Starting phenix.real_space_refine on Tue Nov 21 20:46:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/11_2023/7wob_32647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/11_2023/7wob_32647.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/7wob_32647/11_2023/7wob_32647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/11_2023/7wob_32647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/11_2023/7wob_32647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/11_2023/7wob_32647.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 144 5.16 5 C 22315 2.51 5 N 5867 2.21 5 O 6808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 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 GLU 406": "OE1" <-> "OE2" 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 "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" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I 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: 35134 Number of models: 1 Model: "" Number of chains: 12 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: "H" 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: "I" 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 17.21, per 1000 atoms: 0.49 Number of scatterers: 35134 At special positions: 0 Unit cell: (207.46, 193.52, 223.04, 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 144 16.00 O 6808 8.00 N 5867 7.00 C 22315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 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 616 " " NAG E1307 " - " ASN E 709 " " NAG E1308 " - " ASN E 717 " " NAG E1309 " - " ASN E 801 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " Time building additional restraints: 12.69 Conformation dependent library (CDL) restraints added in 6.4 seconds 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 83 sheets defined 16.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.698A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.199A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.543A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) 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 removed outlier: 3.594A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.653A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.897A 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 337 through 343 removed outlier: 4.001A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.798A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.906A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.815A 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 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 783 removed outlier: 3.651A 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 891 removed outlier: 4.031A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.224A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.000A 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 1033 removed outlier: 5.276A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.765A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.778A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 390' Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.761A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 407' Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.793A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.685A pdb=" N LEU E 754 " --> pdb=" O SER E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 783 removed outlier: 3.599A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.817A 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 884 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.324A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 965 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 removed outlier: 4.721A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.567A pdb=" N GLN B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'G' and resid 29 through 32 removed outlier: 4.335A pdb=" N ARG G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.543A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.675A pdb=" N LYS G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.009A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 165 Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'I' and resid 186 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.895A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.524A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AA8, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.232A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.686A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.807A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.579A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.227A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.081A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.868A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.868A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.372A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.965A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.481A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AC6, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AC7, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.658A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.173A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.843A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.695A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.632A pdb=" N PHE C 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.871A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.814A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.140A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.997A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.551A pdb=" N PHE E 55 " --> pdb=" O GLN E 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 65 through 68 removed outlier: 3.659A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.514A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 224 through 230 removed outlier: 3.592A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 127 through 129 removed outlier: 4.292A pdb=" N ILE E 128 " --> pdb=" O TYR E 170 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 135 through 140 removed outlier: 10.827A pdb=" N ASP E 138 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N TYR E 160 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 140 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 151 through 153 removed outlier: 3.591A pdb=" N SER E 151 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS E 146 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.388A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 325 through 327 removed outlier: 3.574A pdb=" N GLY E 548 " --> pdb=" O PHE E 541 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.688A pdb=" N SER E 514 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AF7, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.131A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 673 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 711 through 722 removed outlier: 7.072A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 711 through 722 removed outlier: 7.072A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 725 through 728 Processing sheet with id=AG2, first strand: chain 'E' and resid 733 through 735 removed outlier: 4.098A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.671A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.695A pdb=" N VAL D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 83 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.570A pdb=" N ARG D 50 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 144 through 148 removed outlier: 4.021A pdb=" N SER D 187 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 157 through 160 removed outlier: 3.527A pdb=" N THR D 158 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.539A pdb=" N PHE B 72 " --> pdb=" O CYS B 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.561A pdb=" N LEU B 13 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.561A pdb=" N LEU B 13 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR B 98 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.501A pdb=" N SER B 115 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 138 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR B 174 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AH4, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.743A pdb=" N VAL F 20 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET F 81 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.545A pdb=" N ILE F 57 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU F 46 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 92 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 127 through 129 removed outlier: 4.046A pdb=" N LYS F 150 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS F 147 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER F 187 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 188 " --> pdb=" O HIS F 171 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 157 through 159 Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.789A pdb=" N LEU G 11 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 13 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.546A pdb=" N ALA G 19 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.590A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AI3, first strand: chain 'G' and resid 146 through 149 removed outlier: 4.234A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 198 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN G 148 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU G 196 " --> pdb=" O GLN G 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'H' and resid 20 through 23 Processing sheet with id=AI5, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.981A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL H 37 " --> pdb=" O PHE H 95 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 170 through 172 removed outlier: 3.666A pdb=" N HIS H 171 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AI8, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.645A pdb=" N ALA I 19 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS I 23 " --> pdb=" O PHE I 72 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE I 72 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 36 through 37 removed outlier: 7.027A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 86 through 87 Processing sheet with id=AJ2, first strand: chain 'I' and resid 146 through 148 992 hydrogen bonds defined for protein. 2673 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: 16.49 Time building geometry restraints manager: 13.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11275 1.34 - 1.46: 8654 1.46 - 1.58: 15838 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 35947 Sorted by residual: bond pdb=" C PHE D 153 " pdb=" N PRO D 154 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.12e-02 7.97e+03 7.25e+00 bond pdb=" C PHE F 153 " pdb=" N PRO F 154 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.12e-02 7.97e+03 6.34e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 35942 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.18: 1177 107.18 - 113.88: 20148 113.88 - 120.58: 12840 120.58 - 127.28: 14427 127.28 - 133.98: 349 Bond angle restraints: 48941 Sorted by residual: angle pdb=" N GLN I 125 " pdb=" CA GLN I 125 " pdb=" C GLN I 125 " ideal model delta sigma weight residual 114.56 110.71 3.85 1.27e+00 6.20e-01 9.21e+00 angle pdb=" C PRO D 154 " pdb=" N GLU D 155 " pdb=" CA GLU D 155 " ideal model delta sigma weight residual 120.26 124.30 -4.04 1.34e+00 5.57e-01 9.11e+00 angle pdb=" N LYS E 97 " pdb=" CA LYS E 97 " pdb=" C LYS E 97 " ideal model delta sigma weight residual 114.56 110.87 3.69 1.27e+00 6.20e-01 8.45e+00 angle pdb=" C ASP E 290 " pdb=" N CYS E 291 " pdb=" CA CYS E 291 " ideal model delta sigma weight residual 121.54 126.29 -4.75 1.91e+00 2.74e-01 6.19e+00 angle pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.13e+00 ... (remaining 48936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 20120 16.82 - 33.63: 783 33.63 - 50.45: 161 50.45 - 67.26: 38 67.26 - 84.08: 9 Dihedral angle restraints: 21111 sinusoidal: 8115 harmonic: 12996 Sorted by residual: dihedral pdb=" CA LYS A 150 " pdb=" C LYS A 150 " pdb=" N SER A 151 " pdb=" CA SER A 151 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA THR C 73 " pdb=" C THR C 73 " pdb=" N ASN C 74 " pdb=" CA ASN C 74 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " ideal model delta sinusoidal sigma weight residual 79.00 5.89 73.11 1 2.00e+01 2.50e-03 1.70e+01 ... (remaining 21108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4872 0.058 - 0.116: 751 0.116 - 0.174: 26 0.174 - 0.232: 0 0.232 - 0.290: 1 Chirality restraints: 5650 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2 NAG E1312 " pdb=" C1 NAG E1312 " pdb=" C3 NAG E1312 " pdb=" N2 NAG E1312 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 5647 not shown) Planarity restraints: 6325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 44 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO G 45 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO G 45 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 45 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 986 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO C 986 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.017 5.00e-02 4.00e+02 ... (remaining 6322 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6048 2.77 - 3.31: 32441 3.31 - 3.84: 57642 3.84 - 4.37: 66237 4.37 - 4.90: 116494 Nonbonded interactions: 278862 Sorted by model distance: nonbonded pdb=" OG1 THR E1100 " pdb=" O7 NAG E1311 " model vdw 2.243 2.440 nonbonded pdb=" O GLN E 498 " pdb=" ND2 ASN E 501 " model vdw 2.256 2.520 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.282 2.520 nonbonded pdb=" OD1 ASN B 138 " pdb=" OG SER B 175 " model vdw 2.283 2.440 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.288 2.440 ... (remaining 278857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1147 or resid 1301 through 1312)) selection = (chain 'C' and (resid 14 through 1147 or resid 1301 through 1312)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.570 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 90.590 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.049 35947 Z= 0.157 Angle : 0.468 6.205 48941 Z= 0.250 Chirality : 0.041 0.290 5650 Planarity : 0.003 0.035 6287 Dihedral : 9.198 84.077 12597 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.57 % Allowed : 7.23 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.11), residues: 4428 helix: 0.82 (0.20), residues: 649 sheet: -2.81 (0.15), residues: 936 loop : -3.32 (0.09), residues: 2843 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 864 time to evaluate : 3.918 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 24 residues processed: 981 average time/residue: 0.5033 time to fit residues: 775.0158 Evaluate side-chains 448 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 424 time to evaluate : 3.742 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.3176 time to fit residues: 19.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 30.0000 chunk 336 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 0.0870 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 23 GLN A 49 HIS A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 164 ASN A 173 GLN A 207 HIS A 245 HIS A 439 ASN A 440 ASN A 498 GLN A 540 ASN A 644 GLN A 774 GLN A 784 GLN A 872 GLN A 926 GLN A 954 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1048 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 66 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 148 ASN C 149 ASN C 218 GLN C 394 ASN C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 690 GLN C 762 GLN C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS E 14 GLN E 23 GLN E 148 ASN E 149 ASN E 196 ASN E 207 HIS E 218 GLN E 334 ASN ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 690 GLN E 755 GLN E 762 GLN E 784 GLN E 907 ASN E 969 ASN E1002 GLN E1005 GLN E1048 HIS E1106 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 39 GLN D 62 GLN D 112 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN F 6 GLN F 39 GLN F 104 GLN F 112 GLN F 171 HIS G 27 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 148 GLN G 159 ASN G 161 GLN H 1 GLN H 3 GLN H 39 GLN H 65 GLN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 206 ASN I 90 GLN I 156 GLN I 161 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 35947 Z= 0.439 Angle : 0.726 12.042 48941 Z= 0.364 Chirality : 0.049 0.282 5650 Planarity : 0.005 0.052 6287 Dihedral : 3.989 31.643 4803 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.55 % Allowed : 13.10 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.18 (0.11), residues: 4428 helix: 1.12 (0.20), residues: 635 sheet: -2.29 (0.15), residues: 1054 loop : -3.00 (0.10), residues: 2739 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 451 time to evaluate : 3.912 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 outliers start: 136 outliers final: 73 residues processed: 560 average time/residue: 0.5137 time to fit residues: 457.1450 Evaluate side-chains 429 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 356 time to evaluate : 3.916 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 73 outliers final: 1 residues processed: 73 average time/residue: 0.3272 time to fit residues: 50.4416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 403 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 chunk 359 optimal weight: 0.8980 chunk 400 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 324 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 762 GLN A 992 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 30 ASN ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 969 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 31 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35947 Z= 0.303 Angle : 0.616 9.478 48941 Z= 0.308 Chirality : 0.046 0.302 5650 Planarity : 0.004 0.052 6287 Dihedral : 4.019 32.135 4803 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.50 % Favored : 92.48 % Rotamer: Outliers : 2.40 % Allowed : 14.96 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.84 (0.12), residues: 4428 helix: 1.43 (0.21), residues: 629 sheet: -2.00 (0.15), residues: 1048 loop : -2.80 (0.10), residues: 2751 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 361 time to evaluate : 3.962 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 outliers start: 92 outliers final: 35 residues processed: 442 average time/residue: 0.5107 time to fit residues: 361.9770 Evaluate side-chains 360 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 325 time to evaluate : 3.828 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.3263 time to fit residues: 26.7663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 405 optimal weight: 8.9990 chunk 429 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 384 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 388 ASN A 540 ASN A 542 ASN A 613 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1002 GLN E 450 ASN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN B 125 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 31 ASN G 33 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 35947 Z= 0.486 Angle : 0.717 11.067 48941 Z= 0.363 Chirality : 0.049 0.288 5650 Planarity : 0.005 0.058 6287 Dihedral : 4.624 34.165 4803 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.55 % Favored : 89.43 % Rotamer: Outliers : 2.95 % Allowed : 16.03 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.83 (0.12), residues: 4428 helix: 1.08 (0.20), residues: 626 sheet: -1.92 (0.15), residues: 1075 loop : -2.73 (0.10), residues: 2727 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 350 time to evaluate : 3.910 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: 113 outliers final: 56 residues processed: 446 average time/residue: 0.5338 time to fit residues: 375.5105 Evaluate side-chains 356 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 300 time to evaluate : 3.881 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 56 outliers final: 1 residues processed: 56 average time/residue: 0.3308 time to fit residues: 39.6999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 296 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 385 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 613 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 439 ASN C 440 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 245 HIS ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 ASN E1054 GLN D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 112 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35947 Z= 0.228 Angle : 0.596 12.299 48941 Z= 0.298 Chirality : 0.045 0.454 5650 Planarity : 0.004 0.076 6287 Dihedral : 4.331 30.569 4803 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.43 % Rotamer: Outliers : 1.83 % Allowed : 17.20 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.53 (0.12), residues: 4428 helix: 1.49 (0.21), residues: 629 sheet: -1.63 (0.15), residues: 1074 loop : -2.63 (0.11), residues: 2725 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 350 time to evaluate : 4.066 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 outliers start: 70 outliers final: 31 residues processed: 400 average time/residue: 0.5349 time to fit residues: 337.9405 Evaluate side-chains 331 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 300 time to evaluate : 3.889 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.3230 time to fit residues: 24.1121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 0.3980 chunk 386 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 429 optimal weight: 20.0000 chunk 356 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 164 ASN E 271 GLN E 414 GLN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 ASN ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 35947 Z= 0.404 Angle : 0.670 14.071 48941 Z= 0.336 Chirality : 0.047 0.302 5650 Planarity : 0.005 0.064 6287 Dihedral : 4.619 30.674 4803 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.09 % Favored : 89.88 % Rotamer: Outliers : 1.88 % Allowed : 17.44 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.57 (0.12), residues: 4428 helix: 1.28 (0.21), residues: 628 sheet: -1.65 (0.15), residues: 1081 loop : -2.61 (0.11), residues: 2719 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 320 time to evaluate : 3.963 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: 72 outliers final: 33 residues processed: 374 average time/residue: 0.5342 time to fit residues: 315.8306 Evaluate side-chains 331 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 298 time to evaluate : 4.386 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.3465 time to fit residues: 27.3579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 313 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 361 optimal weight: 0.1980 chunk 239 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 ASN D 162 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 35947 Z= 0.272 Angle : 0.604 12.628 48941 Z= 0.304 Chirality : 0.045 0.274 5650 Planarity : 0.004 0.053 6287 Dihedral : 4.507 41.552 4803 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.18 % Favored : 91.80 % Rotamer: Outliers : 1.17 % Allowed : 18.45 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.38 (0.12), residues: 4428 helix: 1.52 (0.21), residues: 628 sheet: -1.53 (0.15), residues: 1096 loop : -2.51 (0.11), residues: 2704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 324 time to evaluate : 3.925 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 outliers start: 45 outliers final: 23 residues processed: 361 average time/residue: 0.5362 time to fit residues: 305.3814 Evaluate side-chains 323 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 300 time to evaluate : 4.121 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.3434 time to fit residues: 20.0029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5036 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: