Starting phenix.real_space_refine (version: dev) on Tue Feb 28 05:47:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/02_2023/7woa_32646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/02_2023/7woa_32646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/02_2023/7woa_32646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/02_2023/7woa_32646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/02_2023/7woa_32646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/02_2023/7woa_32646.pdb" } resolution = 3.25 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= 0.002 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 "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 457": "NH1" <-> "NH2" Residue "E ARG 466": "NH1" <-> "NH2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 41": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" 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: 31952 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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 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: "E" 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: 17.18, per 1000 atoms: 0.54 Number of scatterers: 31952 At special positions: 0 Unit cell: (170.56, 194.34, 222.22, 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 134 16.00 O 6193 8.00 N 5321 7.00 C 20304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1098 " " NAG C1313 " - " ASN C1134 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 165 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 343 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 709 " " NAG E1309 " - " ASN E 717 " " NAG E1310 " - " ASN E 801 " " NAG E1311 " - " ASN E1074 " " NAG E1312 " - " ASN E1098 " " NAG E1313 " - " ASN E1134 " Time building additional restraints: 11.87 Conformation dependent library (CDL) restraints added in 5.0 seconds 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7578 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 67 sheets defined 18.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.833A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.754A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.984A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.311A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.616A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.539A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.835A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.815A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.655A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.548A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.735A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.557A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.705A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.506A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.360A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.517A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.752A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.630A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 4.205A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.758A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.800A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.582A pdb=" N LEU E 754 " --> pdb=" O SER E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.604A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE E 782 " --> pdb=" O THR E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 910 removed outlier: 3.617A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.327A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.562A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.849A pdb=" N GLN D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.678A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.576A pdb=" N SER B 128 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.051A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.607A pdb=" N LYS G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 removed outlier: 3.540A pdb=" N GLU G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.595A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.595A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.014A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 3.662A pdb=" N THR A 167 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 154 removed outlier: 4.542A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.528A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.661A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.922A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.594A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.811A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.811A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.805A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.725A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.935A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC4, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.778A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.227A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 326 removed outlier: 5.243A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE C 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 396 through 402 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.738A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 722 removed outlier: 6.931A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.631A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.302A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.262A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 27 through 29 removed outlier: 3.570A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 36 through 37 removed outlier: 7.063A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 189 " --> pdb=" O THR E 208 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 48 through 51 removed outlier: 6.343A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.904A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 119 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 151 through 157 removed outlier: 4.430A pdb=" N SER E 151 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS E 146 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.173A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.844A pdb=" N ILE E 358 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 512 " --> pdb=" O ASP E 398 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 510 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'E' and resid 565 through 566 removed outlier: 3.613A pdb=" N GLY E 566 " --> pdb=" O ALA E 575 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.039A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 673 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 711 through 722 removed outlier: 7.052A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 725 through 728 Processing sheet with id=AF3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.207A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.689A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.623A pdb=" N ILE D 57 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP D 36 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 116 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 127 through 129 removed outlier: 4.036A pdb=" N LYS D 150 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 148 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 149 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.667A pdb=" N LEU D 145 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D 188 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS D 171 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.573A pdb=" N LYS D 216 " --> pdb=" O CYS D 203 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.112A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 76 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.112A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.503A pdb=" N LEU B 13 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.747A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.604A pdb=" N PHE B 117 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B 174 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AG7, first strand: chain 'F' and resid 18 through 23 removed outlier: 4.051A pdb=" N VAL F 18 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 45 through 51 removed outlier: 3.507A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 97 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 37 " --> pdb=" O PHE F 95 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.916A pdb=" N LEU F 148 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS F 147 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER F 187 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 149 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL F 188 " --> pdb=" O HIS F 171 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS F 171 " --> pdb=" O VAL F 188 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.526A pdb=" N SER G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR G 50 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN G 91 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AH3, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.996A pdb=" N LEU G 176 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 146 through 149 957 hydrogen bonds defined for protein. 2598 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: 18.64 Time building geometry restraints manager: 12.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10243 1.34 - 1.46: 7593 1.46 - 1.58: 14686 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 32690 Sorted by residual: bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.333 1.350 -0.017 7.80e-03 1.64e+04 4.68e+00 bond pdb=" C TYR G 141 " pdb=" N PRO G 142 " ideal model delta sigma weight residual 1.333 1.353 -0.020 1.01e-02 9.80e+03 3.75e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.20e+00 bond pdb=" C ASP E1139 " pdb=" O ASP E1139 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.77e+00 bond pdb=" C GLN E 607 " pdb=" O GLN E 607 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.17e-02 7.31e+03 1.22e+00 ... (remaining 32685 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 1108 107.24 - 113.93: 18403 113.93 - 120.61: 11871 120.61 - 127.30: 12831 127.30 - 133.99: 300 Bond angle restraints: 44513 Sorted by residual: angle pdb=" N PRO D 156 " pdb=" CA PRO D 156 " pdb=" C PRO D 156 " ideal model delta sigma weight residual 114.68 110.65 4.03 1.28e+00 6.10e-01 9.92e+00 angle pdb=" CA PRO D 156 " pdb=" C PRO D 156 " pdb=" O PRO D 156 " ideal model delta sigma weight residual 118.29 121.11 -2.82 9.60e-01 1.09e+00 8.64e+00 angle pdb=" C PRO F 154 " pdb=" N GLU F 155 " pdb=" CA GLU F 155 " ideal model delta sigma weight residual 120.97 124.89 -3.92 1.48e+00 4.57e-01 7.01e+00 angle pdb=" C VAL G 151 " pdb=" N ASP G 152 " pdb=" CA ASP G 152 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 angle pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.17e+00 ... (remaining 44508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 18591 17.69 - 35.38: 650 35.38 - 53.07: 106 53.07 - 70.76: 29 70.76 - 88.45: 8 Dihedral angle restraints: 19384 sinusoidal: 7591 harmonic: 11793 Sorted by residual: dihedral pdb=" CA VAL G 151 " pdb=" C VAL G 151 " pdb=" N ASP G 152 " pdb=" CA ASP G 152 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU D 155 " pdb=" C GLU D 155 " pdb=" N PRO D 156 " pdb=" CA PRO D 156 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " ideal model delta sinusoidal sigma weight residual 79.00 5.67 73.33 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 19381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3497 0.031 - 0.063: 1059 0.063 - 0.094: 322 0.094 - 0.126: 267 0.126 - 0.157: 11 Chirality restraints: 5156 Sorted by residual: chirality pdb=" C1 NAG E1302 " pdb=" ND2 ASN E 165 " pdb=" C2 NAG E1302 " pdb=" O5 NAG E1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 61 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" C1 NAG E1313 " pdb=" ND2 ASN E1134 " pdb=" C2 NAG E1313 " pdb=" O5 NAG E1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 5153 not shown) Planarity restraints: 5756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 80 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 81 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 119 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 120 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO D 156 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.029 5.00e-02 4.00e+02 ... (remaining 5753 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4650 2.76 - 3.30: 29897 3.30 - 3.83: 52760 3.83 - 4.37: 60605 4.37 - 4.90: 107117 Nonbonded interactions: 255029 Sorted by model distance: nonbonded pdb=" OE1 GLU G 106 " pdb=" OH TYR G 174 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR G 37 " pdb=" OE1 GLN G 90 " model vdw 2.243 2.440 nonbonded pdb=" OE1 GLU E 406 " pdb=" OH TYR E 495 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASN E 122 " pdb=" OG1 THR E 124 " model vdw 2.255 2.440 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.269 2.440 ... (remaining 255024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 20304 2.51 5 N 5321 2.21 5 O 6193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.260 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: 0.000 Extract box with map and model: 13.050 Check model and map are aligned: 0.470 Process input model: 86.990 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.310 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.002 0.052 32690 Z= 0.111 Angle : 0.418 6.149 44513 Z= 0.234 Chirality : 0.040 0.157 5156 Planarity : 0.004 0.052 5717 Dihedral : 8.911 88.449 11656 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 4.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.12), residues: 4020 helix: 0.65 (0.20), residues: 681 sheet: -2.47 (0.16), residues: 866 loop : -3.30 (0.10), residues: 2473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 782 time to evaluate : 4.037 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 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: 147 outliers final: 27 residues processed: 877 average time/residue: 0.4874 time to fit residues: 665.6526 Evaluate side-chains 398 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 371 time to evaluate : 3.679 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.4001 time to fit residues: 23.1537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 365 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 69 HIS A 134 GLN A 137 ASN A 149 ASN A 173 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 218 GLN A 245 HIS A 439 ASN A 493 GLN A 498 GLN A 607 GLN A 613 GLN A 658 ASN A 762 GLN A 784 GLN A 872 GLN A 901 GLN A 926 GLN A 992 GLN A1005 GLN A1048 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN C 14 GLN C 23 GLN C 115 GLN C 149 ASN C 173 GLN C 188 ASN C 211 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 360 ASN C 394 ASN C 414 GLN C 439 ASN C 498 GLN C 613 GLN C 787 GLN C 901 GLN C 954 GLN C 957 GLN C 965 GLN C1048 HIS E 218 GLN E 394 ASN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN E 474 GLN E 493 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 ASN E 655 HIS E 675 GLN E 703 ASN E 755 GLN E 762 GLN E 784 GLN E 949 GLN E 954 GLN E1002 GLN E1011 GLN E1048 HIS E1106 GLN D 1 GLN D 6 GLN D 31 ASN D 39 GLN D 162 ASN B 27 GLN B 30 ASN B 31 ASN B 190 HIS B 199 HIS B 200 GLN F 59 HIS F 112 GLN F 206 ASN G 33 HIS G 39 GLN G 43 GLN G 159 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.147 32690 Z= 0.421 Angle : 0.720 11.536 44513 Z= 0.377 Chirality : 0.049 0.351 5156 Planarity : 0.005 0.065 5717 Dihedral : 4.439 35.673 4590 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.56 % Favored : 92.41 % Rotamer Outliers : 3.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.02 (0.12), residues: 4020 helix: 0.52 (0.19), residues: 708 sheet: -2.04 (0.16), residues: 908 loop : -2.94 (0.11), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 369 time to evaluate : 3.801 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 revert: symmetry clash outliers start: 130 outliers final: 74 residues processed: 472 average time/residue: 0.4909 time to fit residues: 369.4901 Evaluate side-chains 375 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 301 time to evaluate : 3.580 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 2 residues processed: 74 average time/residue: 0.3074 time to fit residues: 48.0402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 366 optimal weight: 0.3980 chunk 396 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 185 ASN A 919 ASN A1088 HIS C 14 GLN C 115 GLN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS E 414 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 690 GLN E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 206 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 32690 Z= 0.174 Angle : 0.533 8.418 44513 Z= 0.275 Chirality : 0.043 0.386 5156 Planarity : 0.004 0.065 5717 Dihedral : 4.017 37.582 4590 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.54 (0.12), residues: 4020 helix: 1.10 (0.20), residues: 712 sheet: -1.65 (0.16), residues: 933 loop : -2.74 (0.11), residues: 2375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 325 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 35 residues processed: 384 average time/residue: 0.4559 time to fit residues: 282.3606 Evaluate side-chains 316 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 281 time to evaluate : 3.545 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.2805 time to fit residues: 23.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 246 optimal weight: 0.4980 chunk 367 optimal weight: 2.9990 chunk 389 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 334 ASN C 115 GLN C 173 GLN C 354 ASN C 856 ASN C 901 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E 901 GLN E 949 GLN G 159 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 32690 Z= 0.295 Angle : 0.585 9.943 44513 Z= 0.301 Chirality : 0.045 0.343 5156 Planarity : 0.004 0.069 5717 Dihedral : 4.260 45.771 4590 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.43 (0.12), residues: 4020 helix: 1.14 (0.20), residues: 704 sheet: -1.65 (0.16), residues: 939 loop : -2.60 (0.11), residues: 2377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 304 time to evaluate : 3.835 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 outliers start: 74 outliers final: 34 residues processed: 364 average time/residue: 0.4851 time to fit residues: 283.6035 Evaluate side-chains 311 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 3.842 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.3480 time to fit residues: 27.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 290 optimal weight: 0.1980 chunk 160 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 198 optimal weight: 0.6980 chunk 349 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN C 173 GLN C 354 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E 949 GLN G 39 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 32690 Z= 0.163 Angle : 0.524 10.998 44513 Z= 0.267 Chirality : 0.043 0.354 5156 Planarity : 0.004 0.067 5717 Dihedral : 4.114 43.844 4590 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % 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: -2.13 (0.13), residues: 4020 helix: 1.45 (0.20), residues: 702 sheet: -1.40 (0.16), residues: 962 loop : -2.45 (0.11), residues: 2356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 306 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 31 residues processed: 360 average time/residue: 0.4759 time to fit residues: 274.6054 Evaluate side-chains 313 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 3.660 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.3030 time to fit residues: 23.2507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 10.0000 chunk 350 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 389 optimal weight: 9.9990 chunk 323 optimal weight: 0.0770 chunk 180 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS C 149 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 804 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN B 153 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 32690 Z= 0.201 Angle : 0.538 14.318 44513 Z= 0.275 Chirality : 0.044 0.439 5156 Planarity : 0.004 0.069 5717 Dihedral : 4.164 43.177 4590 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % 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: -2.01 (0.13), residues: 4020 helix: 1.50 (0.20), residues: 702 sheet: -1.29 (0.16), residues: 953 loop : -2.36 (0.11), residues: 2365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 4.105 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: 43 outliers final: 12 residues processed: 333 average time/residue: 0.4801 time to fit residues: 257.1100 Evaluate side-chains 289 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 277 time to evaluate : 3.969 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.3703 time to fit residues: 12.7716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 0.0570 chunk 43 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 328 optimal weight: 6.9990 chunk 217 optimal weight: 0.3980 chunk 388 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 901 GLN C 149 ASN C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 949 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 32690 Z= 0.341 Angle : 0.619 12.472 44513 Z= 0.319 Chirality : 0.046 0.383 5156 Planarity : 0.005 0.077 5717 Dihedral : 4.608 43.610 4590 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.08 % 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: -2.15 (0.13), residues: 4020 helix: 1.26 (0.20), residues: 686 sheet: -1.43 (0.16), residues: 978 loop : -2.36 (0.11), residues: 2356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 280 time to evaluate : 3.849 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 outliers start: 53 outliers final: 26 residues processed: 320 average time/residue: 0.4921 time to fit residues: 252.1266 Evaluate side-chains 285 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 259 time to evaluate : 3.648 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.2943 time to fit residues: 19.8023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 305 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN C 149 ASN C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN E 957 GLN F 112 GLN G 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 32690 Z= 0.247 Angle : 0.566 14.865 44513 Z= 0.291 Chirality : 0.044 0.307 5156 Planarity : 0.004 0.083 5717 Dihedral : 4.464 43.283 4590 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % 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: -2.01 (0.13), residues: 4020 helix: 1.37 (0.20), residues: 692 sheet: -1.30 (0.16), residues: 956 loop : -2.30 (0.11), residues: 2372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 273 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 304 average time/residue: 0.4957 time to fit residues: 243.4500 Evaluate side-chains 286 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 264 time to evaluate : 3.917 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.3228 time to fit residues: 18.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 0.0980 chunk 372 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 284 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 149 ASN C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN G 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 32690 Z= 0.253 Angle : 0.574 14.353 44513 Z= 0.296 Chirality : 0.045 0.499 5156 Planarity : 0.004 0.101 5717 Dihedral : 4.454 42.364 4590 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 4020 helix: 1.37 (0.20), residues: 692 sheet: -1.25 (0.16), residues: 944 loop : -2.26 (0.11), residues: 2384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 274 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 293 average time/residue: 0.5441 time to fit residues: 255.2812 Evaluate side-chains 276 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 3.637 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.3742 time to fit residues: 14.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 0.0270 chunk 382 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 266 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 319 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 32690 Z= 0.170 Angle : 0.539 13.383 44513 Z= 0.277 Chirality : 0.044 0.409 5156 Planarity : 0.004 0.069 5717 Dihedral : 4.267 42.484 4590 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -1.73 (0.13), residues: 4020 helix: 1.67 (0.20), residues: 683 sheet: -1.09 (0.16), residues: 967 loop : -2.15 (0.12), residues: 2370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 286 average time/residue: 0.5203 time to fit residues: 241.3203 Evaluate side-chains 263 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 260 time to evaluate : 4.239 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.3469 time to fit residues: 7.6738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 253 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 328 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN D 1 GLN G 39 GLN ** G 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.108428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082127 restraints weight = 78898.845| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.13 r_work: 0.3075 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 32690 Z= 0.279 Angle : 0.586 13.899 44513 Z= 0.302 Chirality : 0.045 0.384 5156 Planarity : 0.004 0.072 5717 Dihedral : 4.413 41.383 4590 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 4020 helix: 1.49 (0.20), residues: 686 sheet: -1.14 (0.16), residues: 981 loop : -2.18 (0.12), residues: 2353 =============================================================================== Job complete usr+sys time: 8411.90 seconds wall clock time: 153 minutes 41.22 seconds (9221.22 seconds total)