Starting phenix.real_space_refine on Fri Mar 6 03:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6i_23697/03_2026/7m6i_23697_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6i_23697/03_2026/7m6i_23697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6i_23697/03_2026/7m6i_23697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6i_23697/03_2026/7m6i_23697.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6i_23697/03_2026/7m6i_23697_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6i_23697/03_2026/7m6i_23697_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 116 5.16 5 C 17397 2.51 5 N 4514 2.21 5 O 5332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27359 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7814 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7801 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.28, per 1000 atoms: 0.23 Number of scatterers: 27359 At special positions: 0 Unit cell: (131.219, 140.778, 196.394, 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 116 16.00 O 5332 8.00 N 4514 7.00 C 17397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM27007 O5 NAG A1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM27119 O5 NAG A1309 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 717 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 657 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN B 165 " " NAG F 1 " - " ASN B 709 " " NAG G 1 " - " ASN C 709 " " NAG I 1 " - " ASN C 165 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 879.7 milliseconds 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6422 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 51 sheets defined 23.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.272A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.551A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.746A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.833A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.691A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.504A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.219A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.959A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.991A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.764A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.753A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.889A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.492A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.422A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 501 through 501 No H-bonds generated for 'chain 'C' and resid 501 through 501' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.754A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.625A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.244A 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: 3.866A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (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 1032 removed outlier: 4.660A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.702A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.809A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.769A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.100A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.447A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.900A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.965A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.798A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.869A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.685A pdb=" N ASN A 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.241A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.612A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.530A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.507A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.878A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 195 through 197 removed outlier: 6.897A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.535A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.570A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.730A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.173A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.269A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.813A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.813A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.630A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.608A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.100A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.663A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.742A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.256A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.843A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.271A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.062A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.795A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.677A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET H 80 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.533A pdb=" N ILE H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN H 58 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.654A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.995A pdb=" N LEU L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.786A pdb=" N VAL M 20 " --> pdb=" O MET M 80 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET M 80 " --> pdb=" O VAL M 20 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.552A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF5, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.535A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 53 through 54 removed outlier: 7.099A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2706 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: 8.67 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6971 1.33 - 1.46: 8179 1.46 - 1.59: 12663 1.59 - 1.72: 0 1.72 - 1.85: 145 Bond restraints: 27958 Sorted by residual: bond pdb=" N TYR A 473 " pdb=" CA TYR A 473 " ideal model delta sigma weight residual 1.457 1.490 -0.033 6.40e-03 2.44e+04 2.66e+01 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N VAL L 28 " pdb=" CA VAL L 28 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.14e+01 bond pdb=" N GLU A 471 " pdb=" CA GLU A 471 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 27953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 37028 3.73 - 7.45: 852 7.45 - 11.18: 113 11.18 - 14.91: 25 14.91 - 18.64: 6 Bond angle restraints: 38024 Sorted by residual: angle pdb=" CA TYR N 91 " pdb=" CB TYR N 91 " pdb=" CG TYR N 91 " ideal model delta sigma weight residual 113.90 127.09 -13.19 1.80e+00 3.09e-01 5.37e+01 angle pdb=" CA ARG A 905 " pdb=" CB ARG A 905 " pdb=" CG ARG A 905 " ideal model delta sigma weight residual 114.10 99.79 14.31 2.00e+00 2.50e-01 5.12e+01 angle pdb=" CB ARG A 905 " pdb=" CG ARG A 905 " pdb=" CD ARG A 905 " ideal model delta sigma weight residual 111.30 126.93 -15.63 2.30e+00 1.89e-01 4.62e+01 angle pdb=" C ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 109.95 123.23 -13.28 1.99e+00 2.53e-01 4.45e+01 angle pdb=" C ASN A 616 " pdb=" CA ASN A 616 " pdb=" CB ASN A 616 " ideal model delta sigma weight residual 109.46 121.58 -12.12 1.84e+00 2.95e-01 4.34e+01 ... (remaining 38019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 15983 21.92 - 43.85: 913 43.85 - 65.77: 115 65.77 - 87.69: 75 87.69 - 109.61: 12 Dihedral angle restraints: 17098 sinusoidal: 7098 harmonic: 10000 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA GLU B 471 " pdb=" C GLU B 471 " pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta harmonic sigma weight residual 180.00 -134.91 -45.09 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CA GLN B 474 " pdb=" C GLN B 474 " pdb=" N ALA B 475 " pdb=" CA ALA B 475 " ideal model delta harmonic sigma weight residual 180.00 -136.03 -43.97 0 5.00e+00 4.00e-02 7.73e+01 ... (remaining 17095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 4392 0.306 - 0.612: 21 0.612 - 0.918: 1 0.918 - 1.223: 1 1.223 - 1.529: 1 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.85e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4413 not shown) Planarity restraints: 4903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.151 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" C7 NAG D 2 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.200 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.124 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" C7 NAG F 2 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.093 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.163 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.006 2.00e-02 2.50e+03 8.88e-02 9.85e+01 pdb=" CG ASN A 61 " -0.107 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.093 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.089 2.00e-02 2.50e+03 ... (remaining 4900 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1143 2.71 - 3.26: 27172 3.26 - 3.80: 43095 3.80 - 4.35: 53567 4.35 - 4.90: 88192 Nonbonded interactions: 213169 Sorted by model distance: nonbonded pdb=" OE2 GLU B 988 " pdb=" OG SER C 383 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN A 394 " pdb=" OH TYR C 200 " model vdw 2.198 3.120 nonbonded pdb=" O GLU A 780 " pdb=" NE2 GLN A 784 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.230 3.040 ... (remaining 213164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 501 or res \ id 503 through 524 or (resid 525 and (name N or name CA or name C or name O or n \ ame CB )) or resid 526 through 527 or (resid 528 and (name N or name CA or name \ C or name O or name CB )) or resid 529 through 1308)) selection = (chain 'B' and (resid 27 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O )) or resid 337 through 1308)) selection = (chain 'C' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 524 or (re \ sid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.540 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.007 0.088 28029 Z= 0.367 Angle : 1.470 33.441 38201 Z= 0.775 Chirality : 0.085 1.529 4416 Planarity : 0.009 0.125 4874 Dihedral : 14.420 109.615 10577 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.88 % Favored : 93.88 % Rotamer: Outliers : 0.47 % Allowed : 1.11 % Favored : 98.42 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3384 helix: 0.41 (0.19), residues: 684 sheet: 0.10 (0.19), residues: 719 loop : -1.37 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG B 44 TYR 0.084 0.004 TYR N 91 PHE 0.058 0.004 PHE A 515 TRP 0.062 0.004 TRP A 436 HIS 0.027 0.003 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00692 (27958) covalent geometry : angle 1.39026 (38024) SS BOND : bond 0.00778 ( 34) SS BOND : angle 2.57501 ( 66) hydrogen bonds : bond 0.21370 ( 963) hydrogen bonds : angle 9.66836 ( 2706) link_ALPHA1-3 : bond 0.00374 ( 1) link_ALPHA1-3 : angle 1.88664 ( 3) link_BETA1-4 : bond 0.01179 ( 7) link_BETA1-4 : angle 3.95063 ( 21) link_NAG-ASN : bond 0.01549 ( 29) link_NAG-ASN : angle 9.77018 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 455 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7422 (m) cc_final: 0.7014 (m) REVERT: A 104 TRP cc_start: 0.6481 (m-90) cc_final: 0.6029 (m-90) REVERT: A 200 TYR cc_start: 0.8396 (m-10) cc_final: 0.7906 (m-80) REVERT: A 229 LEU cc_start: 0.9490 (mp) cc_final: 0.8962 (tt) REVERT: A 543 PHE cc_start: 0.8129 (m-80) cc_final: 0.7927 (m-10) REVERT: A 773 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7917 (tm-30) REVERT: A 777 ASN cc_start: 0.9104 (m110) cc_final: 0.8494 (m110) REVERT: B 276 LEU cc_start: 0.9362 (tp) cc_final: 0.8700 (mt) REVERT: B 546 LEU cc_start: 0.9009 (mm) cc_final: 0.7829 (tp) REVERT: B 731 MET cc_start: 0.8723 (ptm) cc_final: 0.8119 (ppp) REVERT: B 763 LEU cc_start: 0.9227 (tt) cc_final: 0.8821 (tt) REVERT: B 882 ILE cc_start: 0.9201 (mt) cc_final: 0.8932 (tt) REVERT: B 902 MET cc_start: 0.9328 (mmt) cc_final: 0.8953 (mmp) REVERT: B 1097 SER cc_start: 0.7951 (t) cc_final: 0.7465 (t) REVERT: B 1120 THR cc_start: 0.8367 (t) cc_final: 0.8075 (t) REVERT: C 55 PHE cc_start: 0.8573 (m-80) cc_final: 0.8112 (m-10) REVERT: C 452 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8467 (mm) REVERT: C 508 TYR cc_start: 0.8191 (m-10) cc_final: 0.7986 (m-10) REVERT: C 514 SER cc_start: 0.9209 (m) cc_final: 0.8958 (p) REVERT: C 740 MET cc_start: 0.7709 (tmm) cc_final: 0.7424 (ttt) REVERT: C 768 THR cc_start: 0.9168 (m) cc_final: 0.8915 (p) REVERT: C 773 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8834 (mt-10) REVERT: H 1 GLN cc_start: 0.7167 (pp30) cc_final: 0.6644 (pp30) REVERT: H 6 GLN cc_start: 0.7342 (tt0) cc_final: 0.7141 (tm-30) REVERT: H 46 GLU cc_start: 0.6451 (pm20) cc_final: 0.6224 (pm20) REVERT: H 64 GLN cc_start: 0.8834 (tm-30) cc_final: 0.7888 (pt0) REVERT: H 69 ILE cc_start: 0.7460 (mm) cc_final: 0.7080 (mm) REVERT: H 80 MET cc_start: 0.7308 (tmm) cc_final: 0.6437 (ppp) REVERT: H 96 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8459 (Cg_exo) REVERT: L 5 THR cc_start: 0.8312 (m) cc_final: 0.7880 (p) REVERT: L 24 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7282 (mpp80) REVERT: L 35 TRP cc_start: 0.7143 (m100) cc_final: 0.6484 (m100) REVERT: L 54 ARG cc_start: 0.8654 (mpt90) cc_final: 0.7169 (tpp-160) REVERT: M 80 MET cc_start: 0.5682 (ppp) cc_final: 0.4703 (ppp) REVERT: M 94 ARG cc_start: 0.6777 (ptp90) cc_final: 0.6527 (ptp90) REVERT: M 100 TYR cc_start: 0.5912 (m-80) cc_final: 0.5402 (m-10) REVERT: N 4 LEU cc_start: 0.2593 (pt) cc_final: 0.2246 (pt) REVERT: N 42 GLN cc_start: 0.7836 (tp40) cc_final: 0.6813 (mt0) outliers start: 14 outliers final: 2 residues processed: 467 average time/residue: 0.1635 time to fit residues: 123.6393 Evaluate side-chains 255 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 699 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0020 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.1980 overall best weight: 3.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 334 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 460 ASN A 487 ASN A 506 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1088 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1036 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 762 GLN C 801 ASN C 928 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.075072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.053962 restraints weight = 137714.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.055517 restraints weight = 74791.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.056542 restraints weight = 48478.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057210 restraints weight = 35508.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.057684 restraints weight = 28491.273| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28029 Z= 0.227 Angle : 0.828 17.434 38201 Z= 0.421 Chirality : 0.052 0.639 4416 Planarity : 0.006 0.075 4874 Dihedral : 9.159 71.965 4520 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 1.89 % Allowed : 10.92 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3384 helix: 0.76 (0.19), residues: 693 sheet: 0.18 (0.18), residues: 753 loop : -1.50 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 77 TYR 0.028 0.002 TYR C 904 PHE 0.022 0.002 PHE M 54 TRP 0.035 0.002 TRP A 436 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00478 (27958) covalent geometry : angle 0.78954 (38024) SS BOND : bond 0.00813 ( 34) SS BOND : angle 1.44734 ( 66) hydrogen bonds : bond 0.05346 ( 963) hydrogen bonds : angle 7.19896 ( 2706) link_ALPHA1-3 : bond 0.01106 ( 1) link_ALPHA1-3 : angle 2.73793 ( 3) link_BETA1-4 : bond 0.00672 ( 7) link_BETA1-4 : angle 2.65644 ( 21) link_NAG-ASN : bond 0.00685 ( 29) link_NAG-ASN : angle 4.98003 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7988 (m) cc_final: 0.7747 (m) REVERT: A 200 TYR cc_start: 0.8480 (m-10) cc_final: 0.8275 (m-80) REVERT: A 229 LEU cc_start: 0.9457 (mp) cc_final: 0.8972 (tt) REVERT: A 460 ASN cc_start: 0.7683 (m-40) cc_final: 0.7153 (p0) REVERT: A 773 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 777 ASN cc_start: 0.8966 (m110) cc_final: 0.8222 (m110) REVERT: A 900 MET cc_start: 0.8844 (mmm) cc_final: 0.8599 (mmm) REVERT: B 731 MET cc_start: 0.8754 (ptm) cc_final: 0.8465 (ppp) REVERT: B 867 ASP cc_start: 0.8600 (p0) cc_final: 0.8335 (p0) REVERT: B 878 LEU cc_start: 0.9444 (tt) cc_final: 0.9214 (mt) REVERT: B 1031 GLU cc_start: 0.7828 (mt-10) cc_final: 0.6582 (mm-30) REVERT: C 300 LYS cc_start: 0.9379 (mttt) cc_final: 0.9109 (mtmm) REVERT: C 508 TYR cc_start: 0.8256 (m-10) cc_final: 0.7936 (m-10) REVERT: C 740 MET cc_start: 0.7929 (tmm) cc_final: 0.7652 (ttt) REVERT: C 773 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8651 (mt-10) REVERT: C 900 MET cc_start: 0.7333 (mpp) cc_final: 0.6981 (ptp) REVERT: C 979 ASP cc_start: 0.9180 (m-30) cc_final: 0.8877 (m-30) REVERT: C 1034 LEU cc_start: 0.9361 (mm) cc_final: 0.9122 (tp) REVERT: H 1 GLN cc_start: 0.6822 (pp30) cc_final: 0.6215 (pp30) REVERT: H 6 GLN cc_start: 0.6964 (tt0) cc_final: 0.6676 (tm-30) REVERT: H 46 GLU cc_start: 0.6693 (pm20) cc_final: 0.6479 (pm20) REVERT: H 54 PHE cc_start: 0.9007 (t80) cc_final: 0.8783 (t80) REVERT: H 69 ILE cc_start: 0.7519 (mm) cc_final: 0.7221 (mm) REVERT: H 96 PRO cc_start: 0.9087 (Cg_endo) cc_final: 0.8850 (Cg_exo) REVERT: L 24 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.6984 (mpp-170) REVERT: L 35 TRP cc_start: 0.7243 (m100) cc_final: 0.6922 (m100) REVERT: L 54 ARG cc_start: 0.8720 (mpt90) cc_final: 0.7365 (tpp-160) REVERT: M 79 TYR cc_start: 0.9221 (m-80) cc_final: 0.8902 (m-10) REVERT: M 94 ARG cc_start: 0.6809 (ptp90) cc_final: 0.6600 (ptp90) REVERT: M 96 PRO cc_start: 0.7744 (Cg_exo) cc_final: 0.7453 (Cg_endo) REVERT: N 58 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4883 (mt) REVERT: N 71 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6974 (m-80) outliers start: 56 outliers final: 39 residues processed: 291 average time/residue: 0.1471 time to fit residues: 71.6043 Evaluate side-chains 248 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 176 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 298 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 501 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.076679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055294 restraints weight = 138445.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.056929 restraints weight = 74142.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058005 restraints weight = 47584.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.058706 restraints weight = 34527.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059193 restraints weight = 27576.697| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28029 Z= 0.141 Angle : 0.705 15.432 38201 Z= 0.354 Chirality : 0.049 0.532 4416 Planarity : 0.005 0.062 4874 Dihedral : 7.934 59.264 4520 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 1.92 % Allowed : 13.12 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 3384 helix: 0.92 (0.19), residues: 684 sheet: 0.04 (0.18), residues: 765 loop : -1.33 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.025 0.002 TYR A 369 PHE 0.019 0.001 PHE A 970 TRP 0.029 0.002 TRP A 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (27958) covalent geometry : angle 0.67014 (38024) SS BOND : bond 0.00756 ( 34) SS BOND : angle 1.22832 ( 66) hydrogen bonds : bond 0.04521 ( 963) hydrogen bonds : angle 6.49786 ( 2706) link_ALPHA1-3 : bond 0.00978 ( 1) link_ALPHA1-3 : angle 2.02497 ( 3) link_BETA1-4 : bond 0.00754 ( 7) link_BETA1-4 : angle 2.47429 ( 21) link_NAG-ASN : bond 0.00708 ( 29) link_NAG-ASN : angle 4.40892 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9447 (mp) cc_final: 0.9017 (tt) REVERT: A 460 ASN cc_start: 0.7710 (m-40) cc_final: 0.7120 (p0) REVERT: A 505 TYR cc_start: 0.8598 (m-80) cc_final: 0.8316 (m-80) REVERT: A 731 MET cc_start: 0.8562 (ppp) cc_final: 0.8063 (ppp) REVERT: A 777 ASN cc_start: 0.8949 (m110) cc_final: 0.8734 (m110) REVERT: A 1050 MET cc_start: 0.7602 (ptp) cc_final: 0.7132 (mtm) REVERT: B 351 TYR cc_start: 0.6488 (p90) cc_final: 0.5977 (p90) REVERT: B 731 MET cc_start: 0.8810 (ptm) cc_final: 0.8339 (ppp) REVERT: B 773 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 867 ASP cc_start: 0.8607 (p0) cc_final: 0.8240 (p0) REVERT: B 878 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9143 (mt) REVERT: B 900 MET cc_start: 0.8090 (mmp) cc_final: 0.7889 (mmp) REVERT: B 902 MET cc_start: 0.9251 (mmp) cc_final: 0.8862 (mmp) REVERT: B 1012 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9324 (mm) REVERT: B 1031 GLU cc_start: 0.7879 (mt-10) cc_final: 0.6736 (mm-30) REVERT: C 300 LYS cc_start: 0.9354 (mttt) cc_final: 0.9087 (mtmm) REVERT: C 508 TYR cc_start: 0.8373 (m-10) cc_final: 0.8074 (m-10) REVERT: C 740 MET cc_start: 0.7805 (tmm) cc_final: 0.7594 (ttt) REVERT: C 754 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8657 (pp) REVERT: C 773 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8621 (mt-10) REVERT: C 878 LEU cc_start: 0.9343 (mt) cc_final: 0.9135 (tp) REVERT: C 979 ASP cc_start: 0.9133 (m-30) cc_final: 0.8818 (m-30) REVERT: H 1 GLN cc_start: 0.6518 (pp30) cc_final: 0.5943 (pp30) REVERT: H 6 GLN cc_start: 0.6750 (tt0) cc_final: 0.6538 (tm-30) REVERT: H 48 MET cc_start: 0.5080 (mtt) cc_final: 0.4677 (mmm) REVERT: H 54 PHE cc_start: 0.9005 (t80) cc_final: 0.8567 (t80) REVERT: H 96 PRO cc_start: 0.9077 (Cg_endo) cc_final: 0.8824 (Cg_exo) REVERT: L 35 TRP cc_start: 0.7316 (m100) cc_final: 0.6530 (m100) REVERT: L 54 ARG cc_start: 0.8672 (mpt90) cc_final: 0.7201 (tpp-160) REVERT: L 81 GLU cc_start: 0.8704 (pp20) cc_final: 0.8473 (pp20) REVERT: M 3 GLN cc_start: 0.8215 (pp30) cc_final: 0.7909 (tm-30) REVERT: M 48 MET cc_start: 0.3629 (mpp) cc_final: 0.3373 (mpp) REVERT: M 94 ARG cc_start: 0.6819 (ptp90) cc_final: 0.6513 (ptp90) REVERT: N 42 GLN cc_start: 0.7782 (tp40) cc_final: 0.6824 (mt0) REVERT: N 71 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6747 (m-80) outliers start: 57 outliers final: 29 residues processed: 295 average time/residue: 0.1540 time to fit residues: 76.3032 Evaluate side-chains 246 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 186 optimal weight: 0.9980 chunk 295 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 422 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.075705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.053895 restraints weight = 136354.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055486 restraints weight = 76681.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056556 restraints weight = 50768.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.057283 restraints weight = 37530.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.057738 restraints weight = 30151.055| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28029 Z= 0.151 Angle : 0.672 13.954 38201 Z= 0.336 Chirality : 0.047 0.468 4416 Planarity : 0.005 0.056 4874 Dihedral : 7.073 59.568 4517 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.80 % Allowed : 14.43 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3384 helix: 1.04 (0.19), residues: 684 sheet: -0.02 (0.18), residues: 772 loop : -1.27 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 905 TYR 0.022 0.002 TYR N 91 PHE 0.026 0.001 PHE A 238 TRP 0.026 0.002 TRP A 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00326 (27958) covalent geometry : angle 0.64173 (38024) SS BOND : bond 0.00474 ( 34) SS BOND : angle 0.99799 ( 66) hydrogen bonds : bond 0.04252 ( 963) hydrogen bonds : angle 6.09551 ( 2706) link_ALPHA1-3 : bond 0.01199 ( 1) link_ALPHA1-3 : angle 2.60509 ( 3) link_BETA1-4 : bond 0.00638 ( 7) link_BETA1-4 : angle 2.42246 ( 21) link_NAG-ASN : bond 0.00637 ( 29) link_NAG-ASN : angle 3.97139 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 233 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9435 (mp) cc_final: 0.9018 (tt) REVERT: A 423 TYR cc_start: 0.7104 (t80) cc_final: 0.6798 (t80) REVERT: A 460 ASN cc_start: 0.7714 (m-40) cc_final: 0.7183 (p0) REVERT: A 505 TYR cc_start: 0.8689 (m-80) cc_final: 0.8405 (m-80) REVERT: A 731 MET cc_start: 0.8550 (ppp) cc_final: 0.7602 (ppp) REVERT: A 777 ASN cc_start: 0.9025 (m110) cc_final: 0.8804 (m110) REVERT: A 1050 MET cc_start: 0.7488 (ptp) cc_final: 0.7244 (mtm) REVERT: B 298 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: B 351 TYR cc_start: 0.6531 (p90) cc_final: 0.6014 (p90) REVERT: B 408 ARG cc_start: 0.6464 (mtp180) cc_final: 0.5921 (mtp180) REVERT: B 697 MET cc_start: 0.7962 (tpp) cc_final: 0.6454 (tpp) REVERT: B 731 MET cc_start: 0.8949 (ptm) cc_final: 0.8368 (ppp) REVERT: B 773 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 867 ASP cc_start: 0.8705 (p0) cc_final: 0.8371 (p0) REVERT: B 878 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9213 (mt) REVERT: B 1012 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9349 (mm) REVERT: B 1031 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 229 LEU cc_start: 0.9158 (mp) cc_final: 0.8951 (mp) REVERT: C 508 TYR cc_start: 0.8455 (m-10) cc_final: 0.8158 (m-10) REVERT: C 754 LEU cc_start: 0.9309 (mt) cc_final: 0.8702 (pp) REVERT: C 773 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8585 (mt-10) REVERT: H 1 GLN cc_start: 0.6465 (pp30) cc_final: 0.5960 (pp30) REVERT: H 6 GLN cc_start: 0.6758 (tt0) cc_final: 0.6532 (tm-30) REVERT: H 32 TYR cc_start: 0.7747 (m-10) cc_final: 0.7213 (m-80) REVERT: H 48 MET cc_start: 0.4976 (mtt) cc_final: 0.4361 (mmm) REVERT: H 54 PHE cc_start: 0.8989 (t80) cc_final: 0.8355 (t80) REVERT: H 98 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: H 101 ASP cc_start: 0.9020 (t0) cc_final: 0.8099 (t0) REVERT: L 46 LEU cc_start: 0.7611 (tp) cc_final: 0.7307 (mt) REVERT: L 54 ARG cc_start: 0.8678 (mpt90) cc_final: 0.7390 (tpp-160) REVERT: L 81 GLU cc_start: 0.8737 (pp20) cc_final: 0.8517 (pp20) REVERT: M 61 GLN cc_start: 0.8492 (mp10) cc_final: 0.8258 (pm20) REVERT: M 94 ARG cc_start: 0.6780 (ptp90) cc_final: 0.6528 (ptp90) REVERT: M 96 PRO cc_start: 0.7526 (Cg_exo) cc_final: 0.7281 (Cg_endo) REVERT: N 42 GLN cc_start: 0.7689 (tp40) cc_final: 0.6740 (mt0) REVERT: N 70 ASP cc_start: 0.8727 (p0) cc_final: 0.8107 (t0) REVERT: N 71 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.6948 (m-80) outliers start: 83 outliers final: 43 residues processed: 300 average time/residue: 0.1533 time to fit residues: 77.9352 Evaluate side-chains 254 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 259 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 274 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 96 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 954 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 437 ASN C 450 ASN C 481 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN L 37 GLN N 42 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.073022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051380 restraints weight = 140993.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052867 restraints weight = 76387.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053833 restraints weight = 49706.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054466 restraints weight = 36685.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054893 restraints weight = 29797.692| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 28029 Z= 0.240 Angle : 0.723 12.686 38201 Z= 0.371 Chirality : 0.047 0.409 4416 Planarity : 0.005 0.056 4874 Dihedral : 6.818 58.818 4517 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.61 % Allowed : 15.31 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3384 helix: 0.91 (0.19), residues: 687 sheet: -0.18 (0.18), residues: 732 loop : -1.28 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 45 TYR 0.030 0.002 TYR N 91 PHE 0.037 0.002 PHE M 54 TRP 0.034 0.002 TRP A 104 HIS 0.006 0.002 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00508 (27958) covalent geometry : angle 0.69763 (38024) SS BOND : bond 0.00509 ( 34) SS BOND : angle 1.23264 ( 66) hydrogen bonds : bond 0.04612 ( 963) hydrogen bonds : angle 6.10394 ( 2706) link_ALPHA1-3 : bond 0.01600 ( 1) link_ALPHA1-3 : angle 2.49331 ( 3) link_BETA1-4 : bond 0.00643 ( 7) link_BETA1-4 : angle 2.27838 ( 21) link_NAG-ASN : bond 0.00662 ( 29) link_NAG-ASN : angle 3.73424 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 206 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9470 (mp) cc_final: 0.9041 (tt) REVERT: A 460 ASN cc_start: 0.7742 (m-40) cc_final: 0.7170 (p0) REVERT: A 505 TYR cc_start: 0.8813 (m-80) cc_final: 0.8466 (m-80) REVERT: A 582 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 720 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 731 MET cc_start: 0.8778 (ppp) cc_final: 0.8025 (ppp) REVERT: A 777 ASN cc_start: 0.9121 (m110) cc_final: 0.8852 (m-40) REVERT: A 902 MET cc_start: 0.9231 (tpp) cc_final: 0.8976 (tpt) REVERT: A 970 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8099 (t80) REVERT: A 1050 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7470 (ptm) REVERT: B 284 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8907 (t) REVERT: B 408 ARG cc_start: 0.6595 (mtp180) cc_final: 0.5899 (mtp180) REVERT: B 697 MET cc_start: 0.8027 (tpp) cc_final: 0.7039 (tpp) REVERT: B 821 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 867 ASP cc_start: 0.8697 (p0) cc_final: 0.8394 (p0) REVERT: B 878 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9225 (mt) REVERT: B 896 ILE cc_start: 0.9215 (pt) cc_final: 0.8977 (mm) REVERT: C 508 TYR cc_start: 0.8564 (m-10) cc_final: 0.8270 (m-10) REVERT: C 731 MET cc_start: 0.8215 (tmm) cc_final: 0.7981 (tmm) REVERT: C 754 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 773 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8469 (mt-10) REVERT: C 873 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8745 (m-10) REVERT: H 1 GLN cc_start: 0.6369 (pp30) cc_final: 0.5903 (pp30) REVERT: H 54 PHE cc_start: 0.9055 (t80) cc_final: 0.8357 (t80) REVERT: H 67 LEU cc_start: 0.8170 (mt) cc_final: 0.7396 (pp) REVERT: H 98 TYR cc_start: 0.7391 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: L 54 ARG cc_start: 0.8706 (mpt90) cc_final: 0.7402 (ttm-80) REVERT: M 4 LEU cc_start: 0.3102 (OUTLIER) cc_final: 0.2812 (pp) REVERT: M 48 MET cc_start: 0.3572 (mpp) cc_final: 0.2899 (mpp) REVERT: N 42 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7040 (mt0) REVERT: N 71 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6392 (m-80) outliers start: 107 outliers final: 58 residues processed: 291 average time/residue: 0.1536 time to fit residues: 75.1246 Evaluate side-chains 245 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 264 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 192 optimal weight: 0.0870 chunk 138 optimal weight: 9.9990 chunk 116 optimal weight: 0.0470 chunk 43 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1010 GLN C 777 ASN C 955 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.074030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.052959 restraints weight = 135301.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.054522 restraints weight = 72901.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.055556 restraints weight = 47147.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.056266 restraints weight = 34524.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056695 restraints weight = 27530.722| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28029 Z= 0.125 Angle : 0.654 12.496 38201 Z= 0.325 Chirality : 0.047 0.416 4416 Planarity : 0.004 0.046 4874 Dihedral : 6.368 59.975 4517 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.56 % Allowed : 16.93 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3384 helix: 1.04 (0.19), residues: 700 sheet: -0.19 (0.18), residues: 742 loop : -1.20 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 408 TYR 0.023 0.001 TYR C1067 PHE 0.015 0.001 PHE C 429 TRP 0.023 0.001 TRP A 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (27958) covalent geometry : angle 0.62865 (38024) SS BOND : bond 0.00348 ( 34) SS BOND : angle 1.18696 ( 66) hydrogen bonds : bond 0.03920 ( 963) hydrogen bonds : angle 5.81469 ( 2706) link_ALPHA1-3 : bond 0.01167 ( 1) link_ALPHA1-3 : angle 2.29477 ( 3) link_BETA1-4 : bond 0.00662 ( 7) link_BETA1-4 : angle 2.19006 ( 21) link_NAG-ASN : bond 0.00646 ( 29) link_NAG-ASN : angle 3.57179 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 210 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9446 (mp) cc_final: 0.9000 (tt) REVERT: A 286 THR cc_start: 0.9293 (m) cc_final: 0.9027 (p) REVERT: A 460 ASN cc_start: 0.7668 (m-40) cc_final: 0.7146 (p0) REVERT: A 505 TYR cc_start: 0.8773 (m-80) cc_final: 0.8410 (m-80) REVERT: A 582 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7801 (tp) REVERT: A 720 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8654 (mt) REVERT: A 731 MET cc_start: 0.8739 (ppp) cc_final: 0.7858 (ppp) REVERT: A 770 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9115 (mt) REVERT: A 934 ILE cc_start: 0.9138 (mm) cc_final: 0.8874 (mm) REVERT: B 408 ARG cc_start: 0.6434 (mtp180) cc_final: 0.5944 (mtp180) REVERT: B 508 TYR cc_start: 0.7469 (m-80) cc_final: 0.6643 (m-80) REVERT: B 697 MET cc_start: 0.7951 (tpp) cc_final: 0.6896 (tpp) REVERT: B 731 MET cc_start: 0.8991 (ptm) cc_final: 0.8298 (ppp) REVERT: B 773 GLU cc_start: 0.8706 (pt0) cc_final: 0.8464 (tm-30) REVERT: B 821 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9070 (tt) REVERT: B 867 ASP cc_start: 0.8727 (p0) cc_final: 0.8361 (p0) REVERT: B 878 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9208 (mt) REVERT: B 896 ILE cc_start: 0.9222 (pt) cc_final: 0.8934 (mm) REVERT: B 1031 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 452 LEU cc_start: 0.8848 (mm) cc_final: 0.8624 (mm) REVERT: C 495 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7326 (t80) REVERT: C 508 TYR cc_start: 0.8531 (m-10) cc_final: 0.8245 (m-10) REVERT: C 754 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.8867 (pp) REVERT: C 773 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8493 (mt-10) REVERT: H 1 GLN cc_start: 0.6190 (pp30) cc_final: 0.5738 (pp30) REVERT: H 54 PHE cc_start: 0.8968 (t80) cc_final: 0.8215 (t80) REVERT: H 67 LEU cc_start: 0.7897 (mt) cc_final: 0.7417 (pp) REVERT: H 98 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: L 54 ARG cc_start: 0.8697 (mpt90) cc_final: 0.7274 (ttm-80) REVERT: M 48 MET cc_start: 0.3432 (mpp) cc_final: 0.3177 (mpp) REVERT: N 42 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7181 (mt0) REVERT: N 70 ASP cc_start: 0.9070 (m-30) cc_final: 0.8215 (t0) REVERT: N 71 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6951 (m-80) outliers start: 76 outliers final: 47 residues processed: 267 average time/residue: 0.1555 time to fit residues: 69.8727 Evaluate side-chains 245 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 151 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.073610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052213 restraints weight = 139925.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.053768 restraints weight = 75277.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.054787 restraints weight = 48561.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.055465 restraints weight = 35509.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.055929 restraints weight = 28579.660| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28029 Z= 0.164 Angle : 0.667 15.670 38201 Z= 0.330 Chirality : 0.046 0.384 4416 Planarity : 0.004 0.048 4874 Dihedral : 6.178 57.866 4517 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.70 % Allowed : 17.90 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3384 helix: 1.05 (0.20), residues: 696 sheet: -0.25 (0.18), residues: 761 loop : -1.19 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.031 0.002 TYR B 453 PHE 0.015 0.001 PHE C 238 TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00353 (27958) covalent geometry : angle 0.64308 (38024) SS BOND : bond 0.00412 ( 34) SS BOND : angle 1.19622 ( 66) hydrogen bonds : bond 0.04078 ( 963) hydrogen bonds : angle 5.80498 ( 2706) link_ALPHA1-3 : bond 0.01275 ( 1) link_ALPHA1-3 : angle 2.12662 ( 3) link_BETA1-4 : bond 0.00626 ( 7) link_BETA1-4 : angle 2.08868 ( 21) link_NAG-ASN : bond 0.00614 ( 29) link_NAG-ASN : angle 3.50897 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 186 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9496 (mp) cc_final: 0.9033 (tt) REVERT: A 582 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7848 (tp) REVERT: A 731 MET cc_start: 0.8713 (ppp) cc_final: 0.7919 (ppp) REVERT: A 934 ILE cc_start: 0.9157 (mm) cc_final: 0.8909 (mm) REVERT: A 1050 MET cc_start: 0.7838 (ptp) cc_final: 0.7234 (mtm) REVERT: B 408 ARG cc_start: 0.6578 (mtp180) cc_final: 0.5999 (mtp180) REVERT: B 697 MET cc_start: 0.7988 (tpp) cc_final: 0.7162 (tpp) REVERT: B 773 GLU cc_start: 0.8728 (pt0) cc_final: 0.8487 (tm-30) REVERT: B 821 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9049 (tt) REVERT: B 867 ASP cc_start: 0.8634 (p0) cc_final: 0.8281 (p0) REVERT: B 878 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9273 (mt) REVERT: B 896 ILE cc_start: 0.9199 (pt) cc_final: 0.8934 (mm) REVERT: B 1031 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 403 ARG cc_start: 0.9048 (tmm-80) cc_final: 0.8648 (tmm-80) REVERT: C 452 LEU cc_start: 0.8835 (mm) cc_final: 0.8582 (mm) REVERT: C 495 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7217 (t80) REVERT: C 508 TYR cc_start: 0.8519 (m-10) cc_final: 0.8206 (m-10) REVERT: C 754 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.8936 (pp) REVERT: C 773 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8417 (mt-10) REVERT: H 1 GLN cc_start: 0.6259 (pp30) cc_final: 0.5803 (pp30) REVERT: H 54 PHE cc_start: 0.9026 (t80) cc_final: 0.8293 (t80) REVERT: L 54 ARG cc_start: 0.8704 (mpt90) cc_final: 0.7265 (ttm-80) REVERT: N 42 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7267 (mt0) REVERT: N 70 ASP cc_start: 0.9080 (m-30) cc_final: 0.8216 (t0) REVERT: N 71 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6851 (m-80) outliers start: 80 outliers final: 54 residues processed: 250 average time/residue: 0.1557 time to fit residues: 65.0094 Evaluate side-chains 232 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 313 optimal weight: 30.0000 chunk 319 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.072384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.050655 restraints weight = 140671.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052175 restraints weight = 74620.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053174 restraints weight = 48032.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053828 restraints weight = 35167.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054235 restraints weight = 28435.803| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28029 Z= 0.209 Angle : 0.692 12.094 38201 Z= 0.349 Chirality : 0.047 0.372 4416 Planarity : 0.004 0.053 4874 Dihedral : 6.336 58.567 4517 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.76 % Allowed : 18.75 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3384 helix: 0.97 (0.20), residues: 689 sheet: -0.49 (0.18), residues: 793 loop : -1.23 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 38 TYR 0.024 0.002 TYR M 79 PHE 0.054 0.002 PHE M 54 TRP 0.012 0.002 TRP A 104 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00444 (27958) covalent geometry : angle 0.66936 (38024) SS BOND : bond 0.00433 ( 34) SS BOND : angle 1.23076 ( 66) hydrogen bonds : bond 0.04276 ( 963) hydrogen bonds : angle 5.90591 ( 2706) link_ALPHA1-3 : bond 0.01330 ( 1) link_ALPHA1-3 : angle 2.04879 ( 3) link_BETA1-4 : bond 0.00629 ( 7) link_BETA1-4 : angle 2.08182 ( 21) link_NAG-ASN : bond 0.00628 ( 29) link_NAG-ASN : angle 3.44754 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 186 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9539 (mp) cc_final: 0.9067 (tt) REVERT: A 582 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8150 (tp) REVERT: A 731 MET cc_start: 0.8722 (ppp) cc_final: 0.7935 (ppp) REVERT: A 896 ILE cc_start: 0.8795 (mm) cc_final: 0.8279 (pt) REVERT: A 934 ILE cc_start: 0.9304 (mm) cc_final: 0.9065 (mm) REVERT: A 965 GLN cc_start: 0.9433 (mm110) cc_final: 0.9226 (mm-40) REVERT: B 408 ARG cc_start: 0.6655 (mtp180) cc_final: 0.5885 (mtp180) REVERT: B 697 MET cc_start: 0.8133 (tpp) cc_final: 0.7912 (tpp) REVERT: B 821 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9121 (tt) REVERT: B 878 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9251 (mt) REVERT: B 896 ILE cc_start: 0.9248 (pt) cc_final: 0.8979 (mm) REVERT: C 369 TYR cc_start: 0.8763 (t80) cc_final: 0.8347 (t80) REVERT: C 403 ARG cc_start: 0.9061 (tmm-80) cc_final: 0.8689 (tmm-80) REVERT: C 452 LEU cc_start: 0.8885 (mm) cc_final: 0.8576 (mm) REVERT: C 495 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7206 (t80) REVERT: C 508 TYR cc_start: 0.8627 (m-10) cc_final: 0.8318 (m-10) REVERT: C 740 MET cc_start: 0.8276 (ttt) cc_final: 0.7874 (tmm) REVERT: C 773 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8447 (mt-10) REVERT: C 873 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8802 (m-10) REVERT: H 1 GLN cc_start: 0.6255 (pp30) cc_final: 0.5883 (pp30) REVERT: H 54 PHE cc_start: 0.9024 (t80) cc_final: 0.8330 (t80) REVERT: L 21 LEU cc_start: 0.5604 (tp) cc_final: 0.5296 (tp) REVERT: L 54 ARG cc_start: 0.8660 (mpt90) cc_final: 0.7365 (tpp80) REVERT: N 42 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7208 (pt0) REVERT: N 69 THR cc_start: 0.7661 (p) cc_final: 0.7452 (p) REVERT: N 70 ASP cc_start: 0.9085 (m-30) cc_final: 0.8177 (t0) REVERT: N 71 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6745 (m-80) outliers start: 82 outliers final: 63 residues processed: 251 average time/residue: 0.1592 time to fit residues: 66.8115 Evaluate side-chains 246 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 297 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 324 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 276 optimal weight: 0.5980 chunk 237 optimal weight: 0.4980 chunk 209 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 777 ASN L 37 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.073783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051945 restraints weight = 135763.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.053537 restraints weight = 74517.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054601 restraints weight = 48720.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.055329 restraints weight = 35884.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055800 restraints weight = 28743.918| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28029 Z= 0.123 Angle : 0.660 12.343 38201 Z= 0.326 Chirality : 0.047 0.380 4416 Planarity : 0.004 0.043 4874 Dihedral : 5.938 59.115 4515 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.66 % Allowed : 19.05 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3384 helix: 1.06 (0.20), residues: 694 sheet: -0.48 (0.18), residues: 773 loop : -1.16 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 94 TYR 0.023 0.001 TYR C1067 PHE 0.031 0.001 PHE M 54 TRP 0.016 0.001 TRP A 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00270 (27958) covalent geometry : angle 0.63773 (38024) SS BOND : bond 0.00328 ( 34) SS BOND : angle 1.21729 ( 66) hydrogen bonds : bond 0.03846 ( 963) hydrogen bonds : angle 5.68756 ( 2706) link_ALPHA1-3 : bond 0.01186 ( 1) link_ALPHA1-3 : angle 1.83352 ( 3) link_BETA1-4 : bond 0.00588 ( 7) link_BETA1-4 : angle 1.96520 ( 21) link_NAG-ASN : bond 0.00645 ( 29) link_NAG-ASN : angle 3.37858 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9510 (mp) cc_final: 0.9024 (tt) REVERT: A 582 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 727 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8911 (mm) REVERT: A 731 MET cc_start: 0.8750 (ppp) cc_final: 0.7965 (ppp) REVERT: A 896 ILE cc_start: 0.8742 (mm) cc_final: 0.8244 (pt) REVERT: A 934 ILE cc_start: 0.9225 (mm) cc_final: 0.8985 (mm) REVERT: A 965 GLN cc_start: 0.9450 (mm110) cc_final: 0.9231 (mm-40) REVERT: A 1050 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7248 (mtm) REVERT: B 821 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9136 (tt) REVERT: B 896 ILE cc_start: 0.9214 (pt) cc_final: 0.8925 (mm) REVERT: B 1031 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 403 ARG cc_start: 0.9088 (tmm-80) cc_final: 0.8693 (tmm-80) REVERT: C 452 LEU cc_start: 0.8908 (mm) cc_final: 0.8646 (mm) REVERT: C 495 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7250 (t80) REVERT: C 508 TYR cc_start: 0.8590 (m-10) cc_final: 0.8289 (m-10) REVERT: C 773 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8571 (mt-10) REVERT: H 1 GLN cc_start: 0.6175 (pp30) cc_final: 0.5800 (pp30) REVERT: H 54 PHE cc_start: 0.9050 (t80) cc_final: 0.8330 (t80) REVERT: L 54 ARG cc_start: 0.8718 (mpt90) cc_final: 0.7199 (tpp80) REVERT: L 59 PRO cc_start: 0.7400 (Cg_exo) cc_final: 0.7132 (Cg_endo) REVERT: L 75 ILE cc_start: 0.6769 (mt) cc_final: 0.6513 (mp) REVERT: L 103 ARG cc_start: 0.6192 (tpt170) cc_final: 0.5217 (ttt180) REVERT: M 48 MET cc_start: 0.3620 (mpp) cc_final: 0.2971 (mpp) REVERT: N 42 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7232 (pt0) REVERT: N 70 ASP cc_start: 0.9108 (m-30) cc_final: 0.8282 (t0) REVERT: N 71 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6979 (m-80) outliers start: 79 outliers final: 57 residues processed: 259 average time/residue: 0.1529 time to fit residues: 66.8060 Evaluate side-chains 249 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 268 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 327 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 26 optimal weight: 0.0020 chunk 166 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 953 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.074242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052454 restraints weight = 135731.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.054065 restraints weight = 74523.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055150 restraints weight = 48738.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055883 restraints weight = 35792.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.056387 restraints weight = 28664.982| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28029 Z= 0.117 Angle : 0.664 14.167 38201 Z= 0.325 Chirality : 0.047 0.369 4416 Planarity : 0.004 0.044 4874 Dihedral : 5.671 57.450 4515 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 2.16 % Allowed : 19.89 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3384 helix: 1.08 (0.20), residues: 684 sheet: -0.37 (0.18), residues: 740 loop : -1.18 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 96 TYR 0.026 0.001 TYR L 91 PHE 0.031 0.001 PHE M 54 TRP 0.016 0.001 TRP A 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00257 (27958) covalent geometry : angle 0.64357 (38024) SS BOND : bond 0.00332 ( 34) SS BOND : angle 1.15013 ( 66) hydrogen bonds : bond 0.03721 ( 963) hydrogen bonds : angle 5.54123 ( 2706) link_ALPHA1-3 : bond 0.01021 ( 1) link_ALPHA1-3 : angle 1.68712 ( 3) link_BETA1-4 : bond 0.00597 ( 7) link_BETA1-4 : angle 1.89734 ( 21) link_NAG-ASN : bond 0.00634 ( 29) link_NAG-ASN : angle 3.27835 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9485 (mp) cc_final: 0.8987 (tt) REVERT: A 582 LEU cc_start: 0.8283 (mm) cc_final: 0.8043 (tp) REVERT: A 727 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8876 (mm) REVERT: A 731 MET cc_start: 0.8725 (ppp) cc_final: 0.7901 (ppp) REVERT: A 896 ILE cc_start: 0.8673 (mm) cc_final: 0.8161 (pt) REVERT: A 965 GLN cc_start: 0.9468 (mm110) cc_final: 0.9185 (mm-40) REVERT: B 697 MET cc_start: 0.8162 (tpp) cc_final: 0.7595 (tpt) REVERT: B 731 MET cc_start: 0.9079 (ptm) cc_final: 0.8475 (ppp) REVERT: B 773 GLU cc_start: 0.8807 (pt0) cc_final: 0.8272 (tm-30) REVERT: B 821 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9149 (tt) REVERT: B 896 ILE cc_start: 0.9202 (pt) cc_final: 0.8928 (mm) REVERT: B 900 MET cc_start: 0.8224 (mmp) cc_final: 0.8011 (mmp) REVERT: B 1029 MET cc_start: 0.8416 (tpp) cc_final: 0.8163 (tpp) REVERT: B 1031 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8014 (mt-10) REVERT: C 403 ARG cc_start: 0.9069 (tmm-80) cc_final: 0.8671 (tmm-80) REVERT: C 452 LEU cc_start: 0.8889 (mm) cc_final: 0.8641 (mm) REVERT: C 495 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 508 TYR cc_start: 0.8570 (m-10) cc_final: 0.8276 (m-10) REVERT: C 740 MET cc_start: 0.8134 (ttt) cc_final: 0.7699 (tmm) REVERT: C 773 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8469 (mt-10) REVERT: C 805 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8505 (tp) REVERT: H 1 GLN cc_start: 0.6103 (pp30) cc_final: 0.5584 (pp30) REVERT: H 54 PHE cc_start: 0.9081 (t80) cc_final: 0.8387 (t80) REVERT: H 101 ASP cc_start: 0.8972 (t0) cc_final: 0.8211 (t0) REVERT: L 54 ARG cc_start: 0.8701 (mpt90) cc_final: 0.7118 (tpp80) REVERT: L 103 ARG cc_start: 0.6108 (tpt170) cc_final: 0.5184 (ttt180) REVERT: M 48 MET cc_start: 0.3482 (mpp) cc_final: 0.2755 (mpp) REVERT: N 42 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7231 (pt0) REVERT: N 70 ASP cc_start: 0.9099 (m-30) cc_final: 0.8260 (t0) REVERT: N 71 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7047 (m-80) outliers start: 64 outliers final: 54 residues processed: 252 average time/residue: 0.1483 time to fit residues: 62.6697 Evaluate side-chains 249 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 264 optimal weight: 0.9980 chunk 299 optimal weight: 0.0040 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.075541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052367 restraints weight = 137689.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053979 restraints weight = 77725.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.055068 restraints weight = 51867.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055801 restraints weight = 38682.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056318 restraints weight = 31360.795| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28029 Z= 0.116 Angle : 0.664 13.347 38201 Z= 0.323 Chirality : 0.046 0.362 4416 Planarity : 0.004 0.043 4874 Dihedral : 5.529 56.972 4515 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 2.06 % Allowed : 20.09 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3384 helix: 1.05 (0.20), residues: 682 sheet: -0.37 (0.18), residues: 742 loop : -1.16 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 103 TYR 0.026 0.001 TYR B 741 PHE 0.025 0.001 PHE C 429 TRP 0.015 0.001 TRP A 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00255 (27958) covalent geometry : angle 0.64384 (38024) SS BOND : bond 0.00341 ( 34) SS BOND : angle 1.07209 ( 66) hydrogen bonds : bond 0.03628 ( 963) hydrogen bonds : angle 5.47450 ( 2706) link_ALPHA1-3 : bond 0.00935 ( 1) link_ALPHA1-3 : angle 1.66921 ( 3) link_BETA1-4 : bond 0.00601 ( 7) link_BETA1-4 : angle 1.86494 ( 21) link_NAG-ASN : bond 0.00629 ( 29) link_NAG-ASN : angle 3.22242 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.74 seconds wall clock time: 82 minutes 54.38 seconds (4974.38 seconds total)