Starting phenix.real_space_refine on Tue Feb 20 13:48:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2a_31639/02_2024/7v2a_31639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2a_31639/02_2024/7v2a_31639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2a_31639/02_2024/7v2a_31639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2a_31639/02_2024/7v2a_31639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2a_31639/02_2024/7v2a_31639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2a_31639/02_2024/7v2a_31639.pdb" } resolution = 3.4 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 123 5.16 5 C 17871 2.51 5 N 4620 2.21 5 O 5403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28017 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7464 Classifications: {'peptide': 988} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 940} Chain breaks: 11 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 190 Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "B" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7464 Classifications: {'peptide': 988} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 940} Chain breaks: 11 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 190 Chain: "C" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7464 Classifications: {'peptide': 988} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 940} Chain breaks: 11 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 190 Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 799 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.43, per 1000 atoms: 0.52 Number of scatterers: 28017 At special positions: 0 Unit cell: (131.04, 135.2, 200.72, 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 123 16.00 O 5403 8.00 N 4620 7.00 C 17871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.49 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 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.36 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.49 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.49 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 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.37 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 89 " distance=2.36 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 282 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 282 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 282 " Time building additional restraints: 11.34 Conformation dependent library (CDL) restraints added in 5.0 seconds 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6774 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 63 sheets defined 22.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.036A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.165A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.572A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.707A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.852A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.802A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.596A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.622A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (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 983 removed outlier: 3.526A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.473A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.728A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.546A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 5.035A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.166A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.572A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.706A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.852A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.802A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.596A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.622A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.525A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.474A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.944A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.037A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.166A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.573A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.707A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.853A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.802A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.826A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.597A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.622A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.527A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.473A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'H' and resid 80 through 84 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.728A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.728A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.848A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.618A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.559A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.442A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.611A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.425A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.531A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.326A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 4.250A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP E 33 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.848A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.616A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.560A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.442A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.610A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.425A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.531A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD3, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.326A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.150A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.899A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.899A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.250A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.637A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.617A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.559A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.441A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.611A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.425A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.530A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF1, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.326A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.150A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.898A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AF6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF8, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.251A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AG1, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.879A pdb=" N ALA F 12 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.879A pdb=" N ALA F 12 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AG4, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA H 12 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.880A pdb=" N ALA H 12 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP G 33 " --> pdb=" O HIS G 99 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP I 33 " --> pdb=" O HIS I 99 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2595 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: 14.10 Time building geometry restraints manager: 12.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5537 1.32 - 1.45: 7273 1.45 - 1.57: 15684 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28650 Sorted by residual: bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.211 0.120 2.07e-02 2.33e+03 3.37e+01 bond pdb=" C HIS A1088 " pdb=" N PHE A1089 " ideal model delta sigma weight residual 1.331 1.211 0.120 2.07e-02 2.33e+03 3.34e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.212 0.119 2.07e-02 2.33e+03 3.33e+01 bond pdb=" C LEU C 335 " pdb=" N CYS C 336 " ideal model delta sigma weight residual 1.328 1.396 -0.068 1.44e-02 4.82e+03 2.23e+01 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.328 1.395 -0.067 1.44e-02 4.82e+03 2.18e+01 ... (remaining 28645 not shown) Histogram of bond angle deviations from ideal: 95.26 - 103.06: 251 103.06 - 110.85: 10825 110.85 - 118.65: 11644 118.65 - 126.44: 15979 126.44 - 134.24: 352 Bond angle restraints: 39051 Sorted by residual: angle pdb=" C TYR G 110 " pdb=" CA TYR G 110 " pdb=" CB TYR G 110 " ideal model delta sigma weight residual 112.82 95.26 17.56 2.17e+00 2.12e-01 6.55e+01 angle pdb=" C TYR I 110 " pdb=" CA TYR I 110 " pdb=" CB TYR I 110 " ideal model delta sigma weight residual 112.82 95.39 17.43 2.17e+00 2.12e-01 6.45e+01 angle pdb=" N LYS B 41 " pdb=" CA LYS B 41 " pdb=" C LYS B 41 " ideal model delta sigma weight residual 114.56 107.60 6.96 1.27e+00 6.20e-01 3.01e+01 angle pdb=" N LYS A 41 " pdb=" CA LYS A 41 " pdb=" C LYS A 41 " ideal model delta sigma weight residual 113.43 106.60 6.83 1.26e+00 6.30e-01 2.94e+01 angle pdb=" C GLU C 324 " pdb=" CA GLU C 324 " pdb=" CB GLU C 324 " ideal model delta sigma weight residual 114.11 100.98 13.13 2.44e+00 1.68e-01 2.90e+01 ... (remaining 39046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 15768 21.92 - 43.84: 1214 43.84 - 65.76: 142 65.76 - 87.69: 37 87.69 - 109.61: 20 Dihedral angle restraints: 17181 sinusoidal: 6621 harmonic: 10560 Sorted by residual: dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta harmonic sigma weight residual -180.00 -125.61 -54.39 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA TYR D 50 " pdb=" C TYR D 50 " pdb=" N ASP D 51 " pdb=" CA ASP D 51 " ideal model delta harmonic sigma weight residual -180.00 -125.61 -54.39 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA TYR F 50 " pdb=" C TYR F 50 " pdb=" N ASP F 51 " pdb=" CA ASP F 51 " ideal model delta harmonic sigma weight residual -180.00 -125.62 -54.38 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 17178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3863 0.077 - 0.153: 635 0.153 - 0.230: 32 0.230 - 0.307: 7 0.307 - 0.384: 5 Chirality restraints: 4542 Sorted by residual: chirality pdb=" CA GLU A 324 " pdb=" N GLU A 324 " pdb=" C GLU A 324 " pdb=" CB GLU A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLU C 324 " pdb=" N GLU C 324 " pdb=" C GLU C 324 " pdb=" CB GLU C 324 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA TYR E 110 " pdb=" N TYR E 110 " pdb=" C TYR E 110 " pdb=" CB TYR E 110 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 4539 not shown) Planarity restraints: 5025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.333 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG A1308 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1308 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " -0.120 2.00e-02 2.50e+03 9.76e-02 1.19e+02 pdb=" C7 NAG C1308 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " 0.025 2.00e-02 2.50e+03 ... (remaining 5022 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 43 1.83 - 2.60: 560 2.60 - 3.36: 37079 3.36 - 4.13: 65053 4.13 - 4.90: 120245 Nonbonded interactions: 222980 Sorted by model distance: nonbonded pdb=" NH2 ARG B 357 " pdb=" CB PRO C 230 " model vdw 1.059 3.520 nonbonded pdb=" NH2 ARG A 357 " pdb=" CB PRO B 230 " model vdw 1.076 3.520 nonbonded pdb=" CB PRO A 230 " pdb=" NH2 ARG C 357 " model vdw 1.079 3.520 nonbonded pdb=" NZ LYS A1045 " pdb=" O GLY B 889 " model vdw 1.225 2.520 nonbonded pdb=" O GLY A 889 " pdb=" NZ LYS C1045 " model vdw 1.241 2.520 ... (remaining 222975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.140 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 77.320 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.210 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.011 0.120 28650 Z= 0.729 Angle : 0.955 17.556 39051 Z= 0.560 Chirality : 0.055 0.384 4542 Planarity : 0.008 0.289 5001 Dihedral : 15.616 109.607 10290 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.54 % Favored : 90.20 % Rotamer: Outliers : 2.50 % Allowed : 18.17 % Favored : 79.33 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.95 (0.12), residues: 3573 helix: -3.84 (0.13), residues: 654 sheet: -1.74 (0.17), residues: 876 loop : -2.66 (0.11), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.006 0.001 HIS G 99 PHE 0.017 0.002 PHE B1089 TYR 0.028 0.003 TYR G 107 ARG 0.006 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 367 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7622 (pttt) cc_final: 0.7394 (pttm) REVERT: D 107 LEU cc_start: 0.7772 (tp) cc_final: 0.7124 (tp) REVERT: E 57 ASP cc_start: 0.8679 (t0) cc_final: 0.8399 (t0) REVERT: E 65 GLN cc_start: 0.8803 (mm110) cc_final: 0.8280 (tp40) REVERT: B 202 LYS cc_start: 0.7689 (pttt) cc_final: 0.7292 (pttt) REVERT: B 994 ASP cc_start: 0.8280 (t0) cc_final: 0.8034 (t0) REVERT: C 202 LYS cc_start: 0.7673 (pttt) cc_final: 0.7069 (pttm) REVERT: G 46 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7584 (mm-30) REVERT: G 65 GLN cc_start: 0.8733 (mm110) cc_final: 0.8253 (tp40) REVERT: G 100 GLN cc_start: 0.8819 (mp10) cc_final: 0.8466 (mp10) REVERT: I 65 GLN cc_start: 0.8749 (mm110) cc_final: 0.7984 (tp40) REVERT: I 67 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7997 (mp10) REVERT: I 100 GLN cc_start: 0.8660 (mp10) cc_final: 0.8305 (mp10) outliers start: 74 outliers final: 61 residues processed: 441 average time/residue: 0.3706 time to fit residues: 266.4036 Evaluate side-chains 290 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 89 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.6980 chunk 275 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 329 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 394 ASN A 437 ASN A 448 ASN A 487 ASN A 536 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 755 GLN A 901 GLN A 965 GLN A1002 GLN A1101 HIS E 104 ASN B 61 ASN B 437 ASN B 448 ASN B 487 ASN B 536 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 755 GLN B 901 GLN B 965 GLN B1002 GLN B1088 HIS B1101 HIS C 61 ASN C 437 ASN C 448 ASN C 487 ASN C 536 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 901 GLN C 965 GLN C1002 GLN C1088 HIS C1101 HIS H 32 ASN G 104 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28650 Z= 0.216 Angle : 0.650 10.997 39051 Z= 0.336 Chirality : 0.045 0.294 4542 Planarity : 0.005 0.055 5001 Dihedral : 8.357 89.651 4468 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.40 % Favored : 94.43 % Rotamer: Outliers : 3.65 % Allowed : 20.57 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.13), residues: 3573 helix: -1.64 (0.19), residues: 651 sheet: -1.22 (0.17), residues: 882 loop : -2.02 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 92 HIS 0.007 0.001 HIS I 99 PHE 0.014 0.001 PHE C1121 TYR 0.022 0.001 TYR I 101 ARG 0.005 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 287 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 887 THR cc_start: 0.8841 (p) cc_final: 0.8378 (t) REVERT: E 57 ASP cc_start: 0.8730 (t0) cc_final: 0.8404 (t0) REVERT: E 65 GLN cc_start: 0.8826 (mm110) cc_final: 0.8350 (tp40) REVERT: B 614 ASP cc_start: 0.8018 (p0) cc_final: 0.7810 (p0) REVERT: B 896 ILE cc_start: 0.7975 (mm) cc_final: 0.7642 (tp) REVERT: C 887 THR cc_start: 0.8826 (p) cc_final: 0.8407 (t) REVERT: C 1123 SER cc_start: 0.8026 (p) cc_final: 0.7729 (p) REVERT: F 92 TRP cc_start: 0.6562 (t-100) cc_final: 0.6280 (t-100) REVERT: G 65 GLN cc_start: 0.8580 (mm110) cc_final: 0.7900 (tp40) REVERT: G 67 GLN cc_start: 0.8097 (mm110) cc_final: 0.7851 (mp10) REVERT: I 65 GLN cc_start: 0.8829 (mm110) cc_final: 0.7951 (tp40) REVERT: I 67 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8092 (mp10) REVERT: I 110 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6881 (t80) REVERT: I 111 TYR cc_start: 0.7499 (m-80) cc_final: 0.7167 (m-10) outliers start: 108 outliers final: 74 residues processed: 371 average time/residue: 0.3372 time to fit residues: 211.8135 Evaluate side-chains 306 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 231 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 330 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 264 optimal weight: 0.0570 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 901 GLN A 955 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 955 ASN B 957 GLN B1108 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 28650 Z= 0.295 Angle : 0.613 8.831 39051 Z= 0.319 Chirality : 0.044 0.246 4542 Planarity : 0.004 0.063 5001 Dihedral : 6.784 70.060 4407 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.52 % Favored : 93.31 % Rotamer: Outliers : 3.88 % Allowed : 22.63 % Favored : 73.49 % 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: -2.02 (0.13), residues: 3573 helix: -0.75 (0.20), residues: 633 sheet: -0.93 (0.17), residues: 918 loop : -1.75 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 92 HIS 0.007 0.001 HIS I 99 PHE 0.014 0.001 PHE C1121 TYR 0.030 0.001 TYR H 50 ARG 0.007 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 240 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 887 THR cc_start: 0.8892 (p) cc_final: 0.8426 (t) REVERT: E 57 ASP cc_start: 0.8745 (t0) cc_final: 0.8430 (t0) REVERT: E 65 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8380 (tp40) REVERT: E 100 GLN cc_start: 0.8811 (mp10) cc_final: 0.8482 (mp10) REVERT: B 202 LYS cc_start: 0.8003 (pttm) cc_final: 0.7597 (pttm) REVERT: B 896 ILE cc_start: 0.8100 (mm) cc_final: 0.7774 (tp) REVERT: C 320 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8847 (m) REVERT: C 488 CYS cc_start: 0.4710 (OUTLIER) cc_final: 0.4325 (m) REVERT: C 585 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 887 THR cc_start: 0.8793 (p) cc_final: 0.8375 (t) REVERT: C 990 GLU cc_start: 0.8364 (pp20) cc_final: 0.8155 (pp20) REVERT: C 1123 SER cc_start: 0.8103 (p) cc_final: 0.7758 (p) REVERT: F 92 TRP cc_start: 0.6640 (t-100) cc_final: 0.6094 (t-100) REVERT: H 50 TYR cc_start: 0.7779 (p90) cc_final: 0.7478 (p90) REVERT: G 65 GLN cc_start: 0.8604 (mm110) cc_final: 0.7990 (tp40) REVERT: G 67 GLN cc_start: 0.8172 (mm110) cc_final: 0.7871 (mp10) REVERT: I 65 GLN cc_start: 0.8811 (mm110) cc_final: 0.7539 (mm-40) REVERT: I 67 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8122 (mp10) REVERT: I 110 TYR cc_start: 0.7545 (OUTLIER) cc_final: 0.6951 (t80) REVERT: I 111 TYR cc_start: 0.7559 (m-80) cc_final: 0.7168 (m-10) outliers start: 115 outliers final: 79 residues processed: 331 average time/residue: 0.3304 time to fit residues: 188.1774 Evaluate side-chains 304 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 219 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 110 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 157 optimal weight: 0.0040 chunk 221 optimal weight: 8.9990 chunk 331 optimal weight: 7.9990 chunk 350 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 314 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28650 Z= 0.227 Angle : 0.577 9.036 39051 Z= 0.298 Chirality : 0.044 0.252 4542 Planarity : 0.004 0.066 5001 Dihedral : 6.420 64.889 4401 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 3.92 % Allowed : 23.47 % Favored : 72.61 % 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: -1.59 (0.13), residues: 3573 helix: -0.10 (0.21), residues: 615 sheet: -0.61 (0.17), residues: 894 loop : -1.60 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 47 HIS 0.005 0.001 HIS I 99 PHE 0.013 0.001 PHE A1121 TYR 0.024 0.001 TYR H 50 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 243 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 887 THR cc_start: 0.8845 (p) cc_final: 0.8374 (t) REVERT: E 57 ASP cc_start: 0.8748 (t0) cc_final: 0.8399 (t0) REVERT: E 65 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8262 (tp40) REVERT: E 67 GLN cc_start: 0.8307 (mm110) cc_final: 0.7891 (mp-120) REVERT: E 100 GLN cc_start: 0.8813 (mp10) cc_final: 0.8444 (mp10) REVERT: B 488 CYS cc_start: 0.4735 (OUTLIER) cc_final: 0.4460 (m) REVERT: B 896 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7815 (tp) REVERT: C 320 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8863 (m) REVERT: C 488 CYS cc_start: 0.4780 (OUTLIER) cc_final: 0.4378 (m) REVERT: C 585 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8439 (mt) REVERT: C 780 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 786 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: C 887 THR cc_start: 0.8704 (p) cc_final: 0.8329 (t) REVERT: C 1123 SER cc_start: 0.8095 (p) cc_final: 0.7749 (p) REVERT: F 92 TRP cc_start: 0.6633 (t-100) cc_final: 0.6241 (t-100) REVERT: H 50 TYR cc_start: 0.7641 (p90) cc_final: 0.7055 (p90) REVERT: G 65 GLN cc_start: 0.8629 (mm110) cc_final: 0.8016 (tp40) REVERT: G 67 GLN cc_start: 0.8123 (mm110) cc_final: 0.7879 (mp10) REVERT: I 65 GLN cc_start: 0.8896 (mm110) cc_final: 0.7966 (tp40) REVERT: I 67 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8097 (mp10) outliers start: 116 outliers final: 72 residues processed: 335 average time/residue: 0.3346 time to fit residues: 194.3620 Evaluate side-chains 299 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 219 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 299 optimal weight: 0.8980 chunk 242 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 314 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28650 Z= 0.254 Angle : 0.584 12.426 39051 Z= 0.299 Chirality : 0.044 0.244 4542 Planarity : 0.004 0.066 5001 Dihedral : 6.269 59.054 4401 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.90 % Rotamer: Outliers : 4.69 % Allowed : 23.78 % Favored : 71.53 % 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: -1.39 (0.14), residues: 3573 helix: 0.15 (0.20), residues: 636 sheet: -0.50 (0.17), residues: 894 loop : -1.49 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 92 HIS 0.006 0.001 HIS I 99 PHE 0.013 0.001 PHE C1121 TYR 0.020 0.001 TYR H 50 ARG 0.005 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 232 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 CYS cc_start: 0.4876 (OUTLIER) cc_final: 0.4345 (m) REVERT: A 585 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 887 THR cc_start: 0.8870 (p) cc_final: 0.8384 (t) REVERT: E 57 ASP cc_start: 0.8681 (t0) cc_final: 0.8332 (t0) REVERT: E 65 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8296 (tp40) REVERT: E 67 GLN cc_start: 0.8286 (mm110) cc_final: 0.7933 (mp10) REVERT: B 495 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.3556 (t80) REVERT: B 896 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7945 (tp) REVERT: C 320 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8870 (m) REVERT: C 495 TYR cc_start: 0.5662 (OUTLIER) cc_final: 0.2585 (t80) REVERT: C 585 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8413 (mt) REVERT: C 887 THR cc_start: 0.8732 (p) cc_final: 0.8343 (t) REVERT: C 1123 SER cc_start: 0.8114 (p) cc_final: 0.7769 (p) REVERT: F 92 TRP cc_start: 0.6689 (t-100) cc_final: 0.6262 (t-100) REVERT: H 50 TYR cc_start: 0.7623 (p90) cc_final: 0.6989 (p90) REVERT: G 65 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8089 (tp40) REVERT: I 65 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7983 (tp40) REVERT: I 67 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8113 (mp10) outliers start: 139 outliers final: 97 residues processed: 347 average time/residue: 0.3326 time to fit residues: 197.8613 Evaluate side-chains 328 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 221 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 351 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 116 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28650 Z= 0.213 Angle : 0.570 12.237 39051 Z= 0.291 Chirality : 0.043 0.246 4542 Planarity : 0.004 0.066 5001 Dihedral : 6.022 59.402 4393 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.29 % Rotamer: Outliers : 4.39 % Allowed : 24.35 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3573 helix: 0.39 (0.20), residues: 648 sheet: -0.42 (0.17), residues: 891 loop : -1.46 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 92 HIS 0.005 0.001 HIS I 99 PHE 0.015 0.001 PHE B 817 TYR 0.019 0.001 TYR H 50 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 233 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 CYS cc_start: 0.4936 (OUTLIER) cc_final: 0.4390 (m) REVERT: A 585 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8362 (mt) REVERT: A 887 THR cc_start: 0.8840 (p) cc_final: 0.8370 (t) REVERT: E 57 ASP cc_start: 0.8742 (t0) cc_final: 0.8461 (t0) REVERT: E 65 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8316 (tp40) REVERT: E 67 GLN cc_start: 0.8323 (mm110) cc_final: 0.8011 (mp10) REVERT: B 495 TYR cc_start: 0.5465 (OUTLIER) cc_final: 0.3574 (t80) REVERT: B 780 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8051 (mp0) REVERT: B 896 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7929 (tp) REVERT: C 320 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8919 (m) REVERT: C 559 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: C 585 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8457 (mt) REVERT: C 887 THR cc_start: 0.8677 (p) cc_final: 0.8298 (t) REVERT: C 1123 SER cc_start: 0.8104 (p) cc_final: 0.7751 (p) REVERT: F 92 TRP cc_start: 0.6630 (t-100) cc_final: 0.6225 (t-100) REVERT: H 50 TYR cc_start: 0.7618 (p90) cc_final: 0.7006 (p90) REVERT: H 110 LEU cc_start: 0.6631 (mt) cc_final: 0.6109 (pp) REVERT: I 65 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8063 (tp40) REVERT: I 67 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8107 (mp10) outliers start: 130 outliers final: 95 residues processed: 340 average time/residue: 0.3226 time to fit residues: 188.2141 Evaluate side-chains 321 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 217 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 198 optimal weight: 0.0010 chunk 295 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 349 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1088 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1106 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28650 Z= 0.152 Angle : 0.541 12.971 39051 Z= 0.274 Chirality : 0.043 0.245 4542 Planarity : 0.004 0.065 5001 Dihedral : 5.613 59.703 4393 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.61 % Allowed : 25.30 % Favored : 71.09 % 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: -0.96 (0.14), residues: 3573 helix: 0.79 (0.20), residues: 657 sheet: -0.27 (0.17), residues: 891 loop : -1.32 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 47 HIS 0.004 0.001 HIS G 99 PHE 0.016 0.001 PHE G 64 TYR 0.020 0.001 TYR H 50 ARG 0.004 0.000 ARG G 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 242 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 CYS cc_start: 0.4816 (OUTLIER) cc_final: 0.4307 (m) REVERT: A 585 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8370 (mt) REVERT: A 786 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8348 (mtmm) REVERT: A 887 THR cc_start: 0.8696 (p) cc_final: 0.8241 (t) REVERT: E 57 ASP cc_start: 0.8702 (t0) cc_final: 0.8459 (t0) REVERT: E 65 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8443 (tp40) REVERT: B 896 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7690 (tp) REVERT: C 488 CYS cc_start: 0.4570 (OUTLIER) cc_final: 0.4254 (m) REVERT: C 559 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: C 585 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8359 (mt) REVERT: C 887 THR cc_start: 0.8590 (p) cc_final: 0.8231 (t) REVERT: C 1123 SER cc_start: 0.8124 (p) cc_final: 0.7724 (p) REVERT: F 17 LYS cc_start: 0.8694 (mmtm) cc_final: 0.7863 (mmpt) REVERT: F 92 TRP cc_start: 0.6568 (t-100) cc_final: 0.6267 (t-100) REVERT: H 17 LYS cc_start: 0.8608 (mmtm) cc_final: 0.7752 (mmpt) REVERT: H 50 TYR cc_start: 0.7481 (p90) cc_final: 0.6886 (p90) REVERT: H 110 LEU cc_start: 0.6635 (mt) cc_final: 0.6063 (pp) REVERT: I 65 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7971 (tp-100) outliers start: 107 outliers final: 75 residues processed: 332 average time/residue: 0.3293 time to fit residues: 188.4405 Evaluate side-chains 309 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 225 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 275 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1106 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28650 Z= 0.173 Angle : 0.548 9.691 39051 Z= 0.277 Chirality : 0.043 0.246 4542 Planarity : 0.004 0.065 5001 Dihedral : 5.509 59.951 4392 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 3.38 % Allowed : 25.97 % Favored : 70.65 % 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: -0.85 (0.14), residues: 3573 helix: 0.95 (0.20), residues: 657 sheet: -0.22 (0.17), residues: 894 loop : -1.26 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 47 HIS 0.011 0.001 HIS A 66 PHE 0.012 0.001 PHE B 817 TYR 0.021 0.001 TYR D 50 ARG 0.003 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 230 time to evaluate : 3.454 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: A 559 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: A 585 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8377 (mt) REVERT: A 786 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8326 (mtmm) REVERT: A 887 THR cc_start: 0.8717 (p) cc_final: 0.8271 (t) REVERT: E 57 ASP cc_start: 0.8662 (t0) cc_final: 0.8431 (t0) REVERT: E 65 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: B 495 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.3232 (t80) REVERT: B 780 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 896 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7761 (tp) REVERT: C 488 CYS cc_start: 0.4626 (OUTLIER) cc_final: 0.4226 (m) REVERT: C 559 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: C 585 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8345 (mt) REVERT: C 887 THR cc_start: 0.8592 (p) cc_final: 0.8235 (t) REVERT: C 1123 SER cc_start: 0.8119 (p) cc_final: 0.7751 (p) REVERT: F 92 TRP cc_start: 0.6582 (t-100) cc_final: 0.6336 (t-100) REVERT: H 50 TYR cc_start: 0.7507 (p90) cc_final: 0.6894 (p90) REVERT: H 110 LEU cc_start: 0.6346 (mt) cc_final: 0.5881 (pp) REVERT: G 103 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6112 (t80) REVERT: I 65 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8499 (tp40) outliers start: 100 outliers final: 73 residues processed: 311 average time/residue: 0.3234 time to fit residues: 174.5778 Evaluate side-chains 305 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 220 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 65 GLN Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 294 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 99 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28650 Z= 0.264 Angle : 0.576 14.787 39051 Z= 0.293 Chirality : 0.044 0.241 4542 Planarity : 0.004 0.065 5001 Dihedral : 5.625 59.807 4391 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.18 % Rotamer: Outliers : 3.55 % Allowed : 25.94 % Favored : 70.52 % 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: -0.84 (0.14), residues: 3573 helix: 0.90 (0.20), residues: 654 sheet: -0.24 (0.17), residues: 876 loop : -1.20 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 92 HIS 0.005 0.001 HIS G 99 PHE 0.016 0.001 PHE B 817 TYR 0.019 0.001 TYR D 50 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 224 time to evaluate : 3.596 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: A 559 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: A 585 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 786 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8297 (mtmm) REVERT: A 887 THR cc_start: 0.8863 (p) cc_final: 0.8393 (t) REVERT: E 57 ASP cc_start: 0.8710 (t0) cc_final: 0.8249 (t0) REVERT: E 65 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8463 (tp40) REVERT: B 495 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.3125 (t80) REVERT: B 559 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: B 896 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7970 (tp) REVERT: C 559 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: C 585 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8402 (mt) REVERT: C 887 THR cc_start: 0.8681 (p) cc_final: 0.8319 (t) REVERT: C 1123 SER cc_start: 0.8138 (p) cc_final: 0.7764 (p) REVERT: F 17 LYS cc_start: 0.8706 (mmtm) cc_final: 0.7946 (mmpt) REVERT: F 50 TYR cc_start: 0.7511 (p90) cc_final: 0.6997 (p90) REVERT: H 50 TYR cc_start: 0.7640 (p90) cc_final: 0.7103 (p90) REVERT: H 110 LEU cc_start: 0.6686 (mt) cc_final: 0.6081 (pp) REVERT: G 103 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6427 (t80) outliers start: 105 outliers final: 86 residues processed: 310 average time/residue: 0.3317 time to fit residues: 178.4642 Evaluate side-chains 313 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 217 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 4.9990 chunk 344 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 287 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28650 Z= 0.280 Angle : 0.581 10.197 39051 Z= 0.297 Chirality : 0.044 0.239 4542 Planarity : 0.004 0.065 5001 Dihedral : 5.662 59.744 4391 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 3.51 % Allowed : 25.97 % Favored : 70.52 % 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: -0.86 (0.14), residues: 3573 helix: 0.87 (0.20), residues: 654 sheet: -0.26 (0.17), residues: 879 loop : -1.21 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 92 HIS 0.010 0.001 HIS A 66 PHE 0.016 0.001 PHE B 817 TYR 0.019 0.001 TYR D 50 ARG 0.004 0.000 ARG A1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 217 time to evaluate : 3.524 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: A 559 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: A 585 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8338 (mt) REVERT: A 786 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: A 887 THR cc_start: 0.8889 (p) cc_final: 0.8415 (t) REVERT: E 57 ASP cc_start: 0.8689 (t0) cc_final: 0.8238 (t0) REVERT: E 65 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8467 (tp40) REVERT: B 495 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.3046 (t80) REVERT: B 559 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 896 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8036 (tp) REVERT: C 495 TYR cc_start: 0.5766 (OUTLIER) cc_final: 0.1568 (t80) REVERT: C 559 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: C 585 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8414 (mt) REVERT: C 887 THR cc_start: 0.8715 (p) cc_final: 0.8319 (t) REVERT: C 1123 SER cc_start: 0.8136 (p) cc_final: 0.7730 (p) REVERT: F 17 LYS cc_start: 0.8718 (mmtm) cc_final: 0.7981 (mmpt) REVERT: H 50 TYR cc_start: 0.7659 (p90) cc_final: 0.7091 (p90) REVERT: G 103 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6549 (t80) REVERT: I 100 GLN cc_start: 0.8786 (mp10) cc_final: 0.8253 (mp10) REVERT: I 103 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6302 (t80) outliers start: 104 outliers final: 85 residues processed: 307 average time/residue: 0.3461 time to fit residues: 181.5668 Evaluate side-chains 310 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 213 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074021 restraints weight = 79027.560| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.85 r_work: 0.3065 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28650 Z= 0.221 Angle : 0.561 10.484 39051 Z= 0.285 Chirality : 0.043 0.237 4542 Planarity : 0.004 0.065 5001 Dihedral : 5.507 59.905 4391 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.40 % Favored : 94.43 % Rotamer: Outliers : 3.44 % Allowed : 25.97 % Favored : 70.58 % 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: -0.76 (0.14), residues: 3573 helix: 1.01 (0.20), residues: 654 sheet: -0.18 (0.17), residues: 876 loop : -1.18 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 92 HIS 0.005 0.001 HIS I 99 PHE 0.012 0.001 PHE B 817 TYR 0.020 0.001 TYR D 50 ARG 0.003 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5691.01 seconds wall clock time: 104 minutes 45.01 seconds (6285.01 seconds total)