cc_start: 0.4422 (t0) cc_final: 0.3252 (p0) REVERT: D 297 MET cc_start: 0.0358 (OUTLIER) cc_final: -0.0093 (mtp) REVERT: D 306 ARG cc_start: 0.4066 (ttt-90) cc_final: 0.3398 (mtp180) REVERT: D 383 MET cc_start: 0.5323 (mtp) cc_final: 0.3878 (tmm) REVERT: D 480 MET cc_start: 0.0259 (mpp) cc_final: -0.0618 (tpp) REVERT: E 270 MET cc_start: 0.4551 (tpp) cc_final: 0.4188 (tpp) REVERT: E 323 MET cc_start: 0.9019 (mmp) cc_final: 0.8669 (mmm) REVERT: E 367 ASP cc_start: 0.9417 (m-30) cc_final: 0.9170 (p0) REVERT: E 510 TYR cc_start: 0.8475 (m-80) cc_final: 0.8222 (m-10) outliers start: 55 outliers final: 36 residues processed: 218 average time/residue: 0.4579 time to fit residues: 170.5830 Evaluate side-chains 201 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 139 optimal weight: 10.0000 chunk 374 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 416 optimal weight: 0.0270 chunk 345 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 330 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35978 Z= 0.321 Angle : 0.577 16.142 48945 Z= 0.286 Chirality : 0.043 0.282 5633 Planarity : 0.004 0.041 6249 Dihedral : 5.088 58.288 6139 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.51 % Allowed : 9.96 % Favored : 88.53 % 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: 0.78 (0.13), residues: 4260 helix: 1.98 (0.14), residues: 1429 sheet: 0.20 (0.19), residues: 657 loop : -0.34 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 168 HIS 0.010 0.001 HIS D 378 PHE 0.018 0.001 PHE C 106 TYR 0.014 0.001 TYR A1067 ARG 0.008 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 166 time to evaluate : 3.739 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 189 LEU cc_start: 0.9676 (tp) cc_final: 0.9291 (mt) REVERT: B 88 ASP cc_start: 0.9060 (m-30) cc_final: 0.8626 (p0) REVERT: B 365 TYR cc_start: 0.8917 (m-80) cc_final: 0.8292 (m-80) REVERT: C 135 PHE cc_start: 0.8234 (m-10) cc_final: 0.7799 (m-80) REVERT: C 540 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8914 (p0) REVERT: D 41 TYR cc_start: 0.3843 (t80) cc_final: 0.3611 (t80) REVERT: D 62 MET cc_start: 0.3676 (tmm) cc_final: 0.3231 (ptm) REVERT: D 152 MET cc_start: 0.0608 (mtm) cc_final: -0.0005 (mtt) REVERT: D 240 LEU cc_start: 0.0916 (tp) cc_final: 0.0388 (pp) REVERT: D 297 MET cc_start: 0.0458 (mtt) cc_final: -0.0131 (mtp) REVERT: D 306 ARG cc_start: 0.3761 (ttt-90) cc_final: 0.3079 (mtp180) REVERT: D 383 MET cc_start: 0.5464 (mtp) cc_final: 0.4043 (tmm) REVERT: E 323 MET cc_start: 0.9065 (mmp) cc_final: 0.8678 (mmm) REVERT: E 360 MET cc_start: 0.5023 (mtp) cc_final: 0.4125 (tpt) REVERT: E 367 ASP cc_start: 0.9415 (m-30) cc_final: 0.9153 (p0) REVERT: E 408 MET cc_start: 0.7745 (mmm) cc_final: 0.7457 (mmm) REVERT: E 462 MET cc_start: 0.6577 (ptp) cc_final: 0.6282 (ptt) REVERT: E 510 TYR cc_start: 0.8531 (m-80) cc_final: 0.8281 (m-10) outliers start: 57 outliers final: 41 residues processed: 211 average time/residue: 0.4594 time to fit residues: 165.8965 Evaluate side-chains 199 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 401 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 303 optimal weight: 0.9990 chunk 235 optimal weight: 0.0000 chunk 350 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 191 optimal weight: 0.7980 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 102 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35978 Z= 0.283 Angle : 0.553 13.592 48945 Z= 0.275 Chirality : 0.042 0.284 5633 Planarity : 0.003 0.041 6249 Dihedral : 5.033 58.169 6139 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.43 % Allowed : 10.54 % Favored : 88.03 % 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: 0.77 (0.13), residues: 4260 helix: 1.99 (0.14), residues: 1432 sheet: 0.19 (0.19), residues: 657 loop : -0.36 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 165 HIS 0.009 0.001 HIS D 378 PHE 0.015 0.001 PHE C 106 TYR 0.016 0.001 TYR B 904 ARG 0.007 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 161 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9662 (tp) cc_final: 0.9312 (mt) REVERT: B 88 ASP cc_start: 0.9110 (m-30) cc_final: 0.8699 (p0) REVERT: B 365 TYR cc_start: 0.8926 (m-80) cc_final: 0.8341 (m-80) REVERT: B 369 TYR cc_start: 0.9066 (t80) cc_final: 0.8836 (t80) REVERT: C 135 PHE cc_start: 0.8380 (m-10) cc_final: 0.7868 (m-80) REVERT: C 540 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8892 (p0) REVERT: D 62 MET cc_start: 0.3706 (tmm) cc_final: 0.3245 (ptm) REVERT: D 240 LEU cc_start: 0.0779 (tp) cc_final: 0.0273 (pp) REVERT: D 297 MET cc_start: 0.0645 (mtt) cc_final: 0.0229 (mtp) REVERT: D 306 ARG cc_start: 0.3692 (ttt-90) cc_final: 0.3062 (mtp180) REVERT: D 480 MET cc_start: 0.0457 (mpp) cc_final: -0.0340 (tpt) REVERT: D 579 MET cc_start: -0.2576 (ptt) cc_final: -0.2805 (ptt) REVERT: E 367 ASP cc_start: 0.9411 (m-30) cc_final: 0.9147 (p0) REVERT: E 408 MET cc_start: 0.7736 (mmm) cc_final: 0.7446 (mmm) REVERT: E 462 MET cc_start: 0.6450 (ptp) cc_final: 0.6150 (ptt) REVERT: E 510 TYR cc_start: 0.8574 (m-80) cc_final: 0.8351 (m-10) outliers start: 54 outliers final: 40 residues processed: 201 average time/residue: 0.4609 time to fit residues: 158.3415 Evaluate side-chains 196 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 256 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 76 GLN D 378 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35978 Z= 0.166 Angle : 0.525 12.835 48945 Z= 0.259 Chirality : 0.042 0.277 5633 Planarity : 0.003 0.047 6249 Dihedral : 4.761 57.653 6139 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.11 % Allowed : 11.10 % Favored : 87.79 % 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: 0.85 (0.13), residues: 4260 helix: 2.02 (0.14), residues: 1428 sheet: 0.21 (0.20), residues: 661 loop : -0.28 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 165 HIS 0.009 0.001 HIS D 378 PHE 0.014 0.001 PHE D 356 TYR 0.041 0.001 TYR D 510 ARG 0.009 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 4.117 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 189 LEU cc_start: 0.9637 (tp) cc_final: 0.9306 (mt) REVERT: B 88 ASP cc_start: 0.9105 (m-30) cc_final: 0.8674 (p0) REVERT: B 365 TYR cc_start: 0.8908 (m-80) cc_final: 0.8324 (m-80) REVERT: B 369 TYR cc_start: 0.9023 (t80) cc_final: 0.8790 (t80) REVERT: C 135 PHE cc_start: 0.8225 (m-10) cc_final: 0.7776 (m-80) REVERT: C 540 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8909 (p0) REVERT: D 41 TYR cc_start: 0.4029 (t80) cc_final: 0.3171 (t80) REVERT: D 240 LEU cc_start: 0.0742 (tp) cc_final: 0.0331 (pp) REVERT: D 297 MET cc_start: 0.0456 (mtt) cc_final: 0.0003 (mtp) REVERT: D 306 ARG cc_start: 0.3952 (ttt-90) cc_final: 0.3342 (mtp180) REVERT: D 315 PHE cc_start: 0.0315 (OUTLIER) cc_final: 0.0072 (t80) REVERT: D 383 MET cc_start: 0.4743 (mtp) cc_final: 0.4422 (mpp) REVERT: D 480 MET cc_start: 0.0596 (mpp) cc_final: 0.0025 (tpp) REVERT: D 579 MET cc_start: -0.2520 (ptt) cc_final: -0.2785 (ptt) REVERT: E 270 MET cc_start: 0.4702 (tpt) cc_final: 0.4068 (tpt) REVERT: E 360 MET cc_start: 0.4592 (mtp) cc_final: 0.4146 (tpt) REVERT: E 367 ASP cc_start: 0.9367 (m-30) cc_final: 0.9096 (p0) REVERT: E 408 MET cc_start: 0.7872 (mmm) cc_final: 0.7618 (mmm) REVERT: E 462 MET cc_start: 0.6482 (ptp) cc_final: 0.6187 (ptt) REVERT: E 510 TYR cc_start: 0.8647 (m-80) cc_final: 0.8371 (m-10) outliers start: 42 outliers final: 29 residues processed: 201 average time/residue: 0.4729 time to fit residues: 162.0234 Evaluate side-chains 192 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 377 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 362 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 396 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 365 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 493 GLN A 856 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN E 508 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 35978 Z= 0.401 Angle : 0.632 13.544 48945 Z= 0.314 Chirality : 0.044 0.298 5633 Planarity : 0.004 0.041 6249 Dihedral : 5.223 59.107 6139 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.29 % Allowed : 11.12 % Favored : 87.58 % 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: 0.66 (0.13), residues: 4260 helix: 1.86 (0.14), residues: 1424 sheet: 0.16 (0.19), residues: 664 loop : -0.40 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 165 HIS 0.012 0.001 HIS D 378 PHE 0.020 0.002 PHE D 314 TYR 0.024 0.002 TYR B 904 ARG 0.007 0.001 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9634 (tp) cc_final: 0.9269 (mt) REVERT: B 88 ASP cc_start: 0.9142 (m-30) cc_final: 0.8713 (p0) REVERT: B 365 TYR cc_start: 0.8960 (m-80) cc_final: 0.8470 (m-80) REVERT: B 369 TYR cc_start: 0.9100 (t80) cc_final: 0.8847 (t80) REVERT: C 135 PHE cc_start: 0.8405 (m-10) cc_final: 0.7889 (m-80) REVERT: C 540 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8935 (p0) REVERT: D 240 LEU cc_start: 0.0757 (tp) cc_final: 0.0225 (pp) REVERT: D 297 MET cc_start: 0.0450 (mtt) cc_final: 0.0046 (mtp) REVERT: D 306 ARG cc_start: 0.3697 (ttt-90) cc_final: 0.2996 (mtp180) REVERT: D 480 MET cc_start: 0.0305 (mpp) cc_final: -0.0549 (tpp) REVERT: E 367 ASP cc_start: 0.9424 (m-30) cc_final: 0.9116 (p0) REVERT: E 408 MET cc_start: 0.7829 (mmm) cc_final: 0.7568 (mmm) REVERT: E 462 MET cc_start: 0.6601 (ptp) cc_final: 0.6298 (ptt) outliers start: 49 outliers final: 39 residues processed: 196 average time/residue: 0.4549 time to fit residues: 154.1645 Evaluate side-chains 188 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 384 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 408 optimal weight: 20.0000 chunk 249 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 428 optimal weight: 8.9990 chunk 394 optimal weight: 0.9990 chunk 341 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 263 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 580 GLN A 856 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS E 508 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35978 Z= 0.162 Angle : 0.539 17.285 48945 Z= 0.266 Chirality : 0.042 0.283 5633 Planarity : 0.003 0.041 6249 Dihedral : 4.880 57.464 6139 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.03 % Allowed : 11.62 % Favored : 87.34 % 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: 0.79 (0.13), residues: 4260 helix: 1.97 (0.14), residues: 1421 sheet: 0.18 (0.20), residues: 630 loop : -0.30 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 165 HIS 0.012 0.001 HIS D 378 PHE 0.015 0.001 PHE D 314 TYR 0.022 0.001 TYR D 510 ARG 0.004 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9636 (tp) cc_final: 0.9274 (mt) REVERT: B 88 ASP cc_start: 0.9109 (m-30) cc_final: 0.8678 (p0) REVERT: B 365 TYR cc_start: 0.8929 (m-80) cc_final: 0.8379 (m-80) REVERT: B 369 TYR cc_start: 0.9012 (t80) cc_final: 0.8774 (t80) REVERT: C 135 PHE cc_start: 0.8430 (m-10) cc_final: 0.7899 (m-80) REVERT: C 153 MET cc_start: 0.8035 (ptt) cc_final: 0.7382 (pmm) REVERT: C 540 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8912 (p0) REVERT: D 240 LEU cc_start: 0.0776 (tp) cc_final: 0.0255 (pp) REVERT: D 297 MET cc_start: 0.0607 (mtt) cc_final: 0.0134 (mtp) REVERT: D 306 ARG cc_start: 0.3719 (ttt-90) cc_final: 0.3072 (mtp180) REVERT: D 480 MET cc_start: 0.0329 (mpp) cc_final: -0.0614 (tpp) REVERT: E 367 ASP cc_start: 0.9385 (m-30) cc_final: 0.9096 (p0) REVERT: E 408 MET cc_start: 0.7945 (mmm) cc_final: 0.7703 (mmm) REVERT: E 462 MET cc_start: 0.6550 (ptp) cc_final: 0.6252 (ptt) outliers start: 39 outliers final: 33 residues processed: 185 average time/residue: 0.4790 time to fit residues: 151.0388 Evaluate side-chains 186 residues out of total 3785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 209 optimal weight: 0.0050 chunk 270 optimal weight: 0.0040 chunk 363 optimal weight: 0.0040 chunk 104 optimal weight: 30.0000 chunk 314 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 341 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 350 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 76 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.123364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081137 restraints weight = 142290.420| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.72 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: