Starting phenix.real_space_refine (version: dev) on Sat Feb 25 21:33:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7n_33042/02_2023/7x7n_33042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7n_33042/02_2023/7x7n_33042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7n_33042/02_2023/7x7n_33042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7n_33042/02_2023/7x7n_33042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7n_33042/02_2023/7x7n_33042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7n_33042/02_2023/7x7n_33042_updated.pdb" } resolution = 4.47 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= 0.000 sd= 0.005 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 "B GLU 96": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "G GLU 23": "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: 26493 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 8031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8031 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8033 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7981 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 317 Classifications: {'peptide': 38} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.13, per 1000 atoms: 0.57 Number of scatterers: 26493 At special positions: 0 Unit cell: (145.08, 211.77, 147.42, 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 128 16.00 O 5128 8.00 N 4328 7.00 C 16909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 603 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.58 Conformation dependent library (CDL) restraints added in 4.4 seconds 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 20 " pdb=" CB DAL E 20 " pdb=" CB DAL H 20 " pdb=" CB DAL I 20 " pdb=" CB DAL F 20 " pdb=" CB DAL G 20 " Number of C-beta restraints generated: 6236 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 44 sheets defined 24.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'B' and resid 295 through 302 removed outlier: 4.029A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) 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 404 through 409 removed outlier: 5.483A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 620 through 622 No H-bonds generated for 'chain 'B' and resid 620 through 622' Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 759 through 782 removed outlier: 4.886A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.850A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 882 removed outlier: 3.550A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 887 No H-bonds generated for 'chain 'B' and resid 885 through 887' Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.601A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 920 through 937 removed outlier: 4.034A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 950 Processing helix chain 'B' and resid 953 through 966 removed outlier: 4.692A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 removed outlier: 3.630A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 977 through 983' Processing helix chain 'B' and resid 989 through 1034 removed outlier: 3.525A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B1014 " --> pdb=" O GLN B1010 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1119 No H-bonds generated for 'chain 'B' and resid 1117 through 1119' Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 4.770A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 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 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 620 through 623 No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 739 through 742 No H-bonds generated for 'chain 'C' and resid 739 through 742' Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.585A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 781 removed outlier: 4.163A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.586A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 removed outlier: 3.702A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.884A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 937 removed outlier: 5.883A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.531A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 986 through 991 removed outlier: 6.003A pdb=" N GLU C 990 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1032 removed outlier: 3.724A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.359A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 4.317A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 366 through 371 removed outlier: 4.059A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 419 through 422 No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 5.077A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 removed outlier: 3.683A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 869 through 882 removed outlier: 3.600A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.661A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 937 removed outlier: 5.168A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 967 removed outlier: 4.488A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 954 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN A 957 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 961 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 963 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 964 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 982 No H-bonds generated for 'chain 'A' and resid 979 through 982' Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 990 through 1032 removed outlier: 3.501A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'D' and resid 4 through 18 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'E' and resid 2 through 18 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'H' and resid 3 through 17 Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'I' and resid 2 through 18 Processing helix chain 'I' and resid 24 through 36 Processing helix chain 'F' and resid 2 through 18 Processing helix chain 'F' and resid 24 through 36 Processing helix chain 'G' and resid 2 through 18 Processing helix chain 'G' and resid 24 through 37 Processing sheet with id= A, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.837A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.585A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 279 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 52 through 55 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.827A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.504A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.970A pdb=" N PHE B 318 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 398 through 403 removed outlier: 3.692A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 551 through 554 removed outlier: 3.981A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.818A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 670 through 674 Processing sheet with id= K, first strand: chain 'B' and resid 713 through 715 Processing sheet with id= L, first strand: chain 'B' and resid 717 through 721 removed outlier: 3.576A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B1065 " --> pdb=" O MET B1050 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 726 through 728 Processing sheet with id= N, first strand: chain 'B' and resid 1132 through 1134 removed outlier: 7.140A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.540A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 448 through 454 removed outlier: 7.258A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 28 through 31 Processing sheet with id= R, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.880A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= T, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.529A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.942A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 376 through 378 Processing sheet with id= W, first strand: chain 'C' and resid 539 through 542 removed outlier: 3.979A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 551 through 553 removed outlier: 4.287A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 648 through 651 removed outlier: 4.333A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 670 through 674 Processing sheet with id= AA, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.804A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.718A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AD, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 3.615A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.021A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 48 through 51 Processing sheet with id= AG, first strand: chain 'A' and resid 192 through 194 removed outlier: 3.781A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.774A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.712A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.568A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= AL, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.890A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A' and resid 584 through 586 removed outlier: 6.584A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 611 through 613 removed outlier: 3.529A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 670 through 675 removed outlier: 3.645A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.885A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.628A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 1094 through 1096 removed outlier: 3.686A pdb=" N VAL A1096 " --> pdb=" O PHE A1103 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1734 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: 9.61 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 26888 1.57 - 1.93: 176 1.93 - 2.29: 0 2.29 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 27065 Sorted by residual: bond pdb=" C GLN A 675 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 1.335 2.999 -1.664 1.34e-02 5.57e+03 1.54e+04 bond pdb=" CA GLN C 913 " pdb=" C GLN C 913 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.80e-02 3.09e+03 1.75e+01 bond pdb=" N THR B 333 " pdb=" CA THR B 333 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" C ILE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.20e-02 6.94e+03 1.14e+01 bond pdb=" N LYS C 424 " pdb=" CA LYS C 424 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 ... (remaining 27060 not shown) Histogram of bond angle deviations from ideal: 40.91 - 61.64: 1 61.64 - 82.37: 0 82.37 - 103.11: 262 103.11 - 123.84: 35961 123.84 - 144.57: 570 Bond angle restraints: 36794 Sorted by residual: angle pdb=" O GLN A 675 " pdb=" C GLN A 675 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 121.76 40.91 80.85 1.15e+00 7.56e-01 4.94e+03 angle pdb=" CA GLN A 675 " pdb=" C GLN A 675 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 118.24 144.57 -26.33 1.18e+00 7.18e-01 4.98e+02 angle pdb=" C GLN A 675 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta sigma weight residual 120.28 139.65 -19.37 1.44e+00 4.82e-01 1.81e+02 angle pdb=" N ASN B 334 " pdb=" CA ASN B 334 " pdb=" C ASN B 334 " ideal model delta sigma weight residual 110.97 102.83 8.14 1.09e+00 8.42e-01 5.57e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 111.91 105.78 6.13 8.90e-01 1.26e+00 4.74e+01 ... (remaining 36789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 14872 21.71 - 43.42: 1067 43.42 - 65.13: 96 65.13 - 86.84: 40 86.84 - 108.55: 8 Dihedral angle restraints: 16083 sinusoidal: 6413 harmonic: 9670 Sorted by residual: dihedral pdb=" CA GLN A 675 " pdb=" C GLN A 675 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta harmonic sigma weight residual 180.00 130.16 49.84 0 5.00e+00 4.00e-02 9.94e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -1.99 -84.01 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.49 -75.51 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 16080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4102 0.109 - 0.218: 171 0.218 - 0.327: 8 0.327 - 0.436: 6 0.436 - 0.545: 4 Chirality restraints: 4291 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 4288 not shown) Planarity restraints: 4734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 675 " -0.267 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C GLN A 675 " 0.387 2.00e-02 2.50e+03 pdb=" O GLN A 675 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN A 690 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO B 812 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 490 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO B 491 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.032 5.00e-02 4.00e+02 ... (remaining 4731 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 507 2.55 - 3.13: 25060 3.13 - 3.72: 40957 3.72 - 4.31: 55171 4.31 - 4.90: 83851 Nonbonded interactions: 205546 Sorted by model distance: nonbonded pdb=" O CYS A1032 " pdb=" OG SER A1051 " model vdw 1.956 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.015 2.440 nonbonded pdb=" O VAL A 308 " pdb=" OG1 THR A 602 " model vdw 2.044 2.440 nonbonded pdb=" OG SER B 746 " pdb=" OE2 GLU B 748 " model vdw 2.046 2.440 nonbonded pdb=" O GLN B 580 " pdb=" O6 NAG B1301 " model vdw 2.065 2.440 ... (remaining 205541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 675 or resid 691 through 1149 or resid 1301 thr \ ough 1313)) selection = (chain 'B' and (resid 26 through 480 or (resid 481 and (name N or name CA or nam \ e C or name O or name CB )) or resid 489 through 675 or resid 691 through 1149 o \ r resid 1301 through 1313)) selection = (chain 'C' and (resid 26 through 480 or (resid 481 and (name N or name CA or nam \ e C or name O or name CB )) or resid 489 through 675 or resid 691 through 1149 o \ r resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 128 5.16 5 C 16909 2.51 5 N 4328 2.21 5 O 5128 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 group one per residue 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: 1.000 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: 0.030 Extract box with map and model: 6.340 Check model and map are aligned: 0.490 Process input model: 71.370 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.280 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.013 1.664 27065 Z= 0.980 Angle : 1.037 80.851 36794 Z= 0.641 Chirality : 0.056 0.545 4291 Planarity : 0.006 0.243 4695 Dihedral : 14.743 108.554 9733 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 29.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.61 % Favored : 80.27 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.19 % 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: -5.63 (0.11), residues: 3228 helix: -3.39 (0.13), residues: 708 sheet: -3.47 (0.19), residues: 496 loop : -4.19 (0.11), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 335 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 345 average time/residue: 0.4221 time to fit residues: 225.0922 Evaluate side-chains 164 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 3.310 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2314 time to fit residues: 5.3102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 196 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 437 ASN C 460 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1005 GLN C1054 GLN C1064 HIS ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 27065 Z= 0.366 Angle : 0.804 20.822 36794 Z= 0.416 Chirality : 0.052 0.490 4291 Planarity : 0.005 0.063 4695 Dihedral : 8.346 109.059 3785 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.66 % Favored : 87.28 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.12), residues: 3230 helix: -2.18 (0.16), residues: 761 sheet: -2.93 (0.20), residues: 491 loop : -3.65 (0.12), residues: 1978 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 248 average time/residue: 0.3907 time to fit residues: 155.7689 Evaluate side-chains 161 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2193 time to fit residues: 6.3678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 246 optimal weight: 0.3980 chunk 201 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 320 optimal weight: 0.3980 chunk 264 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 450 ASN B 644 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 501 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 690 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 27065 Z= 0.198 Angle : 0.690 18.863 36794 Z= 0.353 Chirality : 0.050 0.885 4291 Planarity : 0.005 0.075 4695 Dihedral : 7.794 108.956 3785 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.94 % Favored : 90.00 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.83 (0.13), residues: 3230 helix: -1.40 (0.17), residues: 761 sheet: -2.45 (0.21), residues: 502 loop : -3.21 (0.12), residues: 1967 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 280 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 281 average time/residue: 0.4278 time to fit residues: 192.9911 Evaluate side-chains 167 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.076 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 297 optimal weight: 0.7980 chunk 315 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 282 optimal weight: 0.0040 chunk 84 optimal weight: 10.0000 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1083 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 27065 Z= 0.220 Angle : 0.672 18.924 36794 Z= 0.342 Chirality : 0.049 0.803 4291 Planarity : 0.004 0.069 4695 Dihedral : 7.654 109.008 3785 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.43 % Favored : 89.54 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.19 % 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: -3.52 (0.13), residues: 3230 helix: -1.10 (0.18), residues: 755 sheet: -2.24 (0.21), residues: 517 loop : -3.03 (0.13), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 250 average time/residue: 0.3933 time to fit residues: 159.2918 Evaluate side-chains 159 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 27065 Z= 0.235 Angle : 0.671 18.828 36794 Z= 0.342 Chirality : 0.049 0.785 4291 Planarity : 0.004 0.068 4695 Dihedral : 7.590 109.024 3785 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % 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: -3.34 (0.13), residues: 3230 helix: -0.87 (0.18), residues: 745 sheet: -2.14 (0.20), residues: 532 loop : -2.94 (0.13), residues: 1953 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 3.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3924 time to fit residues: 144.5542 Evaluate side-chains 150 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 26 optimal weight: 0.0670 chunk 104 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 27065 Z= 0.214 Angle : 0.664 18.866 36794 Z= 0.335 Chirality : 0.047 0.442 4291 Planarity : 0.004 0.066 4695 Dihedral : 7.505 108.936 3785 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.19 % 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: -3.15 (0.14), residues: 3230 helix: -0.70 (0.18), residues: 745 sheet: -1.84 (0.21), residues: 528 loop : -2.88 (0.13), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.3762 time to fit residues: 141.3791 Evaluate side-chains 156 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 0.0970 chunk 35 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 265 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN A 644 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 27065 Z= 0.177 Angle : 0.640 18.787 36794 Z= 0.322 Chirality : 0.046 0.443 4291 Planarity : 0.004 0.062 4695 Dihedral : 7.334 108.663 3785 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.19 % 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: -2.85 (0.14), residues: 3230 helix: -0.44 (0.19), residues: 751 sheet: -1.62 (0.22), residues: 496 loop : -2.70 (0.13), residues: 1983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.3822 time to fit residues: 152.3029 Evaluate side-chains 153 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 246 optimal weight: 0.2980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A 690 GLN A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 27065 Z= 0.186 Angle : 0.647 17.289 36794 Z= 0.325 Chirality : 0.047 0.450 4291 Planarity : 0.004 0.069 4695 Dihedral : 7.325 108.602 3785 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.72 (0.14), residues: 3230 helix: -0.32 (0.19), residues: 749 sheet: -1.64 (0.22), residues: 517 loop : -2.60 (0.13), residues: 1964 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.3770 time to fit residues: 142.8155 Evaluate side-chains 151 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 264 optimal weight: 0.1980 chunk 276 optimal weight: 4.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 27065 Z= 0.198 Angle : 0.655 17.612 36794 Z= 0.329 Chirality : 0.047 0.452 4291 Planarity : 0.004 0.063 4695 Dihedral : 7.334 108.626 3785 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.63 (0.14), residues: 3230 helix: -0.23 (0.19), residues: 753 sheet: -1.57 (0.21), residues: 545 loop : -2.55 (0.13), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3654 time to fit residues: 132.8568 Evaluate side-chains 149 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 146 optimal weight: 0.4980 chunk 215 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 27065 Z= 0.265 Angle : 0.695 17.670 36794 Z= 0.352 Chirality : 0.048 0.451 4291 Planarity : 0.005 0.065 4695 Dihedral : 7.450 108.906 3785 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.66 (0.14), residues: 3230 helix: -0.34 (0.19), residues: 755 sheet: -1.44 (0.23), residues: 469 loop : -2.57 (0.13), residues: 2006 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3691 time to fit residues: 129.8719 Evaluate side-chains 146 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 265 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.089827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069395 restraints weight = 110593.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067831 restraints weight = 141542.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068320 restraints weight = 138229.475| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 27065 Z= 0.266 Angle : 0.703 17.633 36794 Z= 0.355 Chirality : 0.048 0.447 4291 Planarity : 0.005 0.069 4695 Dihedral : 7.500 109.075 3785 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % 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: -2.67 (0.14), residues: 3230 helix: -0.36 (0.18), residues: 758 sheet: -1.41 (0.23), residues: 471 loop : -2.58 (0.13), residues: 2001 =============================================================================== Job complete usr+sys time: 4261.51 seconds wall clock time: 80 minutes 26.14 seconds (4826.14 seconds total)