Starting phenix.real_space_refine on Tue Feb 20 05:49:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxx_25509/02_2024/7sxx_25509.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxx_25509/02_2024/7sxx_25509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxx_25509/02_2024/7sxx_25509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxx_25509/02_2024/7sxx_25509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxx_25509/02_2024/7sxx_25509.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxx_25509/02_2024/7sxx_25509.pdb" } resolution = 2.66 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 17164 2.51 5 N 4407 2.21 5 O 5277 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 PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26972 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "B" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 14.37, per 1000 atoms: 0.53 Number of scatterers: 26972 At special positions: 0 Unit cell: (140, 156, 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 124 16.00 O 5277 8.00 N 4407 7.00 C 17164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 11.19 Conformation dependent library (CDL) restraints added in 5.0 seconds 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6236 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 38 sheets defined 34.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.893A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.619A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.941A 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: 3.569A 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 1032 removed outlier: 4.242A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.378A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.664A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.094A 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: 3.604A 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: 3.936A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.501A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.525A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.543A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.912A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.503A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.114A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.798A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (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: 3.794A 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: 4.077A 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 146 through 155 removed outlier: 3.944A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.704A 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: 3.740A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.836A 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: 3.823A 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 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.528A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.689A 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: 4.186A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.961A 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: 3.540A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.382A 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: 3.781A 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: 4.375A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.910A 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: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.669A 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: 5.280A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.177A 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: 4.025A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.692A 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: 9.514A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.058A 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 319 removed outlier: 5.253A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.060A 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: 5.048A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.065A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.630A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 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: 3.906A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.288A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.946A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, 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: 6.374A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.054A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, 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: 11.426A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.694A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.160A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.081A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.068A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.840A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, 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: 3.922A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, 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: 6.183A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.122A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, 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: 6.843A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (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=AD4, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.586A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD6, 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: 3.907A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.341A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.736A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.020A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.316A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1107 hydrogen bonds defined for protein. 3125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.68 Time building geometry restraints manager: 11.94 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: 8501 1.34 - 1.47: 6926 1.47 - 1.59: 11985 1.59 - 1.72: 0 1.72 - 1.85: 172 Bond restraints: 27584 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.57e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.49e+00 ... (remaining 27579 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.75: 549 104.75 - 112.08: 13507 112.08 - 119.42: 9253 119.42 - 126.76: 13869 126.76 - 134.10: 354 Bond angle restraints: 37532 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.31 -5.61 1.22e+00 6.72e-01 2.12e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.36 128.86 -6.50 1.42e+00 4.96e-01 2.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.18 -5.48 1.22e+00 6.72e-01 2.02e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.07 -5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA CYS E 141 " pdb=" CB CYS E 141 " pdb=" SG CYS E 141 " ideal model delta sigma weight residual 114.40 123.58 -9.18 2.30e+00 1.89e-01 1.59e+01 ... (remaining 37527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15862 17.91 - 35.83: 1083 35.83 - 53.74: 202 53.74 - 71.66: 61 71.66 - 89.57: 37 Dihedral angle restraints: 17245 sinusoidal: 7582 harmonic: 9663 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 -46.45 -39.55 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 19.57 59.43 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3506 0.068 - 0.136: 783 0.136 - 0.204: 111 0.204 - 0.271: 10 0.271 - 0.339: 3 Chirality restraints: 4413 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 4410 not shown) Planarity restraints: 4819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C ARG E 169 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 902 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C MET A 902 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A 902 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 319 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ARG C 319 " -0.046 2.00e-02 2.50e+03 pdb=" O ARG C 319 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL C 320 " 0.016 2.00e-02 2.50e+03 ... (remaining 4816 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7622 2.82 - 3.34: 23438 3.34 - 3.86: 46856 3.86 - 4.38: 53185 4.38 - 4.90: 91280 Nonbonded interactions: 222381 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.298 2.440 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.304 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.305 2.440 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.315 2.440 ... (remaining 222376 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 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.420 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: 14.670 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 73.400 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 0.059 27584 Z= 0.316 Angle : 0.805 9.993 37532 Z= 0.437 Chirality : 0.057 0.339 4413 Planarity : 0.006 0.065 4775 Dihedral : 13.195 89.574 10901 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -0.02 (0.13), residues: 3264 helix: 0.85 (0.14), residues: 994 sheet: 0.53 (0.20), residues: 630 loop : -0.75 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 886 HIS 0.007 0.001 HIS E 378 PHE 0.033 0.002 PHE C 238 TYR 0.032 0.002 TYR E 385 ARG 0.008 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7300 (m-80) cc_final: 0.6448 (m-80) REVERT: A 173 GLN cc_start: 0.8667 (mp10) cc_final: 0.8347 (tp-100) REVERT: A 174 PRO cc_start: 0.6589 (Cg_endo) cc_final: 0.5203 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8856 (m-80) cc_final: 0.8377 (t80) REVERT: A 1029 MET cc_start: 0.9147 (tpp) cc_final: 0.8861 (tpp) REVERT: B 237 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7652 (ttm110) REVERT: B 340 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8459 (pt0) REVERT: B 365 TYR cc_start: 0.8763 (m-80) cc_final: 0.8469 (m-80) REVERT: B 378 LYS cc_start: 0.9340 (tptt) cc_final: 0.9046 (tptm) REVERT: B 380 TYR cc_start: 0.8061 (m-80) cc_final: 0.7189 (m-10) REVERT: B 1029 MET cc_start: 0.9201 (tpp) cc_final: 0.8946 (tpp) REVERT: C 54 LEU cc_start: 0.9058 (mm) cc_final: 0.8614 (mt) REVERT: C 79 PHE cc_start: 0.7283 (t80) cc_final: 0.6912 (t80) REVERT: C 129 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8006 (tttp) REVERT: C 197 ILE cc_start: 0.9039 (mm) cc_final: 0.8715 (mp) REVERT: C 571 ASP cc_start: 0.8491 (m-30) cc_final: 0.8163 (p0) REVERT: C 1029 MET cc_start: 0.9156 (tpp) cc_final: 0.8900 (tpt) REVERT: E 360 MET cc_start: 0.4013 (ttm) cc_final: 0.3765 (ttt) REVERT: E 474 MET cc_start: -0.0013 (mmt) cc_final: -0.1355 (mtp) outliers start: 0 outliers final: 1 residues processed: 220 average time/residue: 1.4916 time to fit residues: 379.9077 Evaluate side-chains 105 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 20.0000 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 259 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 300 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 856 ASN B 926 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 472 GLN E 552 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27584 Z= 0.401 Angle : 0.611 10.995 37532 Z= 0.312 Chirality : 0.045 0.264 4413 Planarity : 0.004 0.047 4775 Dihedral : 6.592 109.186 4839 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.23 % Allowed : 6.14 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3264 helix: 1.88 (0.16), residues: 994 sheet: 0.44 (0.21), residues: 605 loop : -0.49 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 886 HIS 0.006 0.001 HIS E 374 PHE 0.018 0.002 PHE A 238 TYR 0.020 0.002 TYR B1067 ARG 0.009 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 113 time to evaluate : 2.949 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 133 PHE cc_start: 0.7260 (m-80) cc_final: 0.6687 (m-80) REVERT: A 173 GLN cc_start: 0.8677 (mp10) cc_final: 0.8257 (tp-100) REVERT: A 174 PRO cc_start: 0.6574 (Cg_endo) cc_final: 0.5209 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8808 (m-80) cc_final: 0.8467 (t80) REVERT: B 237 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7771 (mtm110) REVERT: B 314 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: B 365 TYR cc_start: 0.8762 (m-80) cc_final: 0.8385 (m-80) REVERT: B 378 LYS cc_start: 0.9250 (tptt) cc_final: 0.8990 (tptm) REVERT: B 380 TYR cc_start: 0.8167 (m-80) cc_final: 0.7524 (m-80) REVERT: B 387 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8552 (mm) REVERT: B 950 ASP cc_start: 0.8261 (m-30) cc_final: 0.7983 (m-30) REVERT: C 79 PHE cc_start: 0.7584 (t80) cc_final: 0.7108 (t80) REVERT: C 129 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8217 (tttp) REVERT: C 238 PHE cc_start: 0.6941 (p90) cc_final: 0.6718 (p90) REVERT: C 571 ASP cc_start: 0.8712 (m-30) cc_final: 0.8332 (p0) REVERT: E 82 MET cc_start: 0.7441 (mtt) cc_final: 0.7120 (mtt) REVERT: E 123 MET cc_start: 0.4737 (mmm) cc_final: 0.4386 (mmm) REVERT: E 295 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7719 (t0) REVERT: E 455 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.5043 (ppp) REVERT: E 557 MET cc_start: 0.7266 (tmm) cc_final: 0.7023 (tmm) outliers start: 36 outliers final: 9 residues processed: 143 average time/residue: 1.3845 time to fit residues: 232.8938 Evaluate side-chains 106 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 455 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 301 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 298 optimal weight: 0.0570 chunk 102 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 856 ASN A 926 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 926 GLN C 173 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27584 Z= 0.183 Angle : 0.516 9.744 37532 Z= 0.260 Chirality : 0.043 0.268 4413 Planarity : 0.004 0.051 4775 Dihedral : 5.768 57.485 4837 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.13 % Allowed : 7.20 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.87 (0.14), residues: 3264 helix: 2.25 (0.16), residues: 995 sheet: 0.54 (0.21), residues: 575 loop : -0.41 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.005 0.001 HIS E 374 PHE 0.023 0.001 PHE A 135 TYR 0.017 0.001 TYR A 170 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8566 (mp10) cc_final: 0.8188 (tp-100) REVERT: A 174 PRO cc_start: 0.6595 (Cg_endo) cc_final: 0.5182 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8850 (m-80) cc_final: 0.8438 (t80) REVERT: A 780 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 118 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 237 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7826 (mtm110) REVERT: B 314 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: B 340 GLU cc_start: 0.8543 (pt0) cc_final: 0.8011 (pp20) REVERT: B 365 TYR cc_start: 0.8736 (m-80) cc_final: 0.8368 (m-80) REVERT: B 378 LYS cc_start: 0.9257 (tptt) cc_final: 0.8979 (tptm) REVERT: B 380 TYR cc_start: 0.8313 (m-80) cc_final: 0.7521 (m-10) REVERT: B 387 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 950 ASP cc_start: 0.8197 (m-30) cc_final: 0.7916 (m-30) REVERT: C 79 PHE cc_start: 0.7598 (t80) cc_final: 0.7096 (t80) REVERT: C 571 ASP cc_start: 0.8735 (m-30) cc_final: 0.8377 (p0) REVERT: E 82 MET cc_start: 0.7509 (mtt) cc_final: 0.7233 (mtt) REVERT: E 123 MET cc_start: 0.4709 (mmm) cc_final: 0.4461 (mmm) REVERT: E 285 PHE cc_start: 0.2801 (OUTLIER) cc_final: -0.0196 (m-80) REVERT: E 295 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (t0) REVERT: E 408 MET cc_start: 0.8157 (mpt) cc_final: 0.7894 (mpm) outliers start: 33 outliers final: 9 residues processed: 124 average time/residue: 1.5039 time to fit residues: 219.1702 Evaluate side-chains 102 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 202 optimal weight: 0.0670 chunk 302 optimal weight: 2.9990 chunk 319 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 286 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 926 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27584 Z= 0.256 Angle : 0.526 9.566 37532 Z= 0.265 Chirality : 0.043 0.281 4413 Planarity : 0.003 0.051 4775 Dihedral : 5.358 56.036 4837 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.41 % Allowed : 8.47 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.89 (0.14), residues: 3264 helix: 2.27 (0.16), residues: 1012 sheet: 0.57 (0.22), residues: 549 loop : -0.42 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.006 0.001 HIS E 374 PHE 0.024 0.001 PHE C 238 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 91 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7244 (m-80) cc_final: 0.6567 (m-10) REVERT: A 173 GLN cc_start: 0.8470 (mp10) cc_final: 0.8163 (tp-100) REVERT: A 174 PRO cc_start: 0.6665 (Cg_endo) cc_final: 0.5295 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8872 (m-80) cc_final: 0.8411 (t80) REVERT: A 780 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 118 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8169 (mm) REVERT: B 237 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7726 (mtm110) REVERT: B 314 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: B 340 GLU cc_start: 0.8599 (pt0) cc_final: 0.8183 (pp20) REVERT: B 365 TYR cc_start: 0.8780 (m-80) cc_final: 0.8339 (m-80) REVERT: B 378 LYS cc_start: 0.9272 (tptt) cc_final: 0.9013 (tptm) REVERT: B 380 TYR cc_start: 0.8331 (m-80) cc_final: 0.7414 (m-10) REVERT: B 387 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 486 PHE cc_start: 0.7472 (t80) cc_final: 0.7086 (t80) REVERT: B 950 ASP cc_start: 0.8304 (m-30) cc_final: 0.7991 (m-30) REVERT: C 1002 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: E 82 MET cc_start: 0.7872 (mtt) cc_final: 0.7112 (tmm) REVERT: E 123 MET cc_start: 0.4538 (mmm) cc_final: 0.4301 (mmm) REVERT: E 285 PHE cc_start: 0.2773 (OUTLIER) cc_final: -0.0175 (m-80) REVERT: E 295 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7817 (t0) REVERT: E 366 MET cc_start: 0.5870 (tpt) cc_final: 0.3336 (mtp) REVERT: E 408 MET cc_start: 0.8245 (mpt) cc_final: 0.7996 (mpm) outliers start: 41 outliers final: 10 residues processed: 123 average time/residue: 1.4117 time to fit residues: 203.8832 Evaluate side-chains 103 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 273 optimal weight: 20.0000 chunk 221 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 287 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 87 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 926 GLN B 955 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 27584 Z= 0.313 Angle : 0.540 9.685 37532 Z= 0.272 Chirality : 0.044 0.441 4413 Planarity : 0.004 0.067 4775 Dihedral : 5.356 55.889 4837 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 9.67 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.92 (0.14), residues: 3264 helix: 2.38 (0.16), residues: 990 sheet: 0.46 (0.21), residues: 561 loop : -0.38 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.007 0.001 HIS B 519 PHE 0.023 0.001 PHE C 238 TYR 0.018 0.001 TYR B1067 ARG 0.016 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7210 (m-80) cc_final: 0.6550 (m-10) REVERT: A 173 GLN cc_start: 0.8471 (mp10) cc_final: 0.8085 (tp-100) REVERT: A 174 PRO cc_start: 0.6713 (Cg_endo) cc_final: 0.5216 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8872 (m-80) cc_final: 0.8391 (t80) REVERT: B 118 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8187 (mm) REVERT: B 237 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7784 (mtm110) REVERT: B 314 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: B 340 GLU cc_start: 0.8560 (pt0) cc_final: 0.8243 (pp20) REVERT: B 365 TYR cc_start: 0.8732 (m-80) cc_final: 0.8446 (m-80) REVERT: B 378 LYS cc_start: 0.9268 (tptt) cc_final: 0.8997 (tptm) REVERT: B 380 TYR cc_start: 0.8360 (m-80) cc_final: 0.7812 (m-80) REVERT: B 486 PHE cc_start: 0.7539 (t80) cc_final: 0.7187 (t80) REVERT: C 1002 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: E 82 MET cc_start: 0.7858 (mtt) cc_final: 0.7106 (tmm) REVERT: E 123 MET cc_start: 0.4494 (mmm) cc_final: 0.4247 (mmm) REVERT: E 285 PHE cc_start: 0.2759 (OUTLIER) cc_final: -0.0230 (m-80) REVERT: E 295 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7779 (t0) REVERT: E 323 MET cc_start: 0.7250 (mmp) cc_final: 0.6906 (mmm) REVERT: E 408 MET cc_start: 0.8284 (mpt) cc_final: 0.8056 (mpm) outliers start: 30 outliers final: 10 residues processed: 112 average time/residue: 1.5386 time to fit residues: 202.9456 Evaluate side-chains 98 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 295 ASP Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 63 optimal weight: 0.0770 chunk 187 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 168 optimal weight: 3.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27584 Z= 0.223 Angle : 0.509 11.442 37532 Z= 0.255 Chirality : 0.043 0.278 4413 Planarity : 0.003 0.065 4775 Dihedral : 5.130 56.629 4837 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.10 % Allowed : 10.29 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3264 helix: 2.50 (0.16), residues: 987 sheet: 0.44 (0.21), residues: 596 loop : -0.31 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.006 0.001 HIS E 374 PHE 0.020 0.001 PHE C 238 TYR 0.016 0.001 TYR B1067 ARG 0.011 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7241 (m-80) cc_final: 0.6525 (m-10) REVERT: A 173 GLN cc_start: 0.8363 (mp10) cc_final: 0.8092 (tp-100) REVERT: A 174 PRO cc_start: 0.6885 (Cg_endo) cc_final: 0.5411 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8895 (m-80) cc_final: 0.8378 (t80) REVERT: A 780 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: B 340 GLU cc_start: 0.8567 (pt0) cc_final: 0.8281 (pp20) REVERT: B 365 TYR cc_start: 0.8663 (m-80) cc_final: 0.8423 (m-80) REVERT: B 378 LYS cc_start: 0.9282 (tptt) cc_final: 0.8975 (tptm) REVERT: B 380 TYR cc_start: 0.8330 (m-80) cc_final: 0.7668 (m-80) REVERT: B 486 PHE cc_start: 0.7599 (t80) cc_final: 0.7224 (t80) REVERT: C 1002 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: E 82 MET cc_start: 0.7848 (mtt) cc_final: 0.7114 (tmm) REVERT: E 285 PHE cc_start: 0.2718 (OUTLIER) cc_final: -0.0186 (m-80) REVERT: E 579 MET cc_start: 0.5011 (OUTLIER) cc_final: 0.4162 (tpp) outliers start: 32 outliers final: 9 residues processed: 110 average time/residue: 1.5003 time to fit residues: 193.6392 Evaluate side-chains 97 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 319 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1011 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27584 Z= 0.157 Angle : 0.492 10.488 37532 Z= 0.246 Chirality : 0.042 0.273 4413 Planarity : 0.003 0.060 4775 Dihedral : 4.906 57.065 4837 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.10 % Allowed : 10.26 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3264 helix: 2.58 (0.16), residues: 985 sheet: 0.43 (0.22), residues: 560 loop : -0.21 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 104 HIS 0.004 0.001 HIS E 374 PHE 0.017 0.001 PHE C 238 TYR 0.014 0.001 TYR B1067 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7214 (m-80) cc_final: 0.6477 (m-10) REVERT: A 173 GLN cc_start: 0.8358 (mp10) cc_final: 0.8090 (tp-100) REVERT: A 174 PRO cc_start: 0.6838 (Cg_endo) cc_final: 0.5372 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8831 (m-80) cc_final: 0.8343 (t80) REVERT: A 780 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: B 118 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 340 GLU cc_start: 0.8561 (pt0) cc_final: 0.8255 (pp20) REVERT: B 365 TYR cc_start: 0.8614 (m-80) cc_final: 0.8389 (m-80) REVERT: B 378 LYS cc_start: 0.9282 (tptt) cc_final: 0.8980 (tptm) REVERT: B 380 TYR cc_start: 0.8314 (m-80) cc_final: 0.7640 (m-80) REVERT: B 486 PHE cc_start: 0.7559 (t80) cc_final: 0.7194 (t80) REVERT: B 979 ASP cc_start: 0.8581 (m-30) cc_final: 0.8375 (t0) REVERT: C 1002 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: E 82 MET cc_start: 0.7894 (mtt) cc_final: 0.7152 (tmm) REVERT: E 285 PHE cc_start: 0.2784 (OUTLIER) cc_final: -0.0138 (m-80) REVERT: E 323 MET cc_start: 0.7085 (mmp) cc_final: 0.6795 (mmm) outliers start: 32 outliers final: 11 residues processed: 112 average time/residue: 1.4423 time to fit residues: 190.7290 Evaluate side-chains 103 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 285 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 157 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27584 Z= 0.237 Angle : 0.517 12.266 37532 Z= 0.258 Chirality : 0.043 0.281 4413 Planarity : 0.003 0.056 4775 Dihedral : 4.921 56.304 4837 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.10 % Allowed : 10.36 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3264 helix: 2.60 (0.16), residues: 982 sheet: 0.33 (0.22), residues: 558 loop : -0.23 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.001 PHE C 238 TYR 0.016 0.001 TYR B1067 ARG 0.011 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7196 (m-80) cc_final: 0.6513 (m-10) REVERT: A 173 GLN cc_start: 0.8300 (mp10) cc_final: 0.8040 (tp-100) REVERT: A 174 PRO cc_start: 0.6827 (Cg_endo) cc_final: 0.5453 (Cg_exo) REVERT: A 200 TYR cc_start: 0.8842 (m-80) cc_final: 0.8330 (t80) REVERT: A 211 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6170 (t0) REVERT: A 780 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: B 118 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8110 (mm) REVERT: B 340 GLU cc_start: 0.8592 (pt0) cc_final: 0.8326 (pp20) REVERT: B 365 TYR cc_start: 0.8595 (m-80) cc_final: 0.8359 (m-80) REVERT: B 378 LYS cc_start: 0.9275 (tptt) cc_final: 0.9018 (tptm) REVERT: B 380 TYR cc_start: 0.8313 (m-80) cc_final: 0.7748 (m-80) REVERT: B 486 PHE cc_start: 0.7609 (t80) cc_final: 0.7225 (t80) REVERT: C 129 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8243 (tttp) REVERT: C 1002 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: E 82 MET cc_start: 0.7856 (mtt) cc_final: 0.7122 (tmm) REVERT: E 285 PHE cc_start: 0.2748 (OUTLIER) cc_final: -0.0143 (m-80) REVERT: E 323 MET cc_start: 0.7144 (mmp) cc_final: 0.6858 (mmm) REVERT: E 557 MET cc_start: 0.7218 (tmm) cc_final: 0.6940 (tmm) outliers start: 32 outliers final: 11 residues processed: 112 average time/residue: 1.4872 time to fit residues: 195.7254 Evaluate side-chains 100 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 365 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 chunk 178 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 268 optimal weight: 0.6980 chunk 281 optimal weight: 6.9990 chunk 296 optimal weight: 30.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A1142 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN E 300 GLN E 540 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 27584 Z= 0.429 Angle : 0.612 10.891 37532 Z= 0.307 Chirality : 0.046 0.296 4413 Planarity : 0.004 0.056 4775 Dihedral : 5.462 54.705 4837 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.96 % Allowed : 10.60 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.82 (0.14), residues: 3264 helix: 2.37 (0.16), residues: 981 sheet: 0.21 (0.20), residues: 626 loop : -0.42 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 104 HIS 0.011 0.001 HIS E 374 PHE 0.020 0.002 PHE B 898 TYR 0.020 0.002 TYR B1067 ARG 0.010 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7190 (m-80) cc_final: 0.6569 (m-10) REVERT: A 200 TYR cc_start: 0.8845 (m-80) cc_final: 0.8258 (t80) REVERT: A 211 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6411 (t0) REVERT: B 378 LYS cc_start: 0.9273 (tptt) cc_final: 0.9060 (tptm) REVERT: B 380 TYR cc_start: 0.8327 (m-80) cc_final: 0.7571 (m-10) REVERT: B 486 PHE cc_start: 0.7694 (t80) cc_final: 0.7250 (t80) REVERT: C 1002 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: E 82 MET cc_start: 0.7755 (mtt) cc_final: 0.7067 (tmm) REVERT: E 285 PHE cc_start: 0.2584 (OUTLIER) cc_final: -0.0411 (m-80) REVERT: E 323 MET cc_start: 0.7341 (mmp) cc_final: 0.7000 (mmm) REVERT: E 366 MET cc_start: 0.6088 (tpt) cc_final: 0.5391 (mmm) REVERT: E 557 MET cc_start: 0.7275 (tmm) cc_final: 0.6986 (tmm) outliers start: 28 outliers final: 9 residues processed: 105 average time/residue: 1.3931 time to fit residues: 173.3371 Evaluate side-chains 92 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 609 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 329 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27584 Z= 0.241 Angle : 0.538 10.658 37532 Z= 0.268 Chirality : 0.044 0.384 4413 Planarity : 0.003 0.055 4775 Dihedral : 5.235 56.574 4837 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.62 % Allowed : 10.98 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.99 (0.15), residues: 3264 helix: 2.53 (0.16), residues: 979 sheet: 0.32 (0.20), residues: 655 loop : -0.34 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 104 HIS 0.006 0.001 HIS E 374 PHE 0.035 0.001 PHE E 315 TYR 0.018 0.001 TYR B1067 ARG 0.010 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6528 Ramachandran restraints generated. 3264 Oldfield, 0 Emsley, 3264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7201 (m-80) cc_final: 0.6566 (m-10) REVERT: A 200 TYR cc_start: 0.8798 (m-80) cc_final: 0.8300 (m-80) REVERT: A 211 ASN cc_start: 0.7013 (OUTLIER) cc_final: 0.6444 (t0) REVERT: A 957 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 365 TYR cc_start: 0.8633 (m-80) cc_final: 0.8337 (m-80) REVERT: B 378 LYS cc_start: 0.9294 (tptt) cc_final: 0.9042 (tptm) REVERT: B 380 TYR cc_start: 0.8253 (m-80) cc_final: 0.7619 (m-80) REVERT: B 486 PHE cc_start: 0.7689 (t80) cc_final: 0.7225 (t80) REVERT: B 979 ASP cc_start: 0.8658 (m-30) cc_final: 0.8386 (t0) REVERT: C 1002 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: E 82 MET cc_start: 0.7757 (mtt) cc_final: 0.7062 (tmm) REVERT: E 285 PHE cc_start: 0.2546 (OUTLIER) cc_final: -0.0408 (m-80) REVERT: E 323 MET cc_start: 0.7299 (mmp) cc_final: 0.6951 (mmm) REVERT: E 366 MET cc_start: 0.6010 (tpt) cc_final: 0.5293 (mmm) REVERT: E 557 MET cc_start: 0.7239 (tmm) cc_final: 0.6982 (tmm) outliers start: 18 outliers final: 7 residues processed: 98 average time/residue: 1.4792 time to fit residues: 172.1823 Evaluate side-chains 91 residues out of total 2915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 907 ASN E 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.094254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057320 restraints weight = 95254.891| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.67 r_work: 0.2940 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27584 Z= 0.165 Angle : 0.511 10.466 37532 Z= 0.253 Chirality : 0.043 0.310 4413 Planarity : 0.003 0.054 4775 Dihedral : 4.862 56.815 4837 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.51 % Allowed : 11.01 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3264 helix: 2.68 (0.16), residues: 981 sheet: 0.41 (0.21), residues: 605 loop : -0.26 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 104 HIS 0.004 0.001 HIS E 374 PHE 0.034 0.001 PHE E 315 TYR 0.014 0.001 TYR C1067 ARG 0.010 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7098.40 seconds wall clock time: 129 minutes 17.53 seconds (7757.53 seconds total)