Starting phenix.real_space_refine on Tue Mar 19 14:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/03_2024/6zb5_11145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/03_2024/6zb5_11145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/03_2024/6zb5_11145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/03_2024/6zb5_11145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/03_2024/6zb5_11145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/03_2024/6zb5_11145_updated.pdb" } resolution = 2.85 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= 0.012 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 15646 2.51 5 N 4043 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 722": "OE1" <-> "OE2" Residue "C ASP 742": "OD1" <-> "OD2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C ASP 805": "OD1" <-> "OD2" Residue "C PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 845": "OD1" <-> "OD2" Residue "C ASP 864": "OD1" <-> "OD2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C ASP 982": "OD1" <-> "OD2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C ASP 1038": "OD1" <-> "OD2" Residue "C GLU 1069": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B ASP 742": "OD1" <-> "OD2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B ASP 805": "OD1" <-> "OD2" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 845": "OD1" <-> "OD2" Residue "B ASP 864": "OD1" <-> "OD2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B ASP 982": "OD1" <-> "OD2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "B ASP 1038": "OD1" <-> "OD2" Residue "B GLU 1069": "OE1" <-> "OE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "A PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A ASP 982": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24499 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {'EIC': 2, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 13.49, per 1000 atoms: 0.55 Number of scatterers: 24499 At special positions: 0 Unit cell: (141.75, 135.45, 168, 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 4696 8.00 N 4043 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2102 " - " ASN A 343 " " NAG A2104 " - " ASN A 616 " " NAG A2105 " - " ASN A 798 " " NAG B1301 " - " ASN B 798 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 616 " " NAG B1306 " - " ASN B 282 " " NAG B1308 " - " ASN B 17 " " NAG C1401 " - " ASN C 343 " " NAG C1403 " - " ASN C 616 " " NAG C1404 " - " ASN C 798 " " NAG C1405 " - " ASN C1071 " " NAG F 1 " - " ASN A 714 " Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 4.6 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 42 sheets defined 22.0% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.04 Creating SS restraints... Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' 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 368 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: 4.707A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.528A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 421' Processing helix chain 'C' and resid 735 through 739 Processing helix chain 'C' and resid 744 through 751 removed outlier: 3.583A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 779 removed outlier: 3.943A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.598A pdb=" N LYS C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) 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 846 through 853 removed outlier: 3.712A pdb=" N ASN C 853 " --> pdb=" O ALA C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 881 Processing helix chain 'C' and resid 895 through 906 removed outlier: 3.526A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 Processing helix chain 'C' and resid 917 through 935 Processing helix chain 'C' and resid 944 through 964 removed outlier: 3.867A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1029 removed outlier: 3.578A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 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 368 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: 4.706A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.528A 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 751 removed outlier: 3.583A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 779 removed outlier: 3.942A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 822 removed outlier: 3.599A pdb=" N LYS B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 837 No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 846 through 853 removed outlier: 3.711A 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 895 through 906 removed outlier: 3.525A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 917 through 935 Processing helix chain 'B' and resid 944 through 964 removed outlier: 3.866A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 980 Processing helix chain 'B' and resid 983 through 1029 removed outlier: 3.578A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 365 through 368 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: 4.705A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.527A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.583A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 779 removed outlier: 3.943A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.598A pdb=" N LYS A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) 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 846 through 853 removed outlier: 3.713A pdb=" N ASN A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 881 Processing helix chain 'A' and resid 895 through 906 removed outlier: 3.525A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 917 through 935 Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.867A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1029 removed outlier: 3.578A pdb=" N GLU A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.927A 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: 4.261A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 117 through 119 removed outlier: 6.816A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.733A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 324 through 328 Processing sheet with id= F, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (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 472 through 474 Processing sheet with id= I, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.615A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 689 through 693 removed outlier: 6.168A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.566A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.962A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 731 through 733 Processing sheet with id= N, first strand: chain 'C' and resid 133 through 135 removed outlier: 4.017A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 117 through 119 removed outlier: 6.816A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.922A 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 315 removed outlier: 4.733A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 324 through 328 Processing sheet with id= T, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (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 472 through 474 Processing sheet with id= W, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.168A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.565A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.961A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 731 through 733 Processing sheet with id= AB, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.018A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 117 through 119 removed outlier: 6.815A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.734A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 324 through 328 Processing sheet with id= AH, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= AJ, first strand: chain 'A' and resid 472 through 474 Processing sheet with id= AK, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.615A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 689 through 693 removed outlier: 6.168A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.566A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.961A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 731 through 733 Processing sheet with id= AP, first strand: chain 'A' and resid 133 through 135 removed outlier: 4.017A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2241 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: 9.88 Time building geometry restraints manager: 9.94 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: 3987 1.31 - 1.44: 7024 1.44 - 1.57: 13881 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25030 Sorted by residual: bond pdb=" C7 NAG C1406 " pdb=" N2 NAG C1406 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C7 NAG A2101 " pdb=" N2 NAG A2101 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C1 NAG C1406 " pdb=" O5 NAG C1406 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C1 NAG A2101 " pdb=" O5 NAG A2101 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" N ASN B 798 " pdb=" CA ASN B 798 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.27e-02 6.20e+03 9.77e+00 ... (remaining 25025 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 470 106.15 - 113.12: 13493 113.12 - 120.09: 8324 120.09 - 127.06: 11530 127.06 - 134.04: 199 Bond angle restraints: 34016 Sorted by residual: angle pdb=" CA ASN B 798 " pdb=" CB ASN B 798 " pdb=" CG ASN B 798 " ideal model delta sigma weight residual 112.60 128.02 -15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" CB ASN B 798 " pdb=" CG ASN B 798 " pdb=" ND2 ASN B 798 " ideal model delta sigma weight residual 116.40 124.84 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" N GLY B 311 " pdb=" CA GLY B 311 " pdb=" C GLY B 311 " ideal model delta sigma weight residual 110.38 116.82 -6.44 1.28e+00 6.10e-01 2.53e+01 angle pdb=" N GLY C 311 " pdb=" CA GLY C 311 " pdb=" C GLY C 311 " ideal model delta sigma weight residual 110.38 116.81 -6.43 1.28e+00 6.10e-01 2.52e+01 angle pdb=" C ASN B 798 " pdb=" CA ASN B 798 " pdb=" CB ASN B 798 " ideal model delta sigma weight residual 110.79 102.61 8.18 1.63e+00 3.76e-01 2.52e+01 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 14084 27.04 - 54.08: 918 54.08 - 81.12: 128 81.12 - 108.16: 23 108.16 - 135.19: 15 Dihedral angle restraints: 15168 sinusoidal: 6192 harmonic: 8976 Sorted by residual: dihedral pdb=" CA TYR B 704 " pdb=" C TYR B 704 " pdb=" N SER B 705 " pdb=" CA SER B 705 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TYR C 704 " pdb=" C TYR C 704 " pdb=" N SER C 705 " pdb=" CA SER C 705 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TYR A 704 " pdb=" C TYR A 704 " pdb=" N SER A 705 " pdb=" CA SER A 705 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 15165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3902 0.142 - 0.283: 21 0.283 - 0.425: 2 0.425 - 0.566: 3 0.566 - 0.708: 6 Chirality restraints: 3934 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.13e+02 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 -2.82 0.42 2.00e-02 2.50e+03 4.45e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 3931 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.357 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG B1301 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.138 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.341 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG B1302 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2102 " 0.334 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A2102 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A2102 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG A2102 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG A2102 " 0.195 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 162 2.57 - 3.15: 18315 3.15 - 3.73: 33182 3.73 - 4.32: 50665 4.32 - 4.90: 86407 Nonbonded interactions: 188731 Sorted by model distance: nonbonded pdb=" OD2 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 1.985 2.440 nonbonded pdb=" OD2 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 1.985 2.440 nonbonded pdb=" OD2 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 1.986 2.440 nonbonded pdb=" ND2 ASN C 165 " pdb=" O5 NAG C1402 " model vdw 2.008 2.520 nonbonded pdb=" ND2 ASN B 714 " pdb=" C1 NAG E 1 " model vdw 2.055 3.550 ... (remaining 188726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 1136 or resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 1136 or resid 1401 through 1406)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.880 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 67.770 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.160 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:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.009 0.119 25030 Z= 0.584 Angle : 0.769 15.419 34016 Z= 0.412 Chirality : 0.060 0.708 3934 Planarity : 0.015 0.307 4358 Dihedral : 18.164 135.194 9291 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.76 % Allowed : 20.56 % Favored : 75.69 % Cbeta Deviations : 0.03 % 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: -3.22 (0.13), residues: 3024 helix: -1.71 (0.16), residues: 681 sheet: -0.38 (0.18), residues: 693 loop : -3.27 (0.12), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A1061 PHE 0.016 0.002 PHE A 592 TYR 0.021 0.002 TYR A 704 ARG 0.007 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 317 time to evaluate : 2.852 Fit side-chains revert: symmetry clash REVERT: C 187 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.4316 (ttmt) REVERT: C 207 HIS cc_start: 0.7542 (t-90) cc_final: 0.7156 (m90) REVERT: C 298 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: C 493 GLN cc_start: 0.7806 (mt0) cc_final: 0.7595 (mt0) REVERT: C 801 GLN cc_start: 0.7931 (mt0) cc_final: 0.7592 (mm110) REVERT: B 97 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6256 (pttm) REVERT: B 207 HIS cc_start: 0.7546 (t-90) cc_final: 0.7124 (m90) REVERT: B 567 ARG cc_start: 0.8264 (mmt90) cc_final: 0.7993 (mmt90) REVERT: B 801 GLN cc_start: 0.8096 (mt0) cc_final: 0.7775 (mm110) REVERT: A 128 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6653 (mp) REVERT: A 207 HIS cc_start: 0.7568 (t-90) cc_final: 0.7247 (m90) REVERT: A 346 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7232 (tmt170) REVERT: A 567 ARG cc_start: 0.8352 (mmt90) cc_final: 0.7981 (mmt180) REVERT: A 947 ASP cc_start: 0.7498 (m-30) cc_final: 0.7189 (m-30) REVERT: A 1070 LYS cc_start: 0.7411 (mtpp) cc_final: 0.7205 (tttm) outliers start: 100 outliers final: 31 residues processed: 406 average time/residue: 1.0953 time to fit residues: 524.9953 Evaluate side-chains 289 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 254 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 137 ASN C 164 ASN C 188 ASN C 540 ASN C 606 ASN C 675 GLN C 916 ASN C 946 GLN C 951 GLN B 125 ASN B 137 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 603 ASN B 606 ASN B 675 GLN B 687 GLN B 916 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS A 125 ASN A 137 ASN A 165 ASN A 188 ASN A 606 ASN A 675 GLN A 916 ASN A 951 GLN A1002 GLN A1007 GLN A1071 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25030 Z= 0.167 Angle : 0.567 11.187 34016 Z= 0.289 Chirality : 0.046 0.307 3934 Planarity : 0.004 0.060 4358 Dihedral : 10.591 115.892 3939 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.01 % Allowed : 21.72 % Favored : 75.27 % 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: -1.94 (0.14), residues: 3024 helix: 0.31 (0.19), residues: 678 sheet: -0.01 (0.19), residues: 663 loop : -2.66 (0.12), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.006 0.001 HIS B1098 PHE 0.019 0.001 PHE B 799 TYR 0.015 0.001 TYR C 265 ARG 0.005 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 262 time to evaluate : 2.940 Fit side-chains REVERT: C 207 HIS cc_start: 0.7574 (t-90) cc_final: 0.7214 (m90) REVERT: C 493 GLN cc_start: 0.7843 (mt0) cc_final: 0.7626 (mt0) REVERT: C 801 GLN cc_start: 0.8006 (mt0) cc_final: 0.7652 (mm110) REVERT: C 999 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: B 207 HIS cc_start: 0.7593 (t-90) cc_final: 0.7159 (m90) REVERT: B 357 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7089 (ttm170) REVERT: B 567 ARG cc_start: 0.8295 (mmt90) cc_final: 0.8059 (mmt90) REVERT: B 613 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7329 (mt0) REVERT: B 801 GLN cc_start: 0.8075 (mt0) cc_final: 0.7701 (mm110) REVERT: B 947 ASP cc_start: 0.7332 (m-30) cc_final: 0.7015 (m-30) REVERT: B 1007 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: A 202 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8742 (mttp) REVERT: A 207 HIS cc_start: 0.7577 (t-90) cc_final: 0.7264 (m90) REVERT: A 346 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7236 (tmt170) REVERT: A 567 ARG cc_start: 0.8350 (mmt90) cc_final: 0.8025 (mmt90) REVERT: A 947 ASP cc_start: 0.7442 (m-30) cc_final: 0.7115 (m-30) outliers start: 80 outliers final: 44 residues processed: 321 average time/residue: 1.0395 time to fit residues: 400.1456 Evaluate side-chains 297 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 248 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN B 164 ASN B 603 ASN B 687 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS A 474 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 25030 Z= 0.505 Angle : 0.800 12.034 34016 Z= 0.420 Chirality : 0.055 0.272 3934 Planarity : 0.006 0.080 4358 Dihedral : 10.019 116.159 3904 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.07 % Allowed : 18.98 % 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: -1.94 (0.14), residues: 3024 helix: -0.12 (0.19), residues: 696 sheet: 0.12 (0.19), residues: 669 loop : -2.55 (0.12), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 353 HIS 0.009 0.002 HIS B1098 PHE 0.019 0.003 PHE C 59 TYR 0.030 0.003 TYR A 704 ARG 0.011 0.001 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 235 time to evaluate : 2.663 Fit side-chains REVERT: C 207 HIS cc_start: 0.7773 (t-90) cc_final: 0.7509 (m90) REVERT: C 493 GLN cc_start: 0.7937 (mt0) cc_final: 0.7659 (mt0) REVERT: C 554 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7500 (mm-30) REVERT: C 613 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: C 801 GLN cc_start: 0.8040 (mt0) cc_final: 0.7686 (mm110) REVERT: C 999 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: C 1007 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7782 (mt0) REVERT: C 1110 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: B 118 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 207 HIS cc_start: 0.7623 (t-90) cc_final: 0.7361 (m90) REVERT: B 244 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6054 (pp) REVERT: B 321 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7929 (mm110) REVERT: B 357 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: B 613 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7460 (mt0) REVERT: B 801 GLN cc_start: 0.8054 (mt0) cc_final: 0.7773 (mm110) REVERT: B 947 ASP cc_start: 0.7541 (m-30) cc_final: 0.7186 (m-30) REVERT: B 1007 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: B 1110 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7976 (mm-40) REVERT: A 52 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 207 HIS cc_start: 0.7687 (t-90) cc_final: 0.7442 (m90) REVERT: A 244 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6036 (pp) REVERT: A 465 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: A 567 ARG cc_start: 0.8389 (mmt90) cc_final: 0.8114 (mmt90) REVERT: A 613 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: A 730 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8812 (mtpt) REVERT: A 875 LEU cc_start: 0.9002 (mm) cc_final: 0.8586 (mt) REVERT: A 947 ASP cc_start: 0.7610 (m-30) cc_final: 0.7242 (m-30) REVERT: A 1110 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7996 (mm110) outliers start: 135 outliers final: 70 residues processed: 337 average time/residue: 1.1729 time to fit residues: 466.7363 Evaluate side-chains 307 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 221 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 31 optimal weight: 0.0170 chunk 134 optimal weight: 0.1980 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN C 607 GLN C 675 GLN C 904 ASN B 603 ASN B1098 HIS A 234 ASN A 675 GLN A 951 GLN A1002 GLN A1071 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25030 Z= 0.147 Angle : 0.516 9.342 34016 Z= 0.271 Chirality : 0.044 0.309 3934 Planarity : 0.004 0.064 4358 Dihedral : 8.532 114.791 3899 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.41 % Allowed : 21.53 % Favored : 76.06 % 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: -1.30 (0.14), residues: 3024 helix: 0.89 (0.20), residues: 678 sheet: 0.32 (0.19), residues: 687 loop : -2.28 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.008 0.001 HIS B1098 PHE 0.010 0.001 PHE A 592 TYR 0.012 0.001 TYR C1064 ARG 0.003 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 251 time to evaluate : 2.838 Fit side-chains REVERT: C 207 HIS cc_start: 0.7680 (t-90) cc_final: 0.7357 (m90) REVERT: C 613 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: C 801 GLN cc_start: 0.7952 (mt0) cc_final: 0.7639 (mm110) REVERT: C 999 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: C 1007 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7891 (mm-40) REVERT: B 207 HIS cc_start: 0.7485 (t-90) cc_final: 0.7181 (m90) REVERT: B 239 GLN cc_start: 0.8778 (tt0) cc_final: 0.8533 (tt0) REVERT: B 321 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7944 (mm110) REVERT: B 357 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: B 465 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: B 801 GLN cc_start: 0.8051 (mt0) cc_final: 0.7742 (mm110) REVERT: B 947 ASP cc_start: 0.7421 (m-30) cc_final: 0.7200 (m-30) REVERT: B 1007 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: A 207 HIS cc_start: 0.7575 (t-90) cc_final: 0.7315 (m90) REVERT: A 303 LEU cc_start: 0.8610 (mt) cc_final: 0.8388 (mt) REVERT: A 567 ARG cc_start: 0.8343 (mmt90) cc_final: 0.7996 (mmt90) REVERT: A 947 ASP cc_start: 0.7412 (m-30) cc_final: 0.6993 (m-30) REVERT: A 1110 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8009 (mm110) outliers start: 64 outliers final: 25 residues processed: 295 average time/residue: 1.1520 time to fit residues: 400.2778 Evaluate side-chains 263 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.0770 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.0470 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN B 603 ASN B1071 ASN B1098 HIS A 603 ASN A 946 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25030 Z= 0.201 Angle : 0.545 9.394 34016 Z= 0.288 Chirality : 0.045 0.325 3934 Planarity : 0.004 0.068 4358 Dihedral : 7.360 113.381 3894 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.12 % Allowed : 20.93 % 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: -1.20 (0.14), residues: 3024 helix: 0.97 (0.21), residues: 678 sheet: 0.38 (0.19), residues: 687 loop : -2.20 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.008 0.001 HIS B1098 PHE 0.015 0.001 PHE A 32 TYR 0.017 0.001 TYR A 901 ARG 0.005 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 244 time to evaluate : 2.899 Fit side-chains REVERT: C 207 HIS cc_start: 0.7698 (t-90) cc_final: 0.7339 (m90) REVERT: C 357 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7453 (ttm170) REVERT: C 613 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: C 801 GLN cc_start: 0.7982 (mt0) cc_final: 0.7652 (mm110) REVERT: C 999 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: C 1110 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7875 (mm110) REVERT: B 34 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.5620 (mtt180) REVERT: B 207 HIS cc_start: 0.7511 (t-90) cc_final: 0.7214 (m90) REVERT: B 239 GLN cc_start: 0.8791 (tt0) cc_final: 0.8517 (tt0) REVERT: B 321 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8001 (mm110) REVERT: B 357 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7106 (ttm170) REVERT: B 458 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (mttp) REVERT: B 465 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: B 567 ARG cc_start: 0.8298 (mmt90) cc_final: 0.8084 (mmt90) REVERT: B 801 GLN cc_start: 0.8053 (mt0) cc_final: 0.7785 (mm110) REVERT: B 947 ASP cc_start: 0.7417 (m-30) cc_final: 0.7045 (m-30) REVERT: B 1007 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: B 1110 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7967 (mm-40) REVERT: A 207 HIS cc_start: 0.7592 (t-90) cc_final: 0.7332 (m90) REVERT: A 244 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6203 (pp) REVERT: A 303 LEU cc_start: 0.8629 (mt) cc_final: 0.8404 (mt) REVERT: A 567 ARG cc_start: 0.8367 (mmt90) cc_final: 0.8116 (mmt90) REVERT: A 613 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: A 947 ASP cc_start: 0.7444 (m-30) cc_final: 0.6982 (m-30) REVERT: A 1110 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8002 (mm110) outliers start: 83 outliers final: 43 residues processed: 302 average time/residue: 1.2252 time to fit residues: 431.3542 Evaluate side-chains 290 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 0.0970 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN C 951 GLN B 603 ASN B1098 HIS A 603 ASN A 951 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25030 Z= 0.333 Angle : 0.645 9.338 34016 Z= 0.343 Chirality : 0.049 0.332 3934 Planarity : 0.005 0.075 4358 Dihedral : 7.556 110.378 3892 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.91 % Allowed : 20.29 % Favored : 75.80 % 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: -1.45 (0.14), residues: 3024 helix: 0.43 (0.20), residues: 699 sheet: 0.34 (0.19), residues: 687 loop : -2.29 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 353 HIS 0.010 0.001 HIS B1098 PHE 0.016 0.002 PHE A 32 TYR 0.022 0.002 TYR C 704 ARG 0.005 0.001 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 232 time to evaluate : 2.715 Fit side-chains REVERT: C 207 HIS cc_start: 0.7732 (t-90) cc_final: 0.7404 (m90) REVERT: C 294 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6897 (p0) REVERT: C 326 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7606 (mp) REVERT: C 357 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: C 613 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: C 801 GLN cc_start: 0.8011 (mt0) cc_final: 0.7667 (mm110) REVERT: C 897 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8474 (mtt) REVERT: C 999 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: C 1110 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7858 (mm110) REVERT: B 52 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: B 118 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8152 (tp) REVERT: B 207 HIS cc_start: 0.7526 (t-90) cc_final: 0.7305 (m90) REVERT: B 239 GLN cc_start: 0.8786 (tt0) cc_final: 0.8517 (tt0) REVERT: B 244 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5937 (pp) REVERT: B 321 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8024 (mm110) REVERT: B 357 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7093 (ttm170) REVERT: B 458 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8191 (mttp) REVERT: B 465 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: B 730 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8388 (mtmt) REVERT: B 801 GLN cc_start: 0.8042 (mt0) cc_final: 0.7765 (mm110) REVERT: B 947 ASP cc_start: 0.7460 (m-30) cc_final: 0.7073 (m-30) REVERT: B 1007 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: B 1110 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: B 1136 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.6247 (m-30) REVERT: A 52 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: A 207 HIS cc_start: 0.7639 (t-90) cc_final: 0.7355 (m90) REVERT: A 244 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6195 (pp) REVERT: A 303 LEU cc_start: 0.8658 (mt) cc_final: 0.8451 (mt) REVERT: A 465 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: A 554 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: A 567 ARG cc_start: 0.8380 (mmt90) cc_final: 0.8112 (mmt90) REVERT: A 613 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: A 793 ASP cc_start: 0.6547 (t0) cc_final: 0.6244 (t0) REVERT: A 875 LEU cc_start: 0.8995 (mm) cc_final: 0.8628 (mt) REVERT: A 947 ASP cc_start: 0.7527 (m-30) cc_final: 0.7092 (m-30) REVERT: A 1110 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8011 (mm110) outliers start: 104 outliers final: 63 residues processed: 306 average time/residue: 1.1887 time to fit residues: 426.1940 Evaluate side-chains 313 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 227 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 297 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 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 675 GLN C 951 GLN B 370 ASN B 603 ASN B1098 HIS A 951 GLN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25030 Z= 0.205 Angle : 0.546 9.387 34016 Z= 0.292 Chirality : 0.046 0.332 3934 Planarity : 0.004 0.069 4358 Dihedral : 7.276 110.236 3892 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.49 % Allowed : 21.04 % Favored : 75.46 % 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: -1.19 (0.14), residues: 3024 helix: 0.85 (0.20), residues: 678 sheet: 0.40 (0.19), residues: 687 loop : -2.15 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.010 0.001 HIS B1098 PHE 0.014 0.001 PHE A 32 TYR 0.023 0.001 TYR A 901 ARG 0.006 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 237 time to evaluate : 2.741 Fit side-chains REVERT: C 207 HIS cc_start: 0.7740 (t-90) cc_final: 0.7382 (m90) REVERT: C 294 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6795 (p0) REVERT: C 326 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7572 (mp) REVERT: C 357 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7281 (ttm170) REVERT: C 613 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: C 801 GLN cc_start: 0.7978 (mt0) cc_final: 0.7632 (mm110) REVERT: C 899 MET cc_start: 0.8761 (mmp) cc_final: 0.8505 (tpt) REVERT: C 999 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: C 1110 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7856 (mm110) REVERT: B 207 HIS cc_start: 0.7523 (t-90) cc_final: 0.7294 (m90) REVERT: B 239 GLN cc_start: 0.8755 (tt0) cc_final: 0.8471 (tt0) REVERT: B 244 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5912 (pp) REVERT: B 321 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8035 (mm110) REVERT: B 357 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7139 (ttm170) REVERT: B 465 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: B 730 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8289 (mtmt) REVERT: B 801 GLN cc_start: 0.8025 (mt0) cc_final: 0.7595 (mm110) REVERT: B 947 ASP cc_start: 0.7420 (m-30) cc_final: 0.7034 (m-30) REVERT: B 1007 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: B 1047 MET cc_start: 0.8524 (ptm) cc_final: 0.8140 (mtm) REVERT: B 1110 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7944 (mm-40) REVERT: A 207 HIS cc_start: 0.7600 (t-90) cc_final: 0.7340 (m90) REVERT: A 244 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6138 (pp) REVERT: A 303 LEU cc_start: 0.8623 (mt) cc_final: 0.8414 (mt) REVERT: A 465 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: A 554 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: A 567 ARG cc_start: 0.8358 (mmt90) cc_final: 0.8109 (mmt90) REVERT: A 613 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: A 793 ASP cc_start: 0.6596 (t0) cc_final: 0.6293 (t0) REVERT: A 947 ASP cc_start: 0.7450 (m-30) cc_final: 0.6993 (m-30) REVERT: A 1110 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8003 (mm110) outliers start: 93 outliers final: 56 residues processed: 306 average time/residue: 1.1864 time to fit residues: 425.5009 Evaluate side-chains 299 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 226 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN C 951 GLN B 370 ASN B 603 ASN B1098 HIS A 239 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25030 Z= 0.203 Angle : 0.539 9.404 34016 Z= 0.289 Chirality : 0.045 0.331 3934 Planarity : 0.005 0.069 4358 Dihedral : 7.049 109.369 3892 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.49 % Allowed : 21.16 % Favored : 75.35 % 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: -1.09 (0.14), residues: 3024 helix: 0.94 (0.20), residues: 681 sheet: 0.42 (0.19), residues: 687 loop : -2.07 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.010 0.001 HIS B1098 PHE 0.016 0.001 PHE C 830 TYR 0.021 0.001 TYR A 901 ARG 0.007 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 239 time to evaluate : 2.874 Fit side-chains REVERT: C 294 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6769 (p0) REVERT: C 326 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7598 (mp) REVERT: C 357 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7290 (ttm170) REVERT: C 613 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: C 801 GLN cc_start: 0.7984 (mt0) cc_final: 0.7636 (mm110) REVERT: C 899 MET cc_start: 0.8725 (mmp) cc_final: 0.8486 (tpt) REVERT: C 999 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: C 1110 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7828 (mm110) REVERT: B 207 HIS cc_start: 0.7542 (t-90) cc_final: 0.7278 (m90) REVERT: B 239 GLN cc_start: 0.8751 (tt0) cc_final: 0.8448 (tt0) REVERT: B 244 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5876 (pp) REVERT: B 321 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8105 (mm-40) REVERT: B 357 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: B 465 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: B 730 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8292 (mtmt) REVERT: B 801 GLN cc_start: 0.8052 (mt0) cc_final: 0.7623 (mm110) REVERT: B 947 ASP cc_start: 0.7337 (m-30) cc_final: 0.6945 (m-30) REVERT: B 1007 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: B 1136 ASP cc_start: 0.6447 (OUTLIER) cc_final: 0.6217 (m-30) REVERT: A 207 HIS cc_start: 0.7575 (t-90) cc_final: 0.7311 (m90) REVERT: A 244 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6140 (pp) REVERT: A 303 LEU cc_start: 0.8612 (mt) cc_final: 0.8405 (mt) REVERT: A 465 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: A 554 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: A 567 ARG cc_start: 0.8380 (mmt90) cc_final: 0.8115 (mmt90) REVERT: A 613 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: A 793 ASP cc_start: 0.6533 (t0) cc_final: 0.6292 (t0) REVERT: A 875 LEU cc_start: 0.9005 (mm) cc_final: 0.8632 (mt) REVERT: A 947 ASP cc_start: 0.7432 (m-30) cc_final: 0.6973 (m-30) REVERT: A 1110 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8006 (mm110) outliers start: 93 outliers final: 61 residues processed: 307 average time/residue: 1.2437 time to fit residues: 448.7082 Evaluate side-chains 309 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 231 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 2.9990 chunk 285 optimal weight: 0.6980 chunk 260 optimal weight: 6.9990 chunk 277 optimal weight: 0.0770 chunk 167 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 675 GLN C 687 GLN C 759 GLN C 951 GLN B 603 ASN B1007 GLN B1098 HIS A 607 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25030 Z= 0.153 Angle : 0.499 9.442 34016 Z= 0.267 Chirality : 0.044 0.325 3934 Planarity : 0.004 0.068 4358 Dihedral : 6.799 109.150 3892 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.82 % Allowed : 21.83 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3024 helix: 1.18 (0.21), residues: 681 sheet: 0.45 (0.19), residues: 687 loop : -2.00 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.013 0.001 HIS B1098 PHE 0.015 0.001 PHE C 830 TYR 0.022 0.001 TYR A 901 ARG 0.007 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 237 time to evaluate : 2.947 Fit side-chains REVERT: C 357 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7341 (ttm170) REVERT: C 613 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: C 801 GLN cc_start: 0.7976 (mt0) cc_final: 0.7627 (mm110) REVERT: C 999 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: B 207 HIS cc_start: 0.7503 (t-90) cc_final: 0.7229 (m90) REVERT: B 244 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5849 (pp) REVERT: B 321 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8164 (mm-40) REVERT: B 357 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7063 (ttm170) REVERT: B 465 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: B 801 GLN cc_start: 0.8085 (mt0) cc_final: 0.7647 (mm110) REVERT: B 947 ASP cc_start: 0.7214 (m-30) cc_final: 0.6807 (m-30) REVERT: B 1007 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: B 1047 MET cc_start: 0.8403 (ptm) cc_final: 0.8108 (mtm) REVERT: A 207 HIS cc_start: 0.7537 (t-90) cc_final: 0.7278 (m90) REVERT: A 244 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6106 (pp) REVERT: A 303 LEU cc_start: 0.8588 (mt) cc_final: 0.8387 (mt) REVERT: A 554 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6645 (mm-30) REVERT: A 567 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8113 (mmt90) REVERT: A 613 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: A 793 ASP cc_start: 0.6572 (t0) cc_final: 0.6296 (t0) REVERT: A 947 ASP cc_start: 0.7376 (m-30) cc_final: 0.6902 (m-30) REVERT: A 1110 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8004 (mm110) outliers start: 75 outliers final: 50 residues processed: 293 average time/residue: 1.1626 time to fit residues: 400.7135 Evaluate side-chains 291 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 207 HIS C 951 GLN B 603 ASN B1098 HIS A 607 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25030 Z= 0.286 Angle : 0.605 9.395 34016 Z= 0.323 Chirality : 0.048 0.336 3934 Planarity : 0.005 0.073 4358 Dihedral : 7.035 108.019 3892 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.89 % Allowed : 21.87 % Favored : 75.23 % 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: -1.22 (0.14), residues: 3024 helix: 0.65 (0.20), residues: 699 sheet: 0.40 (0.19), residues: 687 loop : -2.12 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.015 0.001 HIS B1098 PHE 0.016 0.002 PHE C 830 TYR 0.034 0.002 TYR B 901 ARG 0.005 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 229 time to evaluate : 3.185 Fit side-chains REVERT: C 294 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6823 (p0) REVERT: C 357 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7317 (ttm170) REVERT: C 493 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7650 (mt0) REVERT: C 613 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: C 801 GLN cc_start: 0.8030 (mt0) cc_final: 0.7670 (mm110) REVERT: C 999 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: C 1110 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7841 (mm110) REVERT: B 207 HIS cc_start: 0.7529 (t-90) cc_final: 0.7312 (m90) REVERT: B 239 GLN cc_start: 0.8844 (tt0) cc_final: 0.8625 (mt0) REVERT: B 244 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5867 (pp) REVERT: B 357 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7053 (ttm170) REVERT: B 465 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: B 801 GLN cc_start: 0.8043 (mt0) cc_final: 0.7604 (mm110) REVERT: B 947 ASP cc_start: 0.7473 (m-30) cc_final: 0.7075 (m-30) REVERT: B 1007 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: B 1047 MET cc_start: 0.8584 (ptm) cc_final: 0.8216 (mtm) REVERT: B 1110 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7978 (mm-40) REVERT: A 207 HIS cc_start: 0.7629 (t-90) cc_final: 0.7321 (m90) REVERT: A 244 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6111 (pp) REVERT: A 554 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: A 567 ARG cc_start: 0.8369 (mmt90) cc_final: 0.8112 (mmt90) REVERT: A 613 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: A 793 ASP cc_start: 0.6536 (t0) cc_final: 0.6210 (t0) REVERT: A 875 LEU cc_start: 0.8989 (mm) cc_final: 0.8611 (mt) REVERT: A 947 ASP cc_start: 0.7496 (m-30) cc_final: 0.7032 (m-30) REVERT: A 1110 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8031 (mm110) outliers start: 77 outliers final: 59 residues processed: 287 average time/residue: 1.1839 time to fit residues: 401.4950 Evaluate side-chains 297 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 224 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.0030 chunk 245 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.0020 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 951 GLN B 603 ASN B1098 HIS A 607 GLN A 951 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.108560 restraints weight = 27000.027| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.57 r_work: 0.2879 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25030 Z= 0.182 Angle : 0.527 9.428 34016 Z= 0.282 Chirality : 0.045 0.323 3934 Planarity : 0.004 0.067 4358 Dihedral : 6.826 107.918 3892 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.89 % Allowed : 21.91 % Favored : 75.20 % 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: -1.01 (0.15), residues: 3024 helix: 1.06 (0.21), residues: 678 sheet: 0.45 (0.19), residues: 687 loop : -2.02 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.013 0.001 HIS B1098 PHE 0.016 0.001 PHE C 830 TYR 0.020 0.001 TYR B 901 ARG 0.004 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7583.62 seconds wall clock time: 135 minutes 26.37 seconds (8126.37 seconds total)