Starting phenix.real_space_refine on Mon Feb 19 13:44:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2024/6zb4_11144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2024/6zb4_11144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2024/6zb4_11144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2024/6zb4_11144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2024/6zb4_11144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2024/6zb4_11144_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 114 5.16 5 C 15856 2.51 5 N 4094 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C ASP 947": "OD1" <-> "OD2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B ARG 844": "NH1" <-> "NH2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B GLU 915": "OE1" <-> "OE2" Residue "B ASP 947": "OD1" <-> "OD2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "B GLU 1069": "OE1" <-> "OE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1124": "OD1" <-> "OD2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ASP 1081": "OD1" <-> "OD2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A ASP 1115": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24841 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8056 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 47, 'TRANS': 987} Chain breaks: 11 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 8189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8189 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 1002} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8158 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 999} Chain breaks: 11 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 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: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'EIC': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.31, per 1000 atoms: 0.54 Number of scatterers: 24841 At special positions: 0 Unit cell: (143.85, 151.2, 161.7, 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 114 16.00 O 4777 8.00 N 4094 7.00 C 15856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM24659 O5 NAG B1309 .*. O " rejected from bonding due to valence issues. Atom "HETATM24443 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2102 " - " ASN A 714 " " NAG A2104 " - " ASN A 343 " " NAG B1309 " - " ASN B 234 " " NAG C1403 " - " ASN C 616 " " NAG C1406 " - " ASN C 234 " " NAG D 1 " - " ASN C 714 " Time building additional restraints: 9.00 Conformation dependent library (CDL) restraints added in 4.0 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 41 sheets defined 20.1% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.602A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.654A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 735 through 739 Processing helix chain 'C' and resid 745 through 752 removed outlier: 4.104A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 779 removed outlier: 3.599A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 820 Processing helix chain 'C' and resid 834 through 837 No H-bonds generated for 'chain 'C' and resid 834 through 837' Processing helix chain 'C' and resid 864 through 886 removed outlier: 8.270A pdb=" N TRP C 883 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR C 884 " --> pdb=" O THR C 880 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C 885 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY C 886 " --> pdb=" O GLY C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 removed outlier: 3.693A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 915 Processing helix chain 'C' and resid 917 through 935 Processing helix chain 'C' and resid 943 through 964 removed outlier: 3.942A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 977 No H-bonds generated for 'chain 'C' and resid 974 through 977' Processing helix chain 'C' and resid 987 through 1028 removed outlier: 3.838A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1015 " --> pdb=" O ARG C1011 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.967A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.673A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 421' Processing helix chain 'B' and resid 735 through 739 Processing helix chain 'B' and resid 744 through 752 removed outlier: 3.910A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 779 removed outlier: 3.850A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 Processing helix chain 'B' and resid 848 through 853 removed outlier: 3.975A pdb=" N ASN B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 881 Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.756A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 914 No H-bonds generated for 'chain 'B' and resid 911 through 914' Processing helix chain 'B' and resid 917 through 935 Processing helix chain 'B' and resid 943 through 964 removed outlier: 4.439A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.628A pdb=" N ARG B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1028 removed outlier: 3.987A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.906A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 745 through 752 removed outlier: 4.552A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 779 removed outlier: 3.772A pdb=" N ALA A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 821 Processing helix chain 'A' and resid 834 through 837 No H-bonds generated for 'chain 'A' and resid 834 through 837' Processing helix chain 'A' and resid 864 through 880 Processing helix chain 'A' and resid 895 through 906 removed outlier: 3.771A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 914 No H-bonds generated for 'chain 'A' and resid 911 through 914' Processing helix chain 'A' and resid 917 through 936 Processing helix chain 'A' and resid 943 through 963 removed outlier: 4.302A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1029 removed outlier: 3.706A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.536A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.072A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 83 through 85 Processing sheet with id= D, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= E, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.293A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.245A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'C' and resid 584 through 586 removed outlier: 6.475A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 689 through 693 removed outlier: 6.384A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 708 through 710 Processing sheet with id= K, first strand: chain 'C' and resid 731 through 733 Processing sheet with id= L, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id= M, first strand: chain 'C' and resid 714 through 725 removed outlier: 3.968A pdb=" N ASN C 714 " --> pdb=" O GLN C1068 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR C 716 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER C 718 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR C1064 " --> pdb=" O SER C 718 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR C 720 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL C1062 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU C 722 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU C1060 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU C 724 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL C1058 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.751A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.541A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.771A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.682A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= S, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.707A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.542A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 539 through 543 Processing sheet with id= W, first strand: chain 'B' and resid 551 through 554 Processing sheet with id= X, first strand: chain 'B' and resid 688 through 693 removed outlier: 6.276A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.577A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 731 through 733 Processing sheet with id= AA, first strand: chain 'B' and resid 1091 through 1093 Processing sheet with id= AB, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= AC, first strand: chain 'A' and resid 48 through 55 Processing sheet with id= AD, first strand: chain 'A' and resid 264 through 267 removed outlier: 5.957A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 127 through 131 removed outlier: 6.821A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= AG, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= AH, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.318A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.571A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'A' and resid 688 through 693 removed outlier: 3.573A pdb=" N SER A 688 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 708 through 712 Processing sheet with id= AM, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.625A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 731 through 733 Processing sheet with id= AO, first strand: chain 'A' and resid 1091 through 1094 702 hydrogen bonds defined for protein. 1926 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: 9.55 Time building geometry restraints manager: 9.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4043 1.31 - 1.44: 7056 1.44 - 1.57: 14142 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25379 Sorted by residual: bond pdb=" C7 NAG B1306 " pdb=" N2 NAG B1306 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C7 NAG B1302 " pdb=" N2 NAG B1302 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1307 " pdb=" N2 NAG B1307 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1303 " pdb=" N2 NAG B1303 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C7 NAG C1401 " pdb=" N2 NAG C1401 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 25374 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 589 106.40 - 113.31: 13769 113.31 - 120.21: 8776 120.21 - 127.12: 11139 127.12 - 134.02: 210 Bond angle restraints: 34483 Sorted by residual: angle pdb=" N ILE B 847 " pdb=" CA ILE B 847 " pdb=" C ILE B 847 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N MET C1047 " pdb=" CA MET C1047 " pdb=" C MET C1047 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.76e+01 angle pdb=" N ALA C 703 " pdb=" CA ALA C 703 " pdb=" C ALA C 703 " ideal model delta sigma weight residual 110.97 115.07 -4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA TYR B 37 " pdb=" CB TYR B 37 " pdb=" CG TYR B 37 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N GLY C 697 " pdb=" CA GLY C 697 " pdb=" C GLY C 697 " ideal model delta sigma weight residual 113.18 121.77 -8.59 2.37e+00 1.78e-01 1.31e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 14507 26.79 - 53.58: 758 53.58 - 80.38: 114 80.38 - 107.17: 16 107.17 - 133.96: 2 Dihedral angle restraints: 15397 sinusoidal: 6309 harmonic: 9088 Sorted by residual: dihedral pdb=" CA ARG C1088 " pdb=" C ARG C1088 " pdb=" N GLU C1089 " pdb=" CA GLU C1089 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP A 88 " pdb=" C ASP A 88 " pdb=" N GLY A 89 " pdb=" CA GLY A 89 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR A 753 " pdb=" C TYR A 753 " pdb=" N GLY A 754 " pdb=" CA GLY A 754 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 15394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 3970 0.258 - 0.516: 2 0.516 - 0.773: 1 0.773 - 1.031: 0 1.031 - 1.289: 1 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.15e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 714 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.15e+00 ... (remaining 3971 not shown) Planarity restraints: 4425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.495 2.00e-02 2.50e+03 5.08e-01 3.23e+03 pdb=" CG ASN B 234 " -0.178 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.796 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.303 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG C1402 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.435 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.299 2.00e-02 2.50e+03 2.52e-01 7.95e+02 pdb=" C7 NAG B1304 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.026 2.00e-02 2.50e+03 ... (remaining 4422 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 88 2.43 - 3.05: 15308 3.05 - 3.67: 32104 3.67 - 4.28: 51766 4.28 - 4.90: 91011 Nonbonded interactions: 190277 Sorted by model distance: nonbonded pdb=" O GLY A 339 " pdb=" OD1 ASN A 343 " model vdw 1.814 3.040 nonbonded pdb=" O ASN C 975 " pdb=" OG SER C 979 " model vdw 1.949 2.440 nonbonded pdb=" ND2 ASN C 343 " pdb=" O5 NAG C1401 " model vdw 1.966 2.520 nonbonded pdb=" O3 NAG B1310 " pdb=" O7 NAG B1310 " model vdw 2.051 2.440 nonbonded pdb=" O ASN A 975 " pdb=" OG SER A 979 " model vdw 2.072 2.440 ... (remaining 190272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ ough 172 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 210 or resid 216 through 245 or resid 255 or resid 257 thro \ ugh 675 or resid 686 through 808 or resid 810 through 825 or resid 829 through 8 \ 40 or resid 845 through 931 or (resid 932 and (name N or name CA or name C or na \ me O or name CB )) or resid 933 through 1136 or resid 2101 through 2106)) selection = (chain 'B' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 172 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ ough 210 or resid 216 through 255 or resid 257 through 675 or resid 686 through \ 807 or (resid 808 and (name N or name CA or name C or name O or name CB )) or re \ sid 810 through 840 or resid 845 through 931 or (resid 932 and (name N or name C \ A or name C or name O or name CB )) or resid 933 through 936 or (resid 937 and ( \ name N or name CA or name C or name O or name CB )) or resid 941 through 1136 or \ resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 18 or resid 25 through 67 or resid 81 through 1 \ 42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ id 157 through 245 or resid 256 through 808 or resid 810 through 936 or (resid 9 \ 37 through 941 and (name N or name CA or name C or name O or name CB )) or resid \ 942 through 1136 or resid 1401 through 1406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 8.090 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 65.250 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.126 25379 Z= 0.415 Angle : 0.691 8.586 34483 Z= 0.366 Chirality : 0.051 1.289 3974 Planarity : 0.009 0.254 4419 Dihedral : 16.161 133.959 9452 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 3.84 % Allowed : 16.85 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.12), residues: 3063 helix: -1.95 (0.17), residues: 659 sheet: -1.71 (0.18), residues: 689 loop : -3.65 (0.11), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B1061 PHE 0.014 0.001 PHE C 592 TYR 0.020 0.001 TYR A 37 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 317 time to evaluate : 2.692 Fit side-chains REVERT: C 88 ASP cc_start: 0.7440 (t70) cc_final: 0.6995 (t0) REVERT: C 702 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7968 (m) REVERT: C 773 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8437 (ttpt) REVERT: C 820 PHE cc_start: 0.7956 (t80) cc_final: 0.7279 (m-80) REVERT: C 983 LYS cc_start: 0.7815 (tptm) cc_final: 0.7485 (mmtm) REVERT: C 1078 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 1104 ARG cc_start: 0.7361 (mtt90) cc_final: 0.7105 (mpt180) REVERT: C 1112 ILE cc_start: 0.8548 (mt) cc_final: 0.8326 (mt) REVERT: B 115 GLN cc_start: 0.8737 (mt0) cc_final: 0.8448 (mt0) REVERT: B 661 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6588 (mm-30) REVERT: B 675 GLN cc_start: 0.7150 (mm110) cc_final: 0.6890 (mm-40) REVERT: B 1088 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6987 (ptm-80) REVERT: B 1133 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7071 (p) REVERT: A 309 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: A 1070 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7257 (mmtp) outliers start: 104 outliers final: 60 residues processed: 398 average time/residue: 0.3628 time to fit residues: 231.0242 Evaluate side-chains 306 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN C 448 ASN C 450 ASN C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 752 GLN C 798 ASN C 952 ASN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 GLN C1045 HIS B 409 GLN B 655 HIS B 798 ASN B 952 ASN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN A 487 ASN A 606 ASN A 616 ASN A 675 GLN A 989 GLN A1068 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25379 Z= 0.219 Angle : 0.614 9.645 34483 Z= 0.317 Chirality : 0.048 0.552 3974 Planarity : 0.005 0.061 4419 Dihedral : 9.119 82.621 4051 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.25 % Allowed : 17.44 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.13), residues: 3063 helix: -0.59 (0.20), residues: 655 sheet: -1.04 (0.19), residues: 677 loop : -3.00 (0.12), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.003 0.001 HIS A1045 PHE 0.015 0.001 PHE A 342 TYR 0.030 0.002 TYR B 170 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 249 time to evaluate : 2.842 Fit side-chains REVERT: C 88 ASP cc_start: 0.7705 (t70) cc_final: 0.7113 (t0) REVERT: C 613 GLN cc_start: 0.8002 (mt0) cc_final: 0.7030 (tt0) REVERT: C 702 VAL cc_start: 0.8112 (p) cc_final: 0.7908 (m) REVERT: C 798 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8145 (t0) REVERT: C 820 PHE cc_start: 0.7903 (t80) cc_final: 0.7269 (m-80) REVERT: C 1104 ARG cc_start: 0.7527 (mtt90) cc_final: 0.7278 (mpt180) REVERT: B 66 HIS cc_start: 0.6573 (m90) cc_final: 0.6331 (m170) REVERT: B 567 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7463 (mmm-85) REVERT: B 787 LYS cc_start: 0.8448 (mttm) cc_final: 0.8232 (mttm) REVERT: B 966 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8670 (m-40) REVERT: B 999 GLN cc_start: 0.7195 (tt0) cc_final: 0.6811 (pt0) REVERT: B 1035 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7790 (mmtm) REVERT: A 1040 CYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8795 (m) REVERT: A 1070 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7230 (mmtp) outliers start: 115 outliers final: 73 residues processed: 339 average time/residue: 0.3368 time to fit residues: 185.8530 Evaluate side-chains 303 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 226 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 966 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1040 CYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 8.9990 chunk 87 optimal weight: 0.0370 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 0.0980 chunk 281 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 overall best weight: 3.6264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 798 ASN C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 606 ASN A 917 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25379 Z= 0.320 Angle : 0.657 9.812 34483 Z= 0.344 Chirality : 0.049 0.291 3974 Planarity : 0.005 0.071 4419 Dihedral : 8.451 80.460 3989 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.80 % Favored : 92.13 % Rotamer: Outliers : 4.91 % Allowed : 17.55 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.14), residues: 3063 helix: -0.45 (0.20), residues: 667 sheet: -0.74 (0.20), residues: 682 loop : -2.82 (0.12), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.005 0.001 HIS B1061 PHE 0.017 0.002 PHE B 201 TYR 0.030 0.002 TYR A 37 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 232 time to evaluate : 2.914 Fit side-chains revert: symmetry clash REVERT: C 88 ASP cc_start: 0.7781 (t70) cc_final: 0.6971 (t0) REVERT: C 613 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: C 820 PHE cc_start: 0.7942 (t80) cc_final: 0.7277 (m-80) REVERT: C 983 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7856 (tmtm) REVERT: B 999 GLN cc_start: 0.7482 (tt0) cc_final: 0.6943 (pt0) REVERT: B 1042 LYS cc_start: 0.8369 (tmtm) cc_final: 0.8063 (mmtt) REVERT: A 309 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: A 776 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: A 1070 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7283 (mmtp) outliers start: 133 outliers final: 90 residues processed: 335 average time/residue: 0.3595 time to fit residues: 195.2707 Evaluate side-chains 317 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 223 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 135 optimal weight: 0.2980 chunk 190 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 798 ASN C 850 GLN C 898 GLN B 414 GLN B 606 ASN B 798 ASN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS A 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25379 Z= 0.220 Angle : 0.581 9.356 34483 Z= 0.306 Chirality : 0.045 0.204 3974 Planarity : 0.004 0.068 4419 Dihedral : 7.921 77.071 3983 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.91 % Allowed : 17.88 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3063 helix: -0.17 (0.20), residues: 667 sheet: -0.55 (0.20), residues: 685 loop : -2.63 (0.13), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.003 0.001 HIS B1061 PHE 0.015 0.001 PHE A 377 TYR 0.025 0.002 TYR A 37 ARG 0.007 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 233 time to evaluate : 3.101 Fit side-chains REVERT: C 32 PHE cc_start: 0.7267 (m-80) cc_final: 0.6986 (m-80) REVERT: C 88 ASP cc_start: 0.7817 (t70) cc_final: 0.6973 (t0) REVERT: C 820 PHE cc_start: 0.7950 (t80) cc_final: 0.7212 (m-80) REVERT: C 983 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7866 (tmtm) REVERT: C 1104 ARG cc_start: 0.7598 (mtt90) cc_final: 0.7371 (mpt180) REVERT: B 567 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7478 (mmm-85) REVERT: B 661 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: B 801 GLN cc_start: 0.7973 (mt0) cc_final: 0.7719 (mt0) REVERT: B 966 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8695 (m-40) REVERT: B 1035 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7830 (mmtp) REVERT: A 309 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: A 776 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7500 (tp40) REVERT: A 932 GLN cc_start: 0.7865 (tt0) cc_final: 0.7616 (tt0) REVERT: A 1070 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7209 (mmtp) outliers start: 133 outliers final: 101 residues processed: 338 average time/residue: 0.3319 time to fit residues: 182.6024 Evaluate side-chains 331 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 224 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 966 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 798 ASN C 898 GLN B 798 ASN B 999 GLN A 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25379 Z= 0.266 Angle : 0.602 9.478 34483 Z= 0.316 Chirality : 0.047 0.382 3974 Planarity : 0.005 0.072 4419 Dihedral : 7.831 74.233 3983 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.25 % Allowed : 17.99 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3063 helix: -0.17 (0.20), residues: 668 sheet: -0.41 (0.20), residues: 671 loop : -2.56 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.004 0.001 HIS B1061 PHE 0.016 0.002 PHE A 377 TYR 0.028 0.002 TYR A 37 ARG 0.006 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 230 time to evaluate : 2.778 Fit side-chains REVERT: C 32 PHE cc_start: 0.7306 (m-80) cc_final: 0.7004 (m-80) REVERT: C 88 ASP cc_start: 0.7821 (t70) cc_final: 0.6948 (t0) REVERT: C 613 GLN cc_start: 0.8004 (mt0) cc_final: 0.7184 (tt0) REVERT: C 820 PHE cc_start: 0.7935 (t80) cc_final: 0.7208 (m-80) REVERT: C 983 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7834 (tmtm) REVERT: C 1104 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7369 (mpt180) REVERT: B 129 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7309 (mtmt) REVERT: B 606 ASN cc_start: 0.7520 (t160) cc_final: 0.7217 (t0) REVERT: B 661 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: B 966 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8697 (m-40) REVERT: B 1035 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7767 (mmtp) REVERT: A 244 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5582 (mt) REVERT: A 309 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: A 675 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6290 (tt0) REVERT: A 776 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7531 (tp40) REVERT: A 932 GLN cc_start: 0.7957 (tt0) cc_final: 0.7693 (tt0) REVERT: A 1070 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7228 (mmtp) REVERT: A 1125 VAL cc_start: 0.6848 (OUTLIER) cc_final: 0.6466 (p) outliers start: 142 outliers final: 113 residues processed: 343 average time/residue: 0.3351 time to fit residues: 185.9781 Evaluate side-chains 345 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 222 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 966 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 25 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 ASN B 613 GLN B 798 ASN A 69 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25379 Z= 0.231 Angle : 0.579 9.234 34483 Z= 0.304 Chirality : 0.046 0.256 3974 Planarity : 0.004 0.072 4419 Dihedral : 7.628 70.313 3983 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.39 % Allowed : 18.25 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3063 helix: -0.04 (0.20), residues: 668 sheet: -0.33 (0.20), residues: 674 loop : -2.47 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.003 0.001 HIS B1061 PHE 0.015 0.001 PHE C 592 TYR 0.026 0.002 TYR A 37 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 229 time to evaluate : 2.813 Fit side-chains REVERT: C 31 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7400 (p) REVERT: C 32 PHE cc_start: 0.7262 (m-80) cc_final: 0.6953 (m-80) REVERT: C 88 ASP cc_start: 0.7844 (t70) cc_final: 0.6950 (t0) REVERT: C 488 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7988 (m) REVERT: C 568 ASP cc_start: 0.6790 (t0) cc_final: 0.6494 (t0) REVERT: C 613 GLN cc_start: 0.8015 (mt0) cc_final: 0.7117 (tt0) REVERT: C 820 PHE cc_start: 0.7934 (t80) cc_final: 0.7231 (m-80) REVERT: C 983 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7859 (tmtm) REVERT: C 1104 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7398 (mpt180) REVERT: B 129 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7401 (mtmt) REVERT: B 606 ASN cc_start: 0.7621 (t160) cc_final: 0.7295 (t0) REVERT: B 661 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: B 801 GLN cc_start: 0.8012 (mt0) cc_final: 0.7696 (mt0) REVERT: B 1108 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: A 244 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.5578 (mt) REVERT: A 309 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: A 500 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7757 (t) REVERT: A 675 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.6175 (tt0) REVERT: A 776 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7478 (tp40) REVERT: A 932 GLN cc_start: 0.7903 (tt0) cc_final: 0.7655 (tt0) REVERT: A 1070 LYS cc_start: 0.7698 (mtpp) cc_final: 0.7189 (mmtp) REVERT: A 1125 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6439 (p) outliers start: 146 outliers final: 116 residues processed: 345 average time/residue: 0.3398 time to fit residues: 189.0049 Evaluate side-chains 349 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 221 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 ASN B 798 ASN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25379 Z= 0.279 Angle : 0.606 9.422 34483 Z= 0.319 Chirality : 0.047 0.235 3974 Planarity : 0.005 0.075 4419 Dihedral : 7.521 66.562 3977 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.47 % Allowed : 18.51 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3063 helix: -0.13 (0.20), residues: 671 sheet: -0.34 (0.20), residues: 676 loop : -2.43 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.004 0.001 HIS B1061 PHE 0.016 0.002 PHE C 592 TYR 0.029 0.002 TYR A 37 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 228 time to evaluate : 2.677 Fit side-chains REVERT: C 32 PHE cc_start: 0.7260 (m-80) cc_final: 0.6935 (m-80) REVERT: C 88 ASP cc_start: 0.7838 (t70) cc_final: 0.6920 (t0) REVERT: C 488 CYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7982 (m) REVERT: C 568 ASP cc_start: 0.6813 (t0) cc_final: 0.6522 (t0) REVERT: C 613 GLN cc_start: 0.8060 (mt0) cc_final: 0.7109 (tt0) REVERT: C 820 PHE cc_start: 0.7945 (t80) cc_final: 0.7237 (m-80) REVERT: C 915 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: C 983 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7872 (tmtm) REVERT: B 66 HIS cc_start: 0.6631 (m90) cc_final: 0.6335 (m170) REVERT: B 129 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7389 (mtmt) REVERT: B 606 ASN cc_start: 0.7691 (t160) cc_final: 0.7357 (t0) REVERT: B 661 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: B 966 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8704 (m-40) REVERT: B 1108 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: A 244 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5575 (mt) REVERT: A 309 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: A 500 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (t) REVERT: A 646 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7607 (ttp-170) REVERT: A 675 GLN cc_start: 0.6509 (OUTLIER) cc_final: 0.6263 (tt0) REVERT: A 776 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: A 932 GLN cc_start: 0.7923 (tt0) cc_final: 0.7680 (tt0) REVERT: A 1070 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7175 (mmtp) REVERT: A 1125 VAL cc_start: 0.6882 (OUTLIER) cc_final: 0.6514 (p) outliers start: 148 outliers final: 125 residues processed: 341 average time/residue: 0.3304 time to fit residues: 181.7757 Evaluate side-chains 365 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 227 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 966 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 236 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 ASN B 613 GLN B 798 ASN B1098 HIS ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25379 Z= 0.208 Angle : 0.562 8.968 34483 Z= 0.297 Chirality : 0.045 0.212 3974 Planarity : 0.004 0.070 4419 Dihedral : 7.271 62.987 3977 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.13 % Allowed : 18.88 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3063 helix: 0.10 (0.21), residues: 669 sheet: -0.26 (0.20), residues: 672 loop : -2.36 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.007 0.001 HIS B1098 PHE 0.014 0.001 PHE C 592 TYR 0.024 0.002 TYR B 901 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 232 time to evaluate : 3.258 Fit side-chains REVERT: C 88 ASP cc_start: 0.7803 (t70) cc_final: 0.7017 (t0) REVERT: C 488 CYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 568 ASP cc_start: 0.6782 (t0) cc_final: 0.6536 (t0) REVERT: C 613 GLN cc_start: 0.8029 (mt0) cc_final: 0.7048 (tt0) REVERT: C 820 PHE cc_start: 0.7978 (t80) cc_final: 0.7244 (m-80) REVERT: C 983 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7847 (tmtm) REVERT: B 129 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7299 (mtmt) REVERT: B 606 ASN cc_start: 0.7745 (t160) cc_final: 0.7422 (t0) REVERT: B 661 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: B 801 GLN cc_start: 0.7948 (mt0) cc_final: 0.7652 (mt0) REVERT: A 244 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5545 (mt) REVERT: A 309 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6184 (mp0) REVERT: A 500 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7759 (t) REVERT: A 675 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6097 (tt0) REVERT: A 776 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7485 (tp40) REVERT: A 1070 LYS cc_start: 0.7713 (mtpp) cc_final: 0.7210 (mmtp) REVERT: A 1125 VAL cc_start: 0.6891 (OUTLIER) cc_final: 0.6519 (p) outliers start: 139 outliers final: 117 residues processed: 337 average time/residue: 0.3292 time to fit residues: 179.6600 Evaluate side-chains 352 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 225 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 ASN B 66 HIS B 798 ASN A 239 GLN A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25379 Z= 0.171 Angle : 0.538 8.627 34483 Z= 0.284 Chirality : 0.044 0.250 3974 Planarity : 0.004 0.067 4419 Dihedral : 7.097 61.662 3975 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.91 % Allowed : 18.95 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3063 helix: 0.27 (0.21), residues: 667 sheet: -0.19 (0.20), residues: 672 loop : -2.29 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.002 0.000 HIS B1061 PHE 0.016 0.001 PHE A 820 TYR 0.022 0.001 TYR B 901 ARG 0.007 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 241 time to evaluate : 2.838 Fit side-chains REVERT: C 32 PHE cc_start: 0.7181 (m-80) cc_final: 0.6955 (m-80) REVERT: C 88 ASP cc_start: 0.7751 (t70) cc_final: 0.6991 (t0) REVERT: C 488 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7735 (m) REVERT: C 568 ASP cc_start: 0.6778 (t0) cc_final: 0.6539 (t0) REVERT: C 613 GLN cc_start: 0.7996 (mt0) cc_final: 0.7030 (tt0) REVERT: C 820 PHE cc_start: 0.7971 (t80) cc_final: 0.7232 (m-80) REVERT: C 983 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7843 (tmtm) REVERT: B 129 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7301 (mtmt) REVERT: B 606 ASN cc_start: 0.7706 (t160) cc_final: 0.7368 (t0) REVERT: B 661 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: B 801 GLN cc_start: 0.7927 (mt0) cc_final: 0.7653 (mt0) REVERT: B 1108 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: A 244 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5520 (mt) REVERT: A 309 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: A 500 THR cc_start: 0.7953 (p) cc_final: 0.7752 (t) REVERT: A 675 GLN cc_start: 0.6303 (OUTLIER) cc_final: 0.5966 (tt0) REVERT: A 776 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7475 (tp40) REVERT: A 1070 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7193 (mmtp) REVERT: A 1125 VAL cc_start: 0.6858 (OUTLIER) cc_final: 0.6472 (p) outliers start: 133 outliers final: 115 residues processed: 343 average time/residue: 0.3320 time to fit residues: 184.2661 Evaluate side-chains 358 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 233 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 180 optimal weight: 0.0000 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 ASN B 66 HIS B 798 ASN A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25379 Z= 0.251 Angle : 0.579 9.103 34483 Z= 0.307 Chirality : 0.046 0.231 3974 Planarity : 0.004 0.073 4419 Dihedral : 7.022 59.960 3972 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.77 % Allowed : 19.28 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3063 helix: 0.13 (0.20), residues: 669 sheet: -0.17 (0.20), residues: 673 loop : -2.31 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.003 0.001 HIS B1061 PHE 0.017 0.002 PHE A 820 TYR 0.027 0.002 TYR A 37 ARG 0.007 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 234 time to evaluate : 3.004 Fit side-chains REVERT: C 32 PHE cc_start: 0.7259 (m-80) cc_final: 0.7012 (m-80) REVERT: C 88 ASP cc_start: 0.7811 (t70) cc_final: 0.7027 (t0) REVERT: C 568 ASP cc_start: 0.6798 (t0) cc_final: 0.6571 (t0) REVERT: C 613 GLN cc_start: 0.8044 (mt0) cc_final: 0.7097 (tt0) REVERT: C 820 PHE cc_start: 0.8039 (t80) cc_final: 0.7276 (m-80) REVERT: C 983 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7875 (tmtm) REVERT: B 129 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7302 (mtmt) REVERT: B 606 ASN cc_start: 0.7689 (t160) cc_final: 0.7347 (t0) REVERT: B 661 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: B 801 GLN cc_start: 0.7968 (mt0) cc_final: 0.7718 (mt0) REVERT: B 1108 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 244 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5531 (mt) REVERT: A 309 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: A 500 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7761 (t) REVERT: A 675 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6098 (tt0) REVERT: A 776 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7496 (tp40) REVERT: A 1070 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7232 (mmtp) REVERT: A 1125 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6495 (p) outliers start: 129 outliers final: 115 residues processed: 332 average time/residue: 0.3362 time to fit residues: 180.6793 Evaluate side-chains 352 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 227 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 930 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 254 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 ASN B 66 HIS B 798 ASN A 115 GLN ** A 932 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 = 0.3577 r_free = 0.3577 target = 0.145341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.121270 restraints weight = 29892.431| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.42 r_work: 0.3054 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25379 Z= 0.225 Angle : 0.566 8.970 34483 Z= 0.300 Chirality : 0.045 0.218 3974 Planarity : 0.004 0.073 4419 Dihedral : 6.922 58.090 3972 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.91 % Allowed : 19.17 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3063 helix: 0.17 (0.21), residues: 669 sheet: -0.13 (0.20), residues: 670 loop : -2.29 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 64 HIS 0.003 0.001 HIS B1061 PHE 0.017 0.001 PHE A 820 TYR 0.025 0.002 TYR A 37 ARG 0.007 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5350.83 seconds wall clock time: 98 minutes 11.64 seconds (5891.64 seconds total)