Starting phenix.real_space_refine on Sat Dec 16 12:55:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/12_2023/7wob_32647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/12_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_32647/12_2023/7wob_32647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/12_2023/7wob_32647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/12_2023/7wob_32647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/12_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-1.21rc1-5172/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 dihedrals: 39 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 dihedrals: 39 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 18.08, per 1000 atoms: 0.51 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: 14.18 Conformation dependent library (CDL) restraints added in 6.6 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: 4.13 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: 16.59 Time building geometry restraints manager: 15.23 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: 20829 16.82 - 33.63: 830 33.63 - 50.45: 184 50.45 - 67.26: 57 67.26 - 84.08: 9 Dihedral angle restraints: 21909 sinusoidal: 8913 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 21906 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: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.940 Check model and map are aligned: 0.490 Set scattering table: 0.340 Process input model: 93.790 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.320 ------------------------------------------------------------------------------- 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 : 9.465 84.077 13395 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 152 HIS 0.002 0.000 HIS C 655 PHE 0.010 0.001 PHE E 562 TYR 0.007 0.000 TYR E 265 ARG 0.002 0.000 ARG C 273 *********************** 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 : 4.051 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: 0.5077 time to fit residues: 782.2278 Evaluate side-chains 448 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 424 time to evaluate : 3.826 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.3222 time to fit residues: 19.8475 ------------------------------------------------------------------------------- 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 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 A1005 GLN A1048 HIS ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN 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 30 ASN 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 Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 35947 Z= 0.425 Angle : 0.729 12.848 48941 Z= 0.364 Chirality : 0.049 0.294 5650 Planarity : 0.005 0.052 6287 Dihedral : 5.935 59.294 5601 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.68 % Allowed : 13.10 % Favored : 83.22 % 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: -3.17 (0.11), residues: 4428 helix: 1.11 (0.21), residues: 630 sheet: -2.30 (0.15), residues: 1039 loop : -2.98 (0.10), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 152 HIS 0.010 0.002 HIS A1064 PHE 0.032 0.003 PHE B 47 TYR 0.024 0.002 TYR A 453 ARG 0.008 0.001 ARG A 158 *********************** 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 590 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 449 time to evaluate : 3.721 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: 141 outliers final: 75 residues processed: 564 average time/residue: 0.5148 time to fit residues: 463.6173 Evaluate side-chains 426 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 351 time to evaluate : 4.326 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 75 outliers final: 1 residues processed: 75 average time/residue: 0.3497 time to fit residues: 54.9519 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 3.9990 chunk 335 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 403 optimal weight: 20.0000 chunk 436 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 400 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 122 ASN A 644 GLN A 762 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 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** 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 B 125 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35947 Z= 0.349 Angle : 0.637 9.485 48941 Z= 0.321 Chirality : 0.047 0.257 5650 Planarity : 0.005 0.057 6287 Dihedral : 5.697 59.225 5601 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.88 % Favored : 92.10 % Rotamer: Outliers : 2.43 % Allowed : 15.11 % Favored : 82.46 % 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: -2.87 (0.12), residues: 4428 helix: 1.30 (0.21), residues: 629 sheet: -1.99 (0.15), residues: 1047 loop : -2.81 (0.10), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 886 HIS 0.009 0.001 HIS B 190 PHE 0.043 0.002 PHE E 65 TYR 0.020 0.002 TYR C 265 ARG 0.006 0.001 ARG A 158 *********************** 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 455 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 362 time to evaluate : 3.945 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: 93 outliers final: 37 residues processed: 444 average time/residue: 0.5388 time to fit residues: 381.8877 Evaluate side-chains 365 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 3.955 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.3510 time to fit residues: 29.3288 ------------------------------------------------------------------------------- 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: 7.9990 chunk 303 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 405 optimal weight: 10.0000 chunk 429 optimal weight: 6.9990 chunk 211 optimal weight: 0.1980 chunk 384 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 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** E 245 HIS E 450 ASN E 506 GLN E 969 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 33 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35947 Z= 0.273 Angle : 0.590 9.967 48941 Z= 0.296 Chirality : 0.045 0.436 5650 Planarity : 0.004 0.057 6287 Dihedral : 5.579 59.295 5601 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.32 % Allowed : 16.03 % Favored : 81.65 % 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: -2.60 (0.12), residues: 4428 helix: 1.54 (0.21), residues: 628 sheet: -1.73 (0.15), residues: 1056 loop : -2.68 (0.10), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 106 HIS 0.006 0.001 HIS H 171 PHE 0.037 0.002 PHE E 65 TYR 0.018 0.001 TYR C 265 ARG 0.009 0.001 ARG H 98 *********************** 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 453 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 364 time to evaluate : 4.356 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: 89 outliers final: 44 residues processed: 436 average time/residue: 0.5421 time to fit residues: 372.3221 Evaluate side-chains 364 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 3.941 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 2 residues processed: 44 average time/residue: 0.3438 time to fit residues: 32.9855 ------------------------------------------------------------------------------- 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: 6.9990 chunk 243 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 10.0000 chunk 296 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 613 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C1002 GLN E 245 HIS ** E1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 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 91 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 35947 Z= 0.425 Angle : 0.679 13.115 48941 Z= 0.341 Chirality : 0.048 0.294 5650 Planarity : 0.005 0.073 6287 Dihedral : 6.012 59.635 5601 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.87 % Favored : 90.11 % Rotamer: Outliers : 2.43 % Allowed : 16.86 % Favored : 80.71 % 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: -2.66 (0.12), residues: 4428 helix: 1.18 (0.21), residues: 628 sheet: -1.70 (0.15), residues: 1090 loop : -2.67 (0.11), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 886 HIS 0.014 0.002 HIS I 190 PHE 0.033 0.002 PHE D 153 TYR 0.026 0.002 TYR I 193 ARG 0.007 0.001 ARG I 24 *********************** 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 433 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 340 time to evaluate : 3.973 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 outliers start: 93 outliers final: 51 residues processed: 417 average time/residue: 0.5365 time to fit residues: 353.6311 Evaluate side-chains 352 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 301 time to evaluate : 4.183 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 51 outliers final: 1 residues processed: 51 average time/residue: 0.3520 time to fit residues: 39.6925 ------------------------------------------------------------------------------- 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: 3.9990 chunk 386 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 429 optimal weight: 0.5980 chunk 356 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 225 optimal weight: 0.0270 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 450 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 422 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 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** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 35947 Z= 0.174 Angle : 0.563 13.199 48941 Z= 0.283 Chirality : 0.044 0.255 5650 Planarity : 0.004 0.068 6287 Dihedral : 5.428 58.373 5601 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.11 % Favored : 92.86 % Rotamer: Outliers : 1.15 % Allowed : 17.88 % 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: -2.30 (0.12), residues: 4428 helix: 1.83 (0.21), residues: 623 sheet: -1.45 (0.15), residues: 1086 loop : -2.52 (0.11), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 149 HIS 0.018 0.001 HIS B 190 PHE 0.030 0.001 PHE E 456 TYR 0.019 0.001 TYR B 50 ARG 0.009 0.000 ARG I 78 *********************** 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 399 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 355 time to evaluate : 4.040 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: 44 outliers final: 13 residues processed: 383 average time/residue: 0.5492 time to fit residues: 332.8894 Evaluate side-chains 319 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 306 time to evaluate : 4.006 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.3472 time to fit residues: 14.0022 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 313 optimal weight: 0.0770 chunk 243 optimal weight: 2.9990 chunk 361 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 427 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 260 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 493 GLN E 164 ASN D 3 GLN B 125 GLN ** 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** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35947 Z= 0.235 Angle : 0.574 12.647 48941 Z= 0.288 Chirality : 0.044 0.262 5650 Planarity : 0.004 0.050 6287 Dihedral : 5.419 59.112 5601 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.24 % Favored : 91.73 % Rotamer: Outliers : 1.23 % Allowed : 18.45 % Favored : 80.32 % 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: -2.22 (0.12), residues: 4428 helix: 1.75 (0.21), residues: 635 sheet: -1.32 (0.15), residues: 1095 loop : -2.49 (0.11), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 106 HIS 0.012 0.001 HIS B 190 PHE 0.032 0.001 PHE D 153 TYR 0.021 0.001 TYR H 105 ARG 0.010 0.000 ARG I 62 *********************** 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 371 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 324 time to evaluate : 3.720 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: 47 outliers final: 20 residues processed: 362 average time/residue: 0.5527 time to fit residues: 313.5632 Evaluate side-chains 329 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 309 time to evaluate : 4.190 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.3339 time to fit residues: 18.5393 ------------------------------------------------------------------------------- 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: 10.0000 chunk 170 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 291 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 336 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 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** C 493 GLN E 164 ASN D 3 GLN D 162 ASN B 125 GLN ** 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** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35947 Z= 0.228 Angle : 0.574 12.119 48941 Z= 0.288 Chirality : 0.044 0.253 5650 Planarity : 0.004 0.050 6287 Dihedral : 5.390 59.181 5601 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.20 % Favored : 91.78 % Rotamer: Outliers : 0.97 % Allowed : 18.53 % Favored : 80.50 % 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: -2.16 (0.12), residues: 4428 helix: 1.83 (0.21), residues: 628 sheet: -1.32 (0.16), residues: 1093 loop : -2.43 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 106 HIS 0.010 0.001 HIS B 190 PHE 0.043 0.001 PHE A 140 TYR 0.021 0.001 TYR H 105 ARG 0.008 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 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 361 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 324 time to evaluate : 3.833 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: 37 outliers final: 15 residues processed: 349 average time/residue: 0.5758 time to fit residues: 314.3147 Evaluate side-chains 321 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 306 time to evaluate : 4.084 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.3658 time to fit residues: 15.2483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 20.0000 chunk 409 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 398 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 360 optimal weight: 1.9990 chunk 377 optimal weight: 40.0000 chunk 397 optimal weight: 30.0000 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 613 GLN A 992 GLN ** 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 762 GLN D 3 GLN ** B 200 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** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 35947 Z= 0.335 Angle : 0.628 14.189 48941 Z= 0.315 Chirality : 0.046 0.278 5650 Planarity : 0.004 0.052 6287 Dihedral : 5.673 58.886 5601 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.67 % Favored : 90.31 % Rotamer: Outliers : 0.86 % Allowed : 18.79 % Favored : 80.34 % 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: -2.24 (0.12), residues: 4428 helix: 1.56 (0.21), residues: 635 sheet: -1.30 (0.16), residues: 1079 loop : -2.46 (0.11), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 36 HIS 0.009 0.001 HIS B 190 PHE 0.035 0.002 PHE A 140 TYR 0.022 0.002 TYR E 380 ARG 0.010 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 9 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 359 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 326 time to evaluate : 3.081 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: 33 outliers final: 17 residues processed: 349 average time/residue: 0.4468 time to fit residues: 244.8466 Evaluate side-chains 323 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 306 time to evaluate : 3.079 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.2766 time to fit residues: 12.9439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.5980 chunk 421 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 442 optimal weight: 5.9990 chunk 407 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: