Starting phenix.real_space_refine on Tue Nov 21 00:53:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/11_2023/7woa_32646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/11_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_32646/11_2023/7woa_32646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/11_2023/7woa_32646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/11_2023/7woa_32646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woa_32646/11_2023/7woa_32646.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 15.49, per 1000 atoms: 0.48 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: 12.01 Conformation dependent library (CDL) restraints added in 6.0 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: 3.79 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: 14.18 Time building geometry restraints manager: 13.01 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=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG E1307 " pdb=" O5 NAG E1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+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: 18357 17.69 - 35.38: 650 35.38 - 53.07: 106 53.07 - 70.76: 29 70.76 - 88.45: 8 Dihedral angle restraints: 19150 sinusoidal: 7357 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 19147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3420 0.031 - 0.063: 1097 0.063 - 0.094: 356 0.094 - 0.126: 272 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 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.260 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 82.790 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.220 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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= 0.158 Angle : 0.451 6.149 44513 Z= 0.240 Chirality : 0.041 0.157 5156 Planarity : 0.004 0.052 5717 Dihedral : 8.938 88.449 11422 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.23 % Allowed : 5.58 % Favored : 90.19 % 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 : 3.336 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: 0.4723 time to fit residues: 643.9695 Evaluate side-chains 398 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 371 time to evaluate : 3.509 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.3682 time to fit residues: 21.2857 ------------------------------------------------------------------------------- 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: 3.9990 chunk 235 optimal weight: 6.9990 chunk 365 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 146 HIS 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 A1119 ASN C 14 GLN C 23 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 211 ASN 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 913 GLN C 954 GLN C 957 GLN C 965 GLN C1048 HIS E 218 GLN E 321 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 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: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 32690 Z= 0.395 Angle : 0.693 10.668 44513 Z= 0.353 Chirality : 0.048 0.282 5156 Planarity : 0.005 0.070 5717 Dihedral : 3.850 33.467 4356 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.16 % Favored : 92.81 % Rotamer: Outliers : 3.48 % Allowed : 12.05 % Favored : 84.46 % 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: -2.97 (0.12), residues: 4020 helix: 0.71 (0.20), residues: 701 sheet: -2.01 (0.16), residues: 894 loop : -2.95 (0.10), residues: 2425 *********************** 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 489 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 368 time to evaluate : 3.624 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: 121 outliers final: 66 residues processed: 462 average time/residue: 0.4453 time to fit residues: 330.5458 Evaluate side-chains 370 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 304 time to evaluate : 3.475 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 2 residues processed: 66 average time/residue: 0.2848 time to fit residues: 40.1600 ------------------------------------------------------------------------------- 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: 2.9990 chunk 113 optimal weight: 9.9990 chunk 304 optimal weight: 0.0020 chunk 249 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 366 optimal weight: 0.0970 chunk 396 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 363 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 294 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A1088 HIS C 115 GLN C 149 ASN C 164 ASN 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** C 913 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS 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 710 ASN E 762 GLN E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32690 Z= 0.153 Angle : 0.526 8.574 44513 Z= 0.267 Chirality : 0.043 0.326 5156 Planarity : 0.004 0.064 5717 Dihedral : 3.595 41.142 4356 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.90 % Allowed : 13.61 % Favored : 84.49 % 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: -2.49 (0.12), residues: 4020 helix: 1.25 (0.20), residues: 709 sheet: -1.68 (0.16), residues: 942 loop : -2.70 (0.11), residues: 2369 *********************** 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 405 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 339 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 29 residues processed: 391 average time/residue: 0.4627 time to fit residues: 290.0019 Evaluate side-chains 318 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 289 time to evaluate : 3.215 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.2769 time to fit residues: 19.6490 ------------------------------------------------------------------------------- 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: 10.0000 chunk 275 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 367 optimal weight: 1.9990 chunk 389 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 613 GLN E 762 GLN E 901 GLN B 199 HIS F 171 HIS G 39 GLN G 159 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32690 Z= 0.308 Angle : 0.617 12.774 44513 Z= 0.311 Chirality : 0.046 0.295 5156 Planarity : 0.004 0.069 5717 Dihedral : 4.003 38.612 4356 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.22 % Allowed : 14.67 % Favored : 83.11 % 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: -2.40 (0.12), residues: 4020 helix: 1.11 (0.20), residues: 699 sheet: -1.62 (0.16), residues: 942 loop : -2.55 (0.11), residues: 2379 *********************** 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 381 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 304 time to evaluate : 3.498 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 outliers start: 77 outliers final: 40 residues processed: 368 average time/residue: 0.4581 time to fit residues: 269.0684 Evaluate side-chains 315 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 3.529 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 1 residues processed: 40 average time/residue: 0.2731 time to fit residues: 25.6350 ------------------------------------------------------------------------------- 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: 7.9990 chunk 221 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 290 optimal weight: 0.0770 chunk 160 optimal weight: 0.9980 chunk 332 optimal weight: 0.0170 chunk 269 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN C 149 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 613 GLN E 762 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: 0.7906 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32690 Z= 0.147 Angle : 0.540 20.255 44513 Z= 0.270 Chirality : 0.043 0.301 5156 Planarity : 0.004 0.065 5717 Dihedral : 3.775 42.627 4356 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.93 % Allowed : 15.07 % Favored : 83.00 % 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: -2.10 (0.13), residues: 4020 helix: 1.44 (0.20), residues: 711 sheet: -1.35 (0.16), residues: 960 loop : -2.45 (0.11), residues: 2349 *********************** 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 368 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 301 time to evaluate : 3.464 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: 67 outliers final: 29 residues processed: 357 average time/residue: 0.4533 time to fit residues: 260.3205 Evaluate side-chains 299 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 3.909 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.3402 time to fit residues: 23.8356 ------------------------------------------------------------------------------- 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: 20.0000 chunk 350 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 389 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 204 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 856 ASN C 149 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 613 GLN E 762 GLN B 153 ASN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 32690 Z= 0.270 Angle : 0.590 19.254 44513 Z= 0.298 Chirality : 0.045 0.340 5156 Planarity : 0.004 0.068 5717 Dihedral : 4.033 40.798 4356 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.38 % Allowed : 16.31 % Favored : 82.31 % 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: -2.11 (0.13), residues: 4020 helix: 1.37 (0.20), residues: 695 sheet: -1.39 (0.16), residues: 948 loop : -2.38 (0.11), residues: 2377 *********************** 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 331 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 3.621 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: 48 outliers final: 21 residues processed: 318 average time/residue: 0.4721 time to fit residues: 240.9020 Evaluate side-chains 290 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 269 time to evaluate : 3.497 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.3191 time to fit residues: 17.7250 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 6.9990 chunk 222 optimal weight: 0.0470 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 328 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 173 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** F 112 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32690 Z= 0.279 Angle : 0.593 14.958 44513 Z= 0.299 Chirality : 0.045 0.408 5156 Planarity : 0.004 0.067 5717 Dihedral : 4.191 39.914 4356 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.35 % Allowed : 16.60 % Favored : 82.05 % 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: -2.05 (0.13), residues: 4020 helix: 1.38 (0.20), residues: 687 sheet: -1.30 (0.16), residues: 938 loop : -2.34 (0.11), residues: 2395 *********************** 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 337 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 290 time to evaluate : 3.717 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: 47 outliers final: 22 residues processed: 324 average time/residue: 0.4655 time to fit residues: 241.8803 Evaluate side-chains 292 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 270 time to evaluate : 3.536 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.2855 time to fit residues: 16.7925 ------------------------------------------------------------------------------- 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: 3.9990 chunk 155 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 246 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 305 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 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 ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** 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** ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4583 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= 0.196 Angle : 0.556 12.580 44513 Z= 0.281 Chirality : 0.044 0.406 5156 Planarity : 0.004 0.068 5717 Dihedral : 4.086 39.345 4356 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % 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: -1.91 (0.13), residues: 4020 helix: 1.47 (0.20), residues: 694 sheet: -1.16 (0.16), residues: 945 loop : -2.28 (0.11), residues: 2381 *********************** 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 306 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 299 average time/residue: 0.4844 time to fit residues: 233.6218 Evaluate side-chains 282 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 271 time to evaluate : 3.803 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.3158 time to fit residues: 11.4074 ------------------------------------------------------------------------------- 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: 4.9990 chunk 372 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 361 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 360 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** C 804 GLN ** 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** E 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32690 Z= 0.343 Angle : 0.641 14.236 44513 Z= 0.325 Chirality : 0.046 0.319 5156 Planarity : 0.004 0.071 5717 Dihedral : 4.455 38.274 4356 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.86 % Allowed : 17.38 % Favored : 81.76 % 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: -2.07 (0.12), residues: 4020 helix: 1.18 (0.20), residues: 690 sheet: -1.27 (0.16), residues: 923 loop : -2.31 (0.11), residues: 2407 *********************** 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 308 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 278 time to evaluate : 3.632 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: 30 outliers final: 16 residues processed: 301 average time/residue: 0.4999 time to fit residues: 239.5779 Evaluate side-chains 280 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 3.752 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.3199 time to fit residues: 14.9276 ------------------------------------------------------------------------------- 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: 3.9990 chunk 382 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 266 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 369 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 901 GLN 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 856 ASN ** 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 G 148 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32690 Z= 0.211 Angle : 0.576 12.704 44513 Z= 0.292 Chirality : 0.045 0.466 5156 Planarity : 0.004 0.067 5717 Dihedral : 4.240 38.968 4356 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.26 % Allowed : 17.81 % Favored : 81.93 % 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: -1.92 (0.13), residues: 4020 helix: 1.38 (0.20), residues: 695 sheet: -1.19 (0.16), residues: 947 loop : -2.24 (0.11), residues: 2378 ********************** 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 283 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 282 average time/residue: 0.5063 time to fit residues: 226.8613 Evaluate side-chains 266 residues out of total 3529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 3.731 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3279 time to fit residues: 7.6985 ------------------------------------------------------------------------------- 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: 7.9990 chunk 340 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 320 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- 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** E 149 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.107106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080383 restraints weight = 79962.423| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.01 r_work: 0.3081 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32690 Z= 0.254 Angle : 0.594 12.602 44513 Z= 0.301 Chirality : 0.045 0.377 5156 Planarity : 0.004 0.069 5717 Dihedral : 4.274 38.803 4356 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.37 % Allowed : 17.95 % Favored : 81.67 % 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: -1.91 (0.13), residues: 4020 helix: 1.31 (0.20), residues: 701 sheet: -1.21 (0.16), residues: 965 loop : -2.22 (0.12), residues: 2354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8603.62 seconds wall clock time: 156 minutes 7.16 seconds (9367.16 seconds total)