Starting phenix.real_space_refine (version: dev) on Sat Feb 25 03:41:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/02_2023/6zb5_11145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/02_2023/6zb5_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_11145/02_2023/6zb5_11145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/02_2023/6zb5_11145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/02_2023/6zb5_11145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/02_2023/6zb5_11145_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 13.90, per 1000 atoms: 0.57 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: 9.73 Conformation dependent library (CDL) restraints added in 3.6 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: 3.95 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: 9.83 Time building geometry restraints manager: 10.62 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 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.35e+02 bond pdb=" C7 NAG A2101 " pdb=" N2 NAG A2101 " ideal model delta sigma weight residual 1.337 1.463 -0.126 1.10e-02 8.26e+03 1.31e+02 bond pdb=" C2 NAG C1406 " pdb=" N2 NAG C1406 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" C2 NAG A2101 " pdb=" N2 NAG A2101 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" C2 NAG C1406 " pdb=" C3 NAG C1406 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.50e-02 4.44e+03 1.09e+01 ... (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=" C2 NAG B1308 " pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 109.64 115.61 -5.97 5.38e-01 3.45e+00 1.23e+02 angle pdb=" C2 NAG A2104 " pdb=" C1 NAG A2104 " pdb=" O5 NAG A2104 " ideal model delta sigma weight residual 109.64 114.34 -4.70 5.38e-01 3.45e+00 7.62e+01 angle pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 109.64 114.21 -4.57 5.38e-01 3.45e+00 7.22e+01 angle pdb=" C2 NAG B1304 " pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 109.64 113.91 -4.27 5.38e-01 3.45e+00 6.29e+01 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 13525 24.45 - 48.89: 1062 48.89 - 73.34: 164 73.34 - 97.79: 20 97.79 - 122.23: 7 Dihedral angle restraints: 14778 sinusoidal: 5802 harmonic: 8976 Sorted by residual: dihedral pdb=" C2 NAG B1305 " pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " pdb=" C5 NAG B1305 " ideal model delta sinusoidal sigma weight residual -50.00 72.23 -122.23 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sinusoidal sigma weight residual -50.00 69.04 -119.04 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" C2 NAG B1302 " pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " pdb=" C5 NAG B1302 " ideal model delta sinusoidal sigma weight residual -50.00 62.38 -112.38 1 2.00e+01 2.50e-03 3.31e+01 ... (remaining 14775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3904 0.142 - 0.283: 19 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 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. 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: 0.620 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: 4.740 Check model and map are aligned: 0.400 Process input model: 65.010 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 0.128 25030 Z= 0.573 Angle : 0.757 15.419 34016 Z= 0.460 Chirality : 0.059 0.708 3934 Planarity : 0.015 0.307 4358 Dihedral : 17.237 122.234 8901 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 % 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 *********************** 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 : 2.901 Fit side-chains revert: symmetry clash outliers start: 100 outliers final: 31 residues processed: 406 average time/residue: 1.1383 time to fit residues: 547.1092 Evaluate side-chains 284 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 3.9788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 25030 Z= 0.237 Angle : 0.575 8.434 34016 Z= 0.317 Chirality : 0.048 0.521 3934 Planarity : 0.005 0.065 4358 Dihedral : 8.886 117.446 3501 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 4.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 3024 helix: 0.11 (0.19), residues: 678 sheet: -0.10 (0.19), residues: 633 loop : -2.63 (0.12), residues: 1713 *********************** 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 370 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 257 time to evaluate : 3.030 Fit side-chains revert: symmetry clash outliers start: 113 outliers final: 70 residues processed: 342 average time/residue: 1.0286 time to fit residues: 425.2633 Evaluate side-chains 313 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 243 time to evaluate : 3.047 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 59 residues processed: 11 average time/residue: 0.7446 time to fit residues: 14.3073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 233 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 281 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 B 613 GLN B 687 GLN B1098 HIS A 474 GLN A 951 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.081 25030 Z= 0.559 Angle : 0.806 9.343 34016 Z= 0.439 Chirality : 0.057 0.524 3934 Planarity : 0.006 0.084 4358 Dihedral : 9.437 120.497 3501 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 5.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3024 helix: -0.28 (0.19), residues: 699 sheet: 0.26 (0.19), residues: 699 loop : -2.66 (0.12), residues: 1626 *********************** 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 390 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 236 time to evaluate : 3.290 Fit side-chains revert: symmetry clash outliers start: 154 outliers final: 95 residues processed: 356 average time/residue: 1.1504 time to fit residues: 487.4134 Evaluate side-chains 314 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 219 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 81 residues processed: 14 average time/residue: 0.7728 time to fit residues: 17.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 31 optimal weight: 0.0670 chunk 134 optimal weight: 0.0980 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 267 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 234 ASN C 607 GLN C 675 GLN C1007 GLN B 603 ASN B 613 GLN B1007 GLN B1098 HIS A 66 HIS A 234 ASN A 675 GLN A 951 GLN A1071 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 25030 Z= 0.146 Angle : 0.487 8.046 34016 Z= 0.270 Chirality : 0.044 0.422 3934 Planarity : 0.004 0.062 4358 Dihedral : 8.643 116.391 3501 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 4.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3024 helix: 0.86 (0.20), residues: 675 sheet: 0.32 (0.19), residues: 687 loop : -2.28 (0.13), residues: 1662 *********************** 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 369 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 254 time to evaluate : 3.140 Fit side-chains revert: symmetry clash outliers start: 115 outliers final: 74 residues processed: 352 average time/residue: 1.0437 time to fit residues: 440.3187 Evaluate side-chains 311 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 237 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 69 residues processed: 5 average time/residue: 0.7118 time to fit residues: 8.0654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.0010 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- 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 C1007 GLN B 603 ASN B1098 HIS A 603 ASN A 951 GLN A1002 GLN A1071 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 25030 Z= 0.326 Angle : 0.621 7.183 34016 Z= 0.338 Chirality : 0.050 0.719 3934 Planarity : 0.005 0.072 4358 Dihedral : 8.828 118.091 3501 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 4.92 % 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: -1.48 (0.14), residues: 3024 helix: 0.44 (0.20), residues: 696 sheet: 0.33 (0.19), residues: 687 loop : -2.34 (0.13), residues: 1641 *********************** 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 369 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 238 time to evaluate : 2.950 Fit side-chains revert: symmetry clash outliers start: 131 outliers final: 95 residues processed: 341 average time/residue: 1.1675 time to fit residues: 474.1324 Evaluate side-chains 319 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 224 time to evaluate : 3.147 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 82 residues processed: 13 average time/residue: 0.9697 time to fit residues: 19.8440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN C 904 ASN C 951 GLN C1007 GLN B 370 ASN B 603 ASN B1098 HIS B1110 GLN A 66 HIS A 603 ASN A 675 GLN A 951 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 25030 Z= 0.253 Angle : 0.567 6.817 34016 Z= 0.312 Chirality : 0.047 0.387 3934 Planarity : 0.005 0.070 4358 Dihedral : 8.740 117.326 3501 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 4.89 % 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: -1.39 (0.14), residues: 3024 helix: 0.55 (0.20), residues: 696 sheet: 0.38 (0.19), residues: 687 loop : -2.28 (0.13), residues: 1641 *********************** 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 373 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 243 time to evaluate : 3.245 Fit side-chains revert: symmetry clash outliers start: 130 outliers final: 97 residues processed: 351 average time/residue: 1.1299 time to fit residues: 472.4391 Evaluate side-chains 330 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 233 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 88 residues processed: 9 average time/residue: 1.0016 time to fit residues: 15.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 170 optimal weight: 7.9990 chunk 218 optimal weight: 0.0980 chunk 169 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 613 GLN C 675 GLN C 951 GLN C1007 GLN B 370 ASN B 603 ASN B1098 HIS A 66 HIS A 603 ASN A 675 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 25030 Z= 0.221 Angle : 0.544 6.481 34016 Z= 0.299 Chirality : 0.047 0.673 3934 Planarity : 0.005 0.068 4358 Dihedral : 8.648 117.170 3501 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3024 helix: 0.80 (0.20), residues: 678 sheet: 0.40 (0.19), residues: 687 loop : -2.17 (0.13), residues: 1659 *********************** 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 363 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 241 time to evaluate : 3.494 Fit side-chains revert: symmetry clash outliers start: 122 outliers final: 98 residues processed: 341 average time/residue: 1.1459 time to fit residues: 469.3168 Evaluate side-chains 329 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 231 time to evaluate : 2.944 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 89 residues processed: 9 average time/residue: 1.2790 time to fit residues: 17.7192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 177 optimal weight: 0.0470 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 0.4980 overall best weight: 1.5084 ------------------------------------------------------------------------------- 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 951 GLN C1007 GLN B 370 ASN B 603 ASN B1098 HIS A 66 HIS A 613 GLN A 951 GLN A1071 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 25030 Z= 0.171 Angle : 0.497 6.024 34016 Z= 0.274 Chirality : 0.044 0.406 3934 Planarity : 0.004 0.066 4358 Dihedral : 8.499 116.858 3501 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 4.13 % 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: -1.05 (0.14), residues: 3024 helix: 1.06 (0.20), residues: 678 sheet: 0.43 (0.19), residues: 687 loop : -2.07 (0.13), residues: 1659 *********************** 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 358 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 248 time to evaluate : 3.197 Fit side-chains revert: symmetry clash outliers start: 110 outliers final: 95 residues processed: 346 average time/residue: 1.1789 time to fit residues: 485.7972 Evaluate side-chains 330 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 235 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 91 residues processed: 4 average time/residue: 0.6638 time to fit residues: 7.4036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 167 optimal weight: 0.0980 chunk 120 optimal weight: 0.8980 chunk 217 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 207 HIS C 675 GLN C 687 GLN C 759 GLN C 951 GLN C1007 GLN B 603 ASN B1007 GLN B1098 HIS A 66 HIS A 239 GLN A 607 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.061 25030 Z= 0.156 Angle : 0.479 5.903 34016 Z= 0.264 Chirality : 0.044 0.366 3934 Planarity : 0.004 0.066 4358 Dihedral : 8.375 116.774 3501 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 3.87 % 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: -0.89 (0.15), residues: 3024 helix: 1.29 (0.21), residues: 678 sheet: 0.46 (0.19), residues: 687 loop : -1.97 (0.13), residues: 1659 *********************** 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 341 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 238 time to evaluate : 3.229 Fit side-chains revert: symmetry clash outliers start: 103 outliers final: 92 residues processed: 334 average time/residue: 1.1666 time to fit residues: 465.6895 Evaluate side-chains 322 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 230 time to evaluate : 2.947 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 88 residues processed: 4 average time/residue: 1.4965 time to fit residues: 10.9216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 C1007 GLN B 603 ASN B1007 GLN B1098 HIS A 607 GLN A 951 GLN A1071 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 25030 Z= 0.318 Angle : 0.609 6.534 34016 Z= 0.333 Chirality : 0.048 0.435 3934 Planarity : 0.005 0.073 4358 Dihedral : 8.711 117.758 3501 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3024 helix: 0.65 (0.20), residues: 696 sheet: 0.37 (0.19), residues: 717 loop : -2.17 (0.13), residues: 1611 ********************** 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 330 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 236 time to evaluate : 2.911 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 87 residues processed: 325 average time/residue: 1.1613 time to fit residues: 451.3247 Evaluate side-chains 311 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 224 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 84 residues processed: 3 average time/residue: 0.8076 time to fit residues: 7.1425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 C1007 GLN B1007 GLN B1098 HIS A 66 HIS A 607 GLN A 951 GLN A1071 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.135213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109003 restraints weight = 26918.304| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.67 r_work: 0.2847 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25030 Z= 0.167 Angle : 0.496 5.873 34016 Z= 0.273 Chirality : 0.044 0.346 3934 Planarity : 0.004 0.067 4358 Dihedral : 8.457 116.873 3501 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 3.57 % 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: -0.95 (0.15), residues: 3024 helix: 1.12 (0.20), residues: 678 sheet: 0.47 (0.19), residues: 687 loop : -1.98 (0.13), residues: 1659 =============================================================================== Job complete usr+sys time: 7496.39 seconds wall clock time: 135 minutes 24.57 seconds (8124.57 seconds total)