Starting phenix.real_space_refine on Thu Feb 22 19:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/02_2024/7wob_32647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/02_2024/7wob_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_32647/02_2024/7wob_32647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/02_2024/7wob_32647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/02_2024/7wob_32647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wob_32647/02_2024/7wob_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 18.24, per 1000 atoms: 0.52 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: 13.43 Conformation dependent library (CDL) restraints added in 6.7 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: 4.34 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: 14.99 Time building geometry restraints manager: 14.63 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: 11.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 15.280 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 92.970 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.310 ------------------------------------------------------------------------------- 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 : 3.921 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 REVERT: A 179 LEU cc_start: 0.6855 (mt) cc_final: 0.6650 (tt) REVERT: A 249 LEU cc_start: 0.8291 (mt) cc_final: 0.8085 (mp) REVERT: A 878 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 1127 ASP cc_start: 0.7426 (p0) cc_final: 0.7047 (p0) REVERT: A 1144 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 368 LEU cc_start: 0.8835 (mt) cc_final: 0.8258 (mt) REVERT: C 495 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6615 (t80) REVERT: C 904 TYR cc_start: 0.7468 (m-10) cc_final: 0.7163 (m-10) REVERT: E 150 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6748 (ttpt) REVERT: E 277 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8358 (pp) REVERT: E 747 THR cc_start: 0.8217 (m) cc_final: 0.7921 (p) REVERT: E 878 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8209 (mt) REVERT: E 934 ILE cc_start: 0.8077 (mm) cc_final: 0.7715 (mm) REVERT: B 119 PHE cc_start: 0.4986 (m-80) cc_final: 0.4377 (m-80) REVERT: B 126 LEU cc_start: 0.5409 (mt) cc_final: 0.4811 (tt) REVERT: B 174 TYR cc_start: 0.5439 (m-80) cc_final: 0.5223 (m-10) REVERT: B 184 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7286 (pttm) REVERT: F 80 TYR cc_start: 0.7939 (m-10) cc_final: 0.7726 (m-10) REVERT: H 18 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6438 (m) REVERT: I 88 TYR cc_start: 0.6280 (m-80) cc_final: 0.6033 (m-10) REVERT: I 155 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5866 (tp) outliers start: 175 outliers final: 24 residues processed: 981 average time/residue: 0.4962 time to fit residues: 759.7190 Evaluate side-chains 463 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 431 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 155 LEU 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: 0.6980 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 403 optimal weight: 0.0870 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 23 GLN A 49 HIS A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 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 23 GLN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 134 GLN C 148 ASN C 149 ASN C 218 GLN C 394 ASN C 414 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 690 GLN C 762 GLN C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS E 14 GLN E 23 GLN E 148 ASN E 149 ASN E 196 ASN E 207 HIS E 218 GLN E 334 ASN E 343 ASN ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** 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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 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 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN I 90 GLN I 156 GLN I 161 GLN ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 35947 Z= 0.362 Angle : 0.684 13.183 48941 Z= 0.341 Chirality : 0.047 0.260 5650 Planarity : 0.005 0.050 6287 Dihedral : 6.364 59.265 5654 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.07 % Allowed : 12.11 % Favored : 83.82 % 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: -3.14 (0.11), residues: 4428 helix: 1.21 (0.21), residues: 641 sheet: -2.35 (0.15), residues: 1046 loop : -2.96 (0.10), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 152 HIS 0.009 0.002 HIS H 59 PHE 0.028 0.002 PHE B 47 TYR 0.023 0.002 TYR A 91 ARG 0.008 0.001 ARG C1014 *********************** 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 612 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 456 time to evaluate : 4.382 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: A 249 LEU cc_start: 0.8369 (mt) cc_final: 0.7967 (mp) REVERT: A 1144 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7143 (mm-30) REVERT: C 119 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8990 (mt) REVERT: C 374 PHE cc_start: 0.7779 (m-80) cc_final: 0.7459 (m-80) REVERT: C 904 TYR cc_start: 0.7685 (m-10) cc_final: 0.7367 (m-10) REVERT: C 1050 MET cc_start: 0.8452 (ptm) cc_final: 0.8154 (ptm) REVERT: E 150 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6807 (ttpt) REVERT: E 198 ASP cc_start: 0.6650 (t0) cc_final: 0.6409 (t0) REVERT: E 277 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8560 (pp) REVERT: E 374 PHE cc_start: 0.6643 (m-10) cc_final: 0.6369 (m-10) REVERT: E 735 SER cc_start: 0.8472 (t) cc_final: 0.8151 (p) REVERT: E 747 THR cc_start: 0.8554 (m) cc_final: 0.8153 (p) REVERT: E 756 TYR cc_start: 0.8398 (m-80) cc_final: 0.8181 (m-80) REVERT: E 878 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8369 (mt) REVERT: E 934 ILE cc_start: 0.8576 (mm) cc_final: 0.8184 (mm) REVERT: B 17 GLU cc_start: 0.7570 (mp0) cc_final: 0.7269 (tt0) REVERT: B 126 LEU cc_start: 0.5409 (mt) cc_final: 0.4945 (tp) REVERT: F 151 ASP cc_start: 0.5880 (t0) cc_final: 0.5602 (t0) REVERT: G 104 LYS cc_start: 0.7561 (pptt) cc_final: 0.6475 (pptt) REVERT: H 171 HIS cc_start: 0.4889 (OUTLIER) cc_final: 0.3688 (t-90) REVERT: I 88 TYR cc_start: 0.6602 (m-80) cc_final: 0.6069 (m-10) REVERT: I 155 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5928 (tp) outliers start: 156 outliers final: 89 residues processed: 582 average time/residue: 0.4982 time to fit residues: 459.5063 Evaluate side-chains 460 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 365 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 370 ASN Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 335 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 644 GLN A 755 GLN A 762 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 30 ASN E 245 HIS ** E 450 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** E1005 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 31 ASN D 112 GLN D 171 HIS ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35947 Z= 0.328 Angle : 0.621 9.507 48941 Z= 0.312 Chirality : 0.046 0.266 5650 Planarity : 0.004 0.052 6287 Dihedral : 6.143 59.916 5646 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.88 % Favored : 92.10 % Rotamer: Outliers : 4.41 % Allowed : 13.81 % Favored : 81.78 % 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: -2.85 (0.12), residues: 4428 helix: 1.34 (0.21), residues: 635 sheet: -1.99 (0.15), residues: 1052 loop : -2.81 (0.10), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 886 HIS 0.006 0.001 HIS A1064 PHE 0.041 0.002 PHE E 65 TYR 0.019 0.002 TYR A 248 ARG 0.005 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 536 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 367 time to evaluate : 4.334 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: A 249 LEU cc_start: 0.8317 (mt) cc_final: 0.8070 (mp) REVERT: A 1144 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 374 PHE cc_start: 0.7883 (m-80) cc_final: 0.7665 (m-80) REVERT: C 599 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8721 (p) REVERT: C 778 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.8998 (p) REVERT: C 856 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8206 (p0) REVERT: C 900 MET cc_start: 0.7985 (mtp) cc_final: 0.7714 (mtp) REVERT: C 1050 MET cc_start: 0.8419 (ptm) cc_final: 0.8208 (ptm) REVERT: E 133 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6361 (p90) REVERT: E 136 CYS cc_start: 0.6351 (OUTLIER) cc_final: 0.6121 (m) REVERT: E 150 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6735 (ttpt) REVERT: E 198 ASP cc_start: 0.6705 (t0) cc_final: 0.6437 (t0) REVERT: E 277 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8579 (pp) REVERT: E 489 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7260 (p90) REVERT: E 934 ILE cc_start: 0.8730 (mm) cc_final: 0.8383 (mm) REVERT: B 17 GLU cc_start: 0.7653 (mp0) cc_final: 0.7322 (tt0) REVERT: B 126 LEU cc_start: 0.5424 (mt) cc_final: 0.4920 (tt) REVERT: G 17 GLU cc_start: 0.7495 (mp0) cc_final: 0.7246 (mp0) REVERT: G 29 ILE cc_start: 0.4950 (pt) cc_final: 0.4701 (pt) REVERT: G 104 LYS cc_start: 0.7249 (pptt) cc_final: 0.6957 (pptt) REVERT: H 171 HIS cc_start: 0.4696 (OUTLIER) cc_final: 0.3206 (t-90) REVERT: I 31 ASN cc_start: 0.7158 (p0) cc_final: 0.6756 (p0) REVERT: I 62 ARG cc_start: 0.7508 (mtm-85) cc_final: 0.7299 (mtm-85) REVERT: I 88 TYR cc_start: 0.6610 (m-80) cc_final: 0.6140 (m-10) REVERT: I 155 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6221 (tp) outliers start: 169 outliers final: 109 residues processed: 514 average time/residue: 0.4858 time to fit residues: 401.8061 Evaluate side-chains 447 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 328 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 271 optimal weight: 10.0000 chunk 405 optimal weight: 6.9990 chunk 429 optimal weight: 0.3980 chunk 211 optimal weight: 0.9990 chunk 384 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A1135 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN C 439 ASN C 440 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN E 164 ASN E 245 HIS ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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: 0.7801 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35947 Z= 0.183 Angle : 0.550 9.564 48941 Z= 0.276 Chirality : 0.044 0.382 5650 Planarity : 0.004 0.047 6287 Dihedral : 5.785 58.894 5643 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.86 % Allowed : 14.85 % Favored : 81.28 % 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: -2.50 (0.12), residues: 4428 helix: 1.73 (0.21), residues: 634 sheet: -1.67 (0.15), residues: 1072 loop : -2.65 (0.11), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 886 HIS 0.011 0.001 HIS B 190 PHE 0.042 0.001 PHE E 65 TYR 0.017 0.001 TYR E 380 ARG 0.006 0.000 ARG I 32 *********************** 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 494 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 346 time to evaluate : 4.318 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: A 249 LEU cc_start: 0.8329 (mt) cc_final: 0.8071 (mp) REVERT: A 774 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7459 (mp-120) REVERT: A 858 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 119 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8981 (mt) REVERT: C 856 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8146 (p0) REVERT: E 133 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6432 (p90) REVERT: E 150 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6700 (ttpt) REVERT: E 198 ASP cc_start: 0.6704 (t0) cc_final: 0.6430 (t0) REVERT: E 277 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (pp) REVERT: E 489 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7399 (p90) REVERT: E 747 THR cc_start: 0.8584 (m) cc_final: 0.8169 (p) REVERT: E 934 ILE cc_start: 0.8652 (mm) cc_final: 0.8279 (mm) REVERT: B 126 LEU cc_start: 0.5433 (mt) cc_final: 0.4918 (tt) REVERT: B 210 PHE cc_start: 0.4329 (t80) cc_final: 0.3965 (t80) REVERT: G 29 ILE cc_start: 0.4324 (pt) cc_final: 0.4111 (pt) REVERT: H 81 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6468 (ptt) REVERT: H 177 LEU cc_start: 0.7881 (mm) cc_final: 0.7680 (mt) REVERT: I 31 ASN cc_start: 0.7138 (p0) cc_final: 0.6680 (p0) REVERT: I 88 TYR cc_start: 0.6663 (m-80) cc_final: 0.6142 (m-10) REVERT: I 190 HIS cc_start: 0.3960 (OUTLIER) cc_final: 0.2892 (t-90) outliers start: 148 outliers final: 98 residues processed: 471 average time/residue: 0.5017 time to fit residues: 380.3677 Evaluate side-chains 427 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 319 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 296 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 385 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 540 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 207 HIS C 218 GLN E 164 ASN E 245 HIS E 271 GLN ** E 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 112 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** 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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 35947 Z= 0.554 Angle : 0.743 14.081 48941 Z= 0.375 Chirality : 0.050 0.399 5650 Planarity : 0.005 0.050 6287 Dihedral : 6.763 59.729 5641 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.34 % Favored : 89.63 % Rotamer: Outliers : 5.04 % Allowed : 14.70 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.73 (0.12), residues: 4428 helix: 1.04 (0.20), residues: 628 sheet: -1.77 (0.15), residues: 1115 loop : -2.68 (0.11), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 886 HIS 0.010 0.002 HIS C 207 PHE 0.031 0.003 PHE A 79 TYR 0.027 0.002 TYR C 265 ARG 0.008 0.001 ARG A 158 *********************** 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 525 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 332 time to evaluate : 4.101 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: A 249 LEU cc_start: 0.8246 (mt) cc_final: 0.7963 (mp) REVERT: A 774 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7634 (mp-120) REVERT: A 858 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8799 (mt) REVERT: C 119 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9038 (mt) REVERT: C 374 PHE cc_start: 0.8123 (m-10) cc_final: 0.7880 (m-80) REVERT: C 778 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9043 (p) REVERT: C 856 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8335 (p0) REVERT: C 995 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8065 (mtt-85) REVERT: E 150 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.6738 (ttpt) REVERT: E 198 ASP cc_start: 0.7155 (t0) cc_final: 0.6849 (t0) REVERT: E 277 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8656 (pp) REVERT: E 460 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7686 (m110) REVERT: B 125 GLN cc_start: 0.3895 (OUTLIER) cc_final: 0.2967 (tp40) REVERT: B 126 LEU cc_start: 0.5312 (mt) cc_final: 0.4908 (tp) REVERT: B 155 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5555 (pp) REVERT: G 29 ILE cc_start: 0.5346 (OUTLIER) cc_final: 0.5135 (pt) REVERT: H 171 HIS cc_start: 0.4829 (OUTLIER) cc_final: 0.3761 (t-90) REVERT: H 177 LEU cc_start: 0.8083 (mm) cc_final: 0.7688 (tp) REVERT: I 31 ASN cc_start: 0.7391 (p0) cc_final: 0.6912 (p0) REVERT: I 88 TYR cc_start: 0.6710 (m-80) cc_final: 0.6181 (m-10) REVERT: I 180 LEU cc_start: 0.2865 (OUTLIER) cc_final: 0.2612 (tt) REVERT: I 190 HIS cc_start: 0.3883 (OUTLIER) cc_final: 0.2904 (t-90) outliers start: 193 outliers final: 135 residues processed: 492 average time/residue: 0.4901 time to fit residues: 385.9506 Evaluate side-chains 445 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 295 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 429 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 613 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 271 GLN E 969 ASN 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** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 35947 Z= 0.182 Angle : 0.565 13.680 48941 Z= 0.285 Chirality : 0.044 0.365 5650 Planarity : 0.004 0.046 6287 Dihedral : 6.125 59.868 5637 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 4.12 % Allowed : 15.77 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.12), residues: 4428 helix: 1.59 (0.21), residues: 628 sheet: -1.53 (0.15), residues: 1106 loop : -2.53 (0.11), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.003 0.001 HIS C1083 PHE 0.030 0.001 PHE E 65 TYR 0.023 0.001 TYR G 141 ARG 0.013 0.000 ARG I 62 *********************** 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 489 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 331 time to evaluate : 4.035 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: A 249 LEU cc_start: 0.8198 (mt) cc_final: 0.7943 (mp) REVERT: A 332 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 774 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7568 (mp-120) REVERT: A 858 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8731 (mt) REVERT: C 69 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.6044 (p-80) REVERT: C 119 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9037 (mt) REVERT: C 856 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8291 (p0) REVERT: C 995 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7621 (mtt90) REVERT: E 150 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6731 (ttpt) REVERT: E 198 ASP cc_start: 0.7027 (t0) cc_final: 0.6798 (t0) REVERT: E 277 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8546 (pp) REVERT: E 460 ASN cc_start: 0.7747 (m-40) cc_final: 0.7482 (m110) REVERT: B 126 LEU cc_start: 0.5286 (mt) cc_final: 0.4858 (tt) REVERT: B 155 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5407 (pp) REVERT: F 12 LYS cc_start: 0.6098 (ptpp) cc_final: 0.5822 (ptpp) REVERT: F 112 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: G 17 GLU cc_start: 0.7427 (mp0) cc_final: 0.7150 (mp0) REVERT: G 29 ILE cc_start: 0.4948 (OUTLIER) cc_final: 0.4726 (pt) REVERT: G 104 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6926 (pttp) REVERT: H 171 HIS cc_start: 0.4644 (OUTLIER) cc_final: 0.3443 (t-90) REVERT: H 177 LEU cc_start: 0.7955 (mm) cc_final: 0.7596 (tp) REVERT: I 31 ASN cc_start: 0.7151 (p0) cc_final: 0.6667 (p0) REVERT: I 190 HIS cc_start: 0.3698 (OUTLIER) cc_final: 0.2852 (t-90) outliers start: 158 outliers final: 102 residues processed: 461 average time/residue: 0.5265 time to fit residues: 390.8382 Evaluate side-chains 419 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 302 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain I residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 243 optimal weight: 0.0000 chunk 361 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 260 optimal weight: 0.0870 chunk 197 optimal weight: 0.2980 overall best weight: 1.2766 ------------------------------------------------------------------------------- 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 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 35947 Z= 0.211 Angle : 0.568 13.064 48941 Z= 0.284 Chirality : 0.044 0.278 5650 Planarity : 0.004 0.047 6287 Dihedral : 6.026 59.082 5635 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.27 % Favored : 91.71 % Rotamer: Outliers : 3.94 % Allowed : 15.92 % Favored : 80.14 % 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: -2.22 (0.12), residues: 4428 helix: 1.67 (0.21), residues: 634 sheet: -1.37 (0.15), residues: 1095 loop : -2.44 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 36 HIS 0.009 0.001 HIS B 190 PHE 0.032 0.001 PHE D 153 TYR 0.023 0.001 TYR B 141 ARG 0.011 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 472 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 321 time to evaluate : 4.210 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: A 249 LEU cc_start: 0.8208 (mt) cc_final: 0.7960 (mp) REVERT: A 332 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 774 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7532 (mp-120) REVERT: A 858 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8717 (mt) REVERT: C 69 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6048 (p-80) REVERT: C 119 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9045 (mt) REVERT: C 856 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8278 (p0) REVERT: C 995 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7619 (mtt90) REVERT: E 150 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6753 (ttpt) REVERT: E 198 ASP cc_start: 0.7056 (t0) cc_final: 0.6815 (t0) REVERT: E 277 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8558 (pp) REVERT: E 460 ASN cc_start: 0.7808 (m-40) cc_final: 0.7555 (m110) REVERT: E 490 PHE cc_start: 0.6442 (m-80) cc_final: 0.6220 (m-80) REVERT: D 50 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8161 (ttt180) REVERT: B 126 LEU cc_start: 0.5247 (mt) cc_final: 0.4747 (tp) REVERT: B 155 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5394 (pp) REVERT: F 12 LYS cc_start: 0.6070 (ptpp) cc_final: 0.5814 (ptpp) REVERT: G 17 GLU cc_start: 0.7445 (mp0) cc_final: 0.7142 (mp0) REVERT: G 29 ILE cc_start: 0.5043 (OUTLIER) cc_final: 0.4829 (pt) REVERT: H 171 HIS cc_start: 0.4588 (OUTLIER) cc_final: 0.3474 (t-90) REVERT: H 177 LEU cc_start: 0.7859 (mm) cc_final: 0.7513 (tp) REVERT: I 31 ASN cc_start: 0.7217 (p0) cc_final: 0.6772 (p0) REVERT: I 190 HIS cc_start: 0.3749 (OUTLIER) cc_final: 0.2931 (t-90) outliers start: 151 outliers final: 116 residues processed: 445 average time/residue: 0.5230 time to fit residues: 370.7333 Evaluate side-chains 437 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 307 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 336 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 218 GLN ** 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 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 101 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4712 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= 0.214 Angle : 0.565 12.474 48941 Z= 0.284 Chirality : 0.044 0.255 5650 Planarity : 0.004 0.048 6287 Dihedral : 5.935 59.077 5635 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.93 % Favored : 92.05 % Rotamer: Outliers : 3.99 % Allowed : 16.03 % Favored : 79.98 % 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: -2.15 (0.12), residues: 4428 helix: 1.70 (0.21), residues: 640 sheet: -1.30 (0.15), residues: 1088 loop : -2.40 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.006 0.001 HIS B 190 PHE 0.032 0.001 PHE A 140 TYR 0.025 0.001 TYR G 141 ARG 0.009 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 485 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 332 time to evaluate : 4.143 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: A 249 LEU cc_start: 0.8215 (mt) cc_final: 0.7966 (mp) REVERT: A 332 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8146 (tt) REVERT: A 752 LEU cc_start: 0.8935 (tp) cc_final: 0.8464 (tt) REVERT: A 774 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7507 (mp-120) REVERT: A 858 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8706 (mt) REVERT: C 69 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6073 (p-80) REVERT: C 119 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9043 (mt) REVERT: C 856 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (p0) REVERT: C 995 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7791 (mtm-85) REVERT: E 150 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.6744 (ttpt) REVERT: E 198 ASP cc_start: 0.7119 (t0) cc_final: 0.6880 (t0) REVERT: E 277 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8573 (pp) REVERT: E 460 ASN cc_start: 0.7823 (m-40) cc_final: 0.7584 (m110) REVERT: E 490 PHE cc_start: 0.6407 (m-80) cc_final: 0.6193 (m-80) REVERT: D 50 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8130 (ttt180) REVERT: B 126 LEU cc_start: 0.5310 (mt) cc_final: 0.4873 (tp) REVERT: B 155 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5377 (pp) REVERT: F 12 LYS cc_start: 0.6044 (ptpp) cc_final: 0.5806 (ptpp) REVERT: F 112 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: G 17 GLU cc_start: 0.7340 (mp0) cc_final: 0.7075 (mp0) REVERT: G 29 ILE cc_start: 0.5097 (OUTLIER) cc_final: 0.4896 (pt) REVERT: G 50 TYR cc_start: 0.6370 (t80) cc_final: 0.5979 (t80) REVERT: H 171 HIS cc_start: 0.4664 (OUTLIER) cc_final: 0.3652 (t-90) REVERT: H 177 LEU cc_start: 0.7844 (mm) cc_final: 0.7497 (tp) REVERT: I 31 ASN cc_start: 0.7141 (p0) cc_final: 0.6696 (p0) REVERT: I 188 GLU cc_start: 0.7163 (mp0) cc_final: 0.6893 (mm-30) REVERT: I 190 HIS cc_start: 0.3803 (OUTLIER) cc_final: 0.3260 (t-90) outliers start: 153 outliers final: 117 residues processed: 459 average time/residue: 0.5229 time to fit residues: 380.7365 Evaluate side-chains 444 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 312 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 3.9990 chunk 409 optimal weight: 0.9980 chunk 374 optimal weight: 20.0000 chunk 398 optimal weight: 30.0000 chunk 240 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 360 optimal weight: 20.0000 chunk 377 optimal weight: 20.0000 chunk 397 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 969 ASN D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35947 Z= 0.272 Angle : 0.596 13.814 48941 Z= 0.298 Chirality : 0.045 0.375 5650 Planarity : 0.004 0.050 6287 Dihedral : 6.112 59.976 5635 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.72 % Favored : 91.26 % Rotamer: Outliers : 3.89 % Allowed : 16.50 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.12), residues: 4428 helix: 1.62 (0.21), residues: 634 sheet: -1.28 (0.15), residues: 1084 loop : -2.38 (0.11), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 36 HIS 0.005 0.001 HIS B 190 PHE 0.039 0.002 PHE A 140 TYR 0.026 0.001 TYR B 141 ARG 0.009 0.001 ARG I 46 *********************** 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 467 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 318 time to evaluate : 3.890 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: A 249 LEU cc_start: 0.8179 (mt) cc_final: 0.7917 (mp) REVERT: A 774 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7521 (mp-120) REVERT: A 858 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8706 (mt) REVERT: C 69 HIS cc_start: 0.6840 (OUTLIER) cc_final: 0.6189 (p-80) REVERT: C 119 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9048 (mt) REVERT: C 387 LEU cc_start: 0.9091 (mt) cc_final: 0.8856 (mt) REVERT: C 778 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8984 (p) REVERT: C 995 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7813 (mtm-85) REVERT: E 150 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6716 (ttpt) REVERT: E 198 ASP cc_start: 0.7178 (t0) cc_final: 0.6849 (t70) REVERT: E 277 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8586 (pp) REVERT: E 460 ASN cc_start: 0.7841 (m-40) cc_final: 0.7626 (m110) REVERT: E 490 PHE cc_start: 0.6508 (m-80) cc_final: 0.6306 (m-80) REVERT: D 50 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8130 (ttt180) REVERT: B 126 LEU cc_start: 0.5178 (mt) cc_final: 0.4756 (tp) REVERT: B 155 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5620 (pp) REVERT: G 17 GLU cc_start: 0.7326 (mp0) cc_final: 0.7071 (mp0) REVERT: G 29 ILE cc_start: 0.5300 (OUTLIER) cc_final: 0.5100 (pt) REVERT: H 171 HIS cc_start: 0.4654 (OUTLIER) cc_final: 0.3675 (t-90) REVERT: H 177 LEU cc_start: 0.7884 (mm) cc_final: 0.7529 (tp) REVERT: I 31 ASN cc_start: 0.7185 (p0) cc_final: 0.6758 (p0) REVERT: I 190 HIS cc_start: 0.4204 (OUTLIER) cc_final: 0.3235 (t-90) outliers start: 149 outliers final: 120 residues processed: 442 average time/residue: 0.5226 time to fit residues: 365.2422 Evaluate side-chains 438 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 305 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 1 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.8980 chunk 421 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 293 optimal weight: 3.9990 chunk 442 optimal weight: 20.0000 chunk 407 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 245 HIS E 969 ASN D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN I 161 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 35947 Z= 0.225 Angle : 0.580 13.502 48941 Z= 0.290 Chirality : 0.044 0.257 5650 Planarity : 0.004 0.053 6287 Dihedral : 5.985 59.193 5635 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.08 % Favored : 91.89 % Rotamer: Outliers : 3.63 % Allowed : 16.81 % Favored : 79.56 % 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: -2.07 (0.12), residues: 4428 helix: 1.66 (0.21), residues: 640 sheet: -1.22 (0.15), residues: 1095 loop : -2.34 (0.11), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.006 0.001 HIS H 59 PHE 0.027 0.001 PHE D 153 TYR 0.021 0.001 TYR B 50 ARG 0.016 0.001 ARG I 212 ********************** REFINEMENT MACRO_CYCLE 10 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 459 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 320 time to evaluate : 3.975 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: A 249 LEU cc_start: 0.8131 (mt) cc_final: 0.7924 (mt) REVERT: A 752 LEU cc_start: 0.8990 (tp) cc_final: 0.8788 (tt) REVERT: A 774 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7499 (mp-120) REVERT: A 858 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8701 (mt) REVERT: C 69 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6183 (p-80) REVERT: C 119 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (mt) REVERT: C 387 LEU cc_start: 0.9074 (mt) cc_final: 0.8832 (mt) REVERT: C 778 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8969 (p) REVERT: C 995 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7781 (mtm-85) REVERT: E 150 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6699 (ttpt) REVERT: E 198 ASP cc_start: 0.7165 (t0) cc_final: 0.6826 (t70) REVERT: E 277 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8573 (pp) REVERT: E 460 ASN cc_start: 0.7850 (m-40) cc_final: 0.7645 (m110) REVERT: D 50 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8088 (ttt180) REVERT: B 126 LEU cc_start: 0.5167 (mt) cc_final: 0.4817 (tp) REVERT: B 155 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5619 (pp) REVERT: G 17 GLU cc_start: 0.7311 (mp0) cc_final: 0.7014 (mp0) REVERT: G 29 ILE cc_start: 0.5316 (OUTLIER) cc_final: 0.5107 (pt) REVERT: H 171 HIS cc_start: 0.4686 (OUTLIER) cc_final: 0.3764 (t-90) REVERT: H 177 LEU cc_start: 0.7830 (mm) cc_final: 0.7482 (tp) REVERT: I 31 ASN cc_start: 0.7197 (p0) cc_final: 0.6760 (p0) REVERT: I 190 HIS cc_start: 0.4256 (OUTLIER) cc_final: 0.3346 (t-90) outliers start: 139 outliers final: 117 residues processed: 435 average time/residue: 0.5078 time to fit residues: 350.2233 Evaluate side-chains 443 residues out of total 3885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 313 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 182 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 508 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 553 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 735 SER Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 939 SER Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 161 TRP Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 171 HIS Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 190 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 2.9990 chunk 375 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 352 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 362 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 271 GLN D 3 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.099631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071232 restraints weight = 97011.522| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.44 r_work: 0.3008 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5120 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= 0.388 Angle : 0.655 14.215 48941 Z= 0.329 Chirality : 0.047 0.289 5650 Planarity : 0.004 0.053 6287 Dihedral : 6.386 59.479 5635 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.98 % Favored : 90.00 % Rotamer: Outliers : 3.81 % Allowed : 16.58 % Favored : 79.61 % 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: -2.22 (0.12), residues: 4428 helix: 1.31 (0.21), residues: 639 sheet: -1.24 (0.16), residues: 1068 loop : -2.40 (0.11), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 104 HIS 0.007 0.001 HIS A1064 PHE 0.034 0.002 PHE E 65 TYR 0.024 0.002 TYR B 141 ARG 0.013 0.001 ARG G 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9547.78 seconds wall clock time: 174 minutes 4.29 seconds (10444.29 seconds total)