Starting phenix.real_space_refine on Sun Feb 18 21:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v20_31632/02_2024/7v20_31632.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v20_31632/02_2024/7v20_31632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v20_31632/02_2024/7v20_31632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v20_31632/02_2024/7v20_31632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v20_31632/02_2024/7v20_31632.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v20_31632/02_2024/7v20_31632.pdb" } resolution = 2.86 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= 0.072 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 101 5.16 5 C 14625 2.51 5 N 3744 2.21 5 O 4483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" 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: 22953 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7431 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 10 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7485 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 53, 'TRANS': 926} Chain breaks: 11 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "C" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7393 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 52, 'TRANS': 927} Chain breaks: 11 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 205 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.01, per 1000 atoms: 0.52 Number of scatterers: 22953 At special positions: 0 Unit cell: (133.92, 136.08, 168.48, 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 101 16.00 O 4483 8.00 N 3744 7.00 C 14625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 Atom "HETATM22321 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " Time building additional restraints: 9.25 Conformation dependent library (CDL) restraints added in 4.2 seconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 43 sheets defined 27.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.602A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.541A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.562A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.843A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.320A 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 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.610A 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 783 removed outlier: 3.720A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.291A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.525A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.572A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.920A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.563A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.827A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 783 removed outlier: 3.818A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.551A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.932A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.286A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.879A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.018A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 984 removed outlier: 3.701A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.422A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.509A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.559A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.680A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.640A 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 783 removed outlier: 4.308A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.629A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.126A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 984 removed outlier: 3.629A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.412A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.801A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.804A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.888A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.771A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.815A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.528A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.486A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.526A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.010A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.625A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.877A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 4.512A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.212A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.864A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.784A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.568A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.637A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.399A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.485A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.323A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.323A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.568A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.502A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.734A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.327A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.986A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.569A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.984A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.573A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.872A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.559A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 1009 hydrogen bonds defined for protein. 2805 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: 11.31 Time building geometry restraints manager: 9.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7308 1.35 - 1.48: 6219 1.48 - 1.61: 9794 1.61 - 1.74: 3 1.74 - 1.87: 122 Bond restraints: 23446 Sorted by residual: bond pdb=" CG ASN A 343 " pdb=" ND2 ASN A 343 " ideal model delta sigma weight residual 1.328 1.474 -0.146 2.10e-02 2.27e+03 4.84e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.533 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" CA ASN C 616 " pdb=" C ASN C 616 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.23e-02 6.61e+03 2.73e+01 bond pdb=" CG ASN B1074 " pdb=" ND2 ASN B1074 " ideal model delta sigma weight residual 1.328 1.233 0.095 2.10e-02 2.27e+03 2.03e+01 bond pdb=" CB ASN B1074 " pdb=" CG ASN B1074 " ideal model delta sigma weight residual 1.516 1.414 0.102 2.50e-02 1.60e+03 1.67e+01 ... (remaining 23441 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.96: 492 104.96 - 112.22: 11940 112.22 - 119.49: 7230 119.49 - 126.75: 12081 126.75 - 134.01: 232 Bond angle restraints: 31975 Sorted by residual: angle pdb=" N ASN C 616 " pdb=" CA ASN C 616 " pdb=" C ASN C 616 " ideal model delta sigma weight residual 110.24 122.41 -12.17 1.30e+00 5.92e-01 8.77e+01 angle pdb=" CA ASN C 616 " pdb=" C ASN C 616 " pdb=" N CYS C 617 " ideal model delta sigma weight residual 115.64 107.66 7.98 1.39e+00 5.18e-01 3.30e+01 angle pdb=" N THR C 761 " pdb=" CA THR C 761 " pdb=" C THR C 761 " ideal model delta sigma weight residual 113.41 106.49 6.92 1.22e+00 6.72e-01 3.22e+01 angle pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 114.40 127.30 -12.90 2.30e+00 1.89e-01 3.14e+01 angle pdb=" CA CYS A 738 " pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 114.40 127.04 -12.64 2.30e+00 1.89e-01 3.02e+01 ... (remaining 31970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13388 17.95 - 35.90: 912 35.90 - 53.84: 156 53.84 - 71.79: 65 71.79 - 89.74: 28 Dihedral angle restraints: 14549 sinusoidal: 6013 harmonic: 8536 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -173.97 87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA VAL C 615 " pdb=" C VAL C 615 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual 180.00 135.04 44.96 0 5.00e+00 4.00e-02 8.09e+01 dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta harmonic sigma weight residual -180.00 -136.68 -43.32 0 5.00e+00 4.00e-02 7.51e+01 ... (remaining 14546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3820 0.166 - 0.333: 25 0.333 - 0.499: 3 0.499 - 0.665: 2 0.665 - 0.832: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CA ASN C 616 " pdb=" N ASN C 616 " pdb=" C ASN C 616 " pdb=" CB ASN C 616 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CG LEU C 229 " pdb=" CB LEU C 229 " pdb=" CD1 LEU C 229 " pdb=" CD2 LEU C 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.34e+00 ... (remaining 3849 not shown) Planarity restraints: 4112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.006 2.00e-02 2.50e+03 6.04e-02 4.56e+01 pdb=" CG ASN A 331 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.041 2.00e-02 2.50e+03 4.62e-02 2.67e+01 pdb=" CG ASN C 616 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 987 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.063 5.00e-02 4.00e+02 ... (remaining 4109 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 196 2.57 - 3.16: 18909 3.16 - 3.74: 33304 3.74 - 4.32: 47327 4.32 - 4.90: 79055 Nonbonded interactions: 178791 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 1.992 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.047 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.052 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.063 2.440 nonbonded pdb=" OG1 THR A 912 " pdb=" OD1 ASN A 914 " model vdw 2.117 2.440 ... (remaining 178786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 344 or (resid 345 through 346 and (name N or name CA or na \ me C or name O or name CB )) or resid 347 through 350 or (resid 351 through 352 \ and (name N or name CA or name C or name O or name CB )) or resid 353 through 36 \ 3 or (resid 364 and (name N or name CA or name C or name O or name CB )) or resi \ d 365 through 368 or (resid 369 and (name N or name CA or name C or name O or na \ me CB )) or resid 370 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 407 or (resid 408 and (name N or n \ ame CA or name C or name O or name CB )) or resid 409 through 441 or (resid 442 \ and (name N or name CA or name C or name O or name CB )) or resid 443 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 496 or (resid 497 through 498 and (name N or name CA or name C or name O or na \ me CB )) or resid 503 through 504 or (resid 505 and (name N or name CA or name C \ or name O or name CB )) or resid 506 through 508 or (resid 509 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 620 or resid 641 t \ hrough 1146 or resid 1301 through 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 333 or (resid 334 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 through 348 or (resid 34 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 350 or (resi \ d 351 through 352 and (name N or name CA or name C or name O or name CB )) or re \ sid 353 through 363 or (resid 364 and (name N or name CA or name C or name O or \ name CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name \ C or name O or name CB )) or resid 375 through 397 or (resid 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 through 426 or (resid 42 \ 7 through 428 and (name N or name CA or name C or name O or name CB )) or resid \ 429 through 441 or (resid 442 and (name N or name CA or name C or name O or name \ CB )) or resid 443 through 454 or resid 491 or (resid 492 through 493 and (name \ N or name CA or name C or name O or name CB )) or resid 494 through 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 508 or (resid 509 and (name N or name CA or name C or name O or \ name CB )) or resid 510 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 th \ rough 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 344 or (r \ esid 345 through 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 454 or resid 491 through 504 or (resid 505 and (name N or nam \ e CA or name C or name O or name CB )) or resid 506 through 1146 or resid 1301 t \ hrough 1307)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.880 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 65.050 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.230 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.006 0.146 23446 Z= 0.429 Angle : 0.866 12.896 31975 Z= 0.474 Chirality : 0.058 0.832 3852 Planarity : 0.006 0.113 4075 Dihedral : 13.327 89.739 8921 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 0.04 % Allowed : 0.21 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.61 (0.15), residues: 2862 helix: 0.26 (0.20), residues: 704 sheet: 0.37 (0.20), residues: 633 loop : -1.06 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 886 HIS 0.012 0.001 HIS A 207 PHE 0.047 0.003 PHE B 275 TYR 0.046 0.002 TYR C 904 ARG 0.020 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: A 1081 ILE cc_start: 0.8113 (pt) cc_final: 0.7801 (pt) outliers start: 1 outliers final: 2 residues processed: 282 average time/residue: 1.0080 time to fit residues: 340.1820 Evaluate side-chains 200 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 808 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 196 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 271 GLN B 544 ASN B 658 ASN B 755 GLN B 804 GLN B 919 ASN B1005 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 23446 Z= 0.402 Angle : 0.757 13.062 31975 Z= 0.389 Chirality : 0.053 0.343 3852 Planarity : 0.006 0.063 4075 Dihedral : 7.768 83.145 4063 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.98 % Allowed : 9.26 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.63 (0.15), residues: 2862 helix: 0.57 (0.20), residues: 704 sheet: 0.20 (0.19), residues: 626 loop : -1.16 (0.14), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.008 0.002 HIS A 655 PHE 0.024 0.002 PHE C 43 TYR 0.029 0.002 TYR B1067 ARG 0.005 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 272 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7390 (pt) cc_final: 0.7167 (pp) REVERT: A 574 ASP cc_start: 0.6935 (t0) cc_final: 0.6694 (t0) REVERT: A 948 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8807 (mp) REVERT: B 314 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: C 388 ASN cc_start: 0.7412 (m110) cc_final: 0.7181 (t0) REVERT: C 697 MET cc_start: 0.7945 (mtp) cc_final: 0.7632 (mtp) outliers start: 72 outliers final: 19 residues processed: 319 average time/residue: 1.0353 time to fit residues: 396.3842 Evaluate side-chains 220 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 287 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 787 GLN A 954 GLN A1058 HIS A1135 ASN B 87 ASN B 271 GLN B 540 ASN B 658 ASN B 919 ASN B 992 GLN B1005 GLN B1010 GLN B1074 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23446 Z= 0.244 Angle : 0.602 10.935 31975 Z= 0.309 Chirality : 0.047 0.259 3852 Planarity : 0.005 0.056 4075 Dihedral : 6.496 55.525 4060 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.35 % Allowed : 12.98 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.34 (0.15), residues: 2862 helix: 0.93 (0.20), residues: 704 sheet: 0.35 (0.19), residues: 625 loop : -1.03 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.003 0.001 HIS B1088 PHE 0.023 0.002 PHE A 168 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 225 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7850 (pt) cc_final: 0.7590 (pp) REVERT: A 587 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (mt) REVERT: B 32 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6871 (t80) REVERT: B 53 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: B 314 GLN cc_start: 0.7941 (tt0) cc_final: 0.7720 (tt0) REVERT: C 388 ASN cc_start: 0.7473 (m110) cc_final: 0.7260 (t0) REVERT: C 697 MET cc_start: 0.7910 (mtp) cc_final: 0.7499 (mtp) outliers start: 81 outliers final: 38 residues processed: 283 average time/residue: 0.8936 time to fit residues: 309.0077 Evaluate side-chains 232 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 263 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 267 optimal weight: 0.2980 chunk 283 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 196 ASN A 919 ASN A 926 GLN A1002 GLN A1135 ASN B 271 GLN B 992 GLN B1005 GLN C 360 ASN C 388 ASN C 544 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 658 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23446 Z= 0.323 Angle : 0.650 10.571 31975 Z= 0.330 Chirality : 0.048 0.264 3852 Planarity : 0.005 0.057 4075 Dihedral : 6.088 59.124 4058 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.92 % Allowed : 13.35 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2862 helix: 1.08 (0.20), residues: 697 sheet: 0.10 (0.19), residues: 656 loop : -1.05 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.004 0.001 HIS B1083 PHE 0.033 0.002 PHE C 565 TYR 0.023 0.002 TYR B1067 ARG 0.008 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 214 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8156 (pt) cc_final: 0.7929 (pp) REVERT: A 129 LYS cc_start: 0.6750 (mttt) cc_final: 0.6071 (tmtt) REVERT: A 269 TYR cc_start: 0.8122 (m-80) cc_final: 0.7844 (m-10) REVERT: A 585 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8033 (pp) REVERT: A 948 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8813 (mp) REVERT: B 53 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: B 194 PHE cc_start: 0.7397 (m-80) cc_final: 0.7051 (m-80) REVERT: B 238 PHE cc_start: 0.6254 (p90) cc_final: 0.5949 (p90) REVERT: B 314 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7754 (tp40) REVERT: C 44 ARG cc_start: 0.6707 (mtt90) cc_final: 0.6473 (mtt-85) REVERT: C 389 ASP cc_start: 0.8113 (p0) cc_final: 0.7829 (p0) REVERT: C 565 PHE cc_start: 0.8427 (p90) cc_final: 0.8224 (p90) REVERT: C 697 MET cc_start: 0.7990 (mtp) cc_final: 0.7522 (mtp) REVERT: C 1050 MET cc_start: 0.8899 (ptm) cc_final: 0.8690 (ptm) outliers start: 119 outliers final: 53 residues processed: 305 average time/residue: 0.9102 time to fit residues: 337.6322 Evaluate side-chains 225 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 235 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 919 ASN A1002 GLN B 751 ASN B 762 GLN B 992 GLN B1005 GLN C 439 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23446 Z= 0.301 Angle : 0.613 12.007 31975 Z= 0.312 Chirality : 0.047 0.255 3852 Planarity : 0.005 0.045 4075 Dihedral : 5.685 56.593 4058 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.50 % Allowed : 14.71 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2862 helix: 1.17 (0.20), residues: 692 sheet: 0.13 (0.19), residues: 644 loop : -1.02 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.003 0.001 HIS B1088 PHE 0.027 0.002 PHE C 565 TYR 0.020 0.001 TYR B 904 ARG 0.008 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 186 time to evaluate : 2.535 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8271 (pt) cc_final: 0.8041 (pp) REVERT: A 129 LYS cc_start: 0.6845 (mttt) cc_final: 0.6201 (tptt) REVERT: A 269 TYR cc_start: 0.8170 (m-80) cc_final: 0.7837 (m-10) REVERT: A 585 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7711 (pp) REVERT: A 1142 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: B 53 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6499 (m-30) REVERT: B 194 PHE cc_start: 0.7477 (m-80) cc_final: 0.7045 (m-80) REVERT: B 314 GLN cc_start: 0.8083 (tt0) cc_final: 0.7834 (tp40) REVERT: C 564 GLN cc_start: 0.6619 (tm-30) cc_final: 0.6095 (tm-30) REVERT: C 1130 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8198 (pt) outliers start: 109 outliers final: 54 residues processed: 267 average time/residue: 0.8825 time to fit residues: 286.5315 Evaluate side-chains 225 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 167 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 95 optimal weight: 0.0470 chunk 255 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 283 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 762 GLN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 658 ASN C 703 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23446 Z= 0.207 Angle : 0.577 11.646 31975 Z= 0.292 Chirality : 0.045 0.246 3852 Planarity : 0.004 0.045 4075 Dihedral : 5.290 58.778 4058 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.64 % Allowed : 16.28 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2862 helix: 1.28 (0.21), residues: 700 sheet: 0.17 (0.19), residues: 654 loop : -0.93 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.003 0.001 HIS B1088 PHE 0.032 0.001 PHE C 565 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 194 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8235 (m-80) cc_final: 0.7961 (m-10) REVERT: A 585 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7597 (pp) REVERT: A 1142 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6702 (mp10) REVERT: B 53 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6505 (m-30) REVERT: B 194 PHE cc_start: 0.7401 (m-80) cc_final: 0.7070 (m-80) REVERT: B 314 GLN cc_start: 0.8078 (tt0) cc_final: 0.7864 (tp40) REVERT: B 994 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: C 564 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6257 (tm-30) REVERT: C 565 PHE cc_start: 0.8383 (p90) cc_final: 0.8144 (p90) outliers start: 88 outliers final: 54 residues processed: 255 average time/residue: 0.8823 time to fit residues: 276.7622 Evaluate side-chains 220 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 273 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 161 optimal weight: 0.3980 chunk 207 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 130 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23446 Z= 0.191 Angle : 0.562 11.256 31975 Z= 0.284 Chirality : 0.045 0.247 3852 Planarity : 0.004 0.044 4075 Dihedral : 5.102 56.654 4058 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.31 % Allowed : 17.40 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 2862 helix: 1.37 (0.21), residues: 700 sheet: 0.19 (0.19), residues: 655 loop : -0.88 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.002 0.000 HIS B1088 PHE 0.029 0.001 PHE C 565 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 179 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8257 (m-80) cc_final: 0.7952 (m-10) REVERT: A 585 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7566 (pp) REVERT: A 790 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8128 (mmtt) REVERT: A 1142 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6695 (mp10) REVERT: B 53 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: B 194 PHE cc_start: 0.7410 (m-80) cc_final: 0.7070 (m-80) REVERT: B 314 GLN cc_start: 0.8055 (tt0) cc_final: 0.7841 (tp40) REVERT: B 994 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: C 564 GLN cc_start: 0.7015 (tm-30) cc_final: 0.6344 (tm-30) REVERT: C 565 PHE cc_start: 0.8434 (p90) cc_final: 0.8143 (p90) REVERT: C 904 TYR cc_start: 0.6023 (t80) cc_final: 0.5761 (t80) REVERT: C 1141 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6909 (tp) outliers start: 80 outliers final: 57 residues processed: 237 average time/residue: 0.9186 time to fit residues: 264.4804 Evaluate side-chains 229 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 167 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 174 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23446 Z= 0.278 Angle : 0.590 11.378 31975 Z= 0.299 Chirality : 0.046 0.247 3852 Planarity : 0.004 0.046 4075 Dihedral : 5.170 57.603 4058 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 17.73 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2862 helix: 1.26 (0.20), residues: 706 sheet: 0.25 (0.19), residues: 647 loop : -0.92 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS B1088 PHE 0.027 0.002 PHE A 168 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 186 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6886 (mttt) cc_final: 0.6241 (ttmm) REVERT: A 269 TYR cc_start: 0.8312 (m-80) cc_final: 0.7974 (m-10) REVERT: A 585 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7543 (pp) REVERT: A 1142 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: B 53 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6507 (m-30) REVERT: B 194 PHE cc_start: 0.7608 (m-80) cc_final: 0.7171 (m-80) REVERT: B 239 GLN cc_start: 0.7079 (tt0) cc_final: 0.6642 (mm-40) REVERT: B 314 GLN cc_start: 0.8097 (tt0) cc_final: 0.7874 (tp40) REVERT: B 356 LYS cc_start: 0.5649 (ptpp) cc_final: 0.4925 (ttpp) REVERT: B 994 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: C 564 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6561 (tm-30) REVERT: C 565 PHE cc_start: 0.8513 (p90) cc_final: 0.8234 (p90) REVERT: C 904 TYR cc_start: 0.6110 (t80) cc_final: 0.5889 (t80) REVERT: C 1141 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6633 (tp) outliers start: 81 outliers final: 58 residues processed: 244 average time/residue: 0.9143 time to fit residues: 271.6739 Evaluate side-chains 235 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 256 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 206 optimal weight: 0.0030 chunk 80 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 262 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 787 GLN A1002 GLN B 580 GLN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23446 Z= 0.216 Angle : 0.582 10.996 31975 Z= 0.294 Chirality : 0.046 0.245 3852 Planarity : 0.004 0.047 4075 Dihedral : 5.064 56.646 4058 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.31 % Allowed : 18.02 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2862 helix: 1.31 (0.20), residues: 705 sheet: 0.27 (0.19), residues: 641 loop : -0.88 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 PHE 0.027 0.001 PHE A 168 TYR 0.018 0.001 TYR B 269 ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 183 time to evaluate : 2.742 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6922 (mttt) cc_final: 0.6292 (mttm) REVERT: A 269 TYR cc_start: 0.8292 (m-80) cc_final: 0.7947 (m-10) REVERT: A 1142 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: B 53 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6541 (m-30) REVERT: B 194 PHE cc_start: 0.7574 (m-80) cc_final: 0.7138 (m-80) REVERT: B 229 LEU cc_start: 0.8156 (mm) cc_final: 0.7953 (mt) REVERT: B 238 PHE cc_start: 0.7370 (p90) cc_final: 0.6975 (p90) REVERT: B 239 GLN cc_start: 0.6561 (tt0) cc_final: 0.6320 (tt0) REVERT: B 314 GLN cc_start: 0.8057 (tt0) cc_final: 0.7776 (tp40) REVERT: B 356 LYS cc_start: 0.5133 (ptpp) cc_final: 0.4707 (ttpp) REVERT: B 919 ASN cc_start: 0.8530 (p0) cc_final: 0.8306 (OUTLIER) REVERT: B 994 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: C 453 TYR cc_start: 0.5670 (p90) cc_final: 0.5364 (p90) REVERT: C 534 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8060 (m) REVERT: C 564 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6556 (tm-30) REVERT: C 565 PHE cc_start: 0.8500 (p90) cc_final: 0.8226 (p90) REVERT: C 1141 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7089 (tp) outliers start: 80 outliers final: 59 residues processed: 241 average time/residue: 0.8697 time to fit residues: 257.6886 Evaluate side-chains 233 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 170 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 172 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 232 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 580 GLN A 787 GLN B 580 GLN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23446 Z= 0.286 Angle : 0.616 11.145 31975 Z= 0.312 Chirality : 0.047 0.247 3852 Planarity : 0.004 0.047 4075 Dihedral : 5.170 57.250 4058 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.02 % Allowed : 18.55 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2862 helix: 1.31 (0.21), residues: 699 sheet: 0.21 (0.18), residues: 656 loop : -0.92 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 353 HIS 0.003 0.001 HIS C1064 PHE 0.028 0.002 PHE A 168 TYR 0.021 0.001 TYR B1067 ARG 0.009 0.001 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 2.608 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6949 (mttt) cc_final: 0.6340 (mttm) REVERT: A 269 TYR cc_start: 0.8333 (m-80) cc_final: 0.7979 (m-10) REVERT: A 1142 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: B 94 SER cc_start: 0.7509 (m) cc_final: 0.7122 (p) REVERT: B 192 PHE cc_start: 0.7999 (m-10) cc_final: 0.7593 (m-10) REVERT: B 194 PHE cc_start: 0.7711 (m-80) cc_final: 0.7433 (m-80) REVERT: B 238 PHE cc_start: 0.7424 (p90) cc_final: 0.6731 (p90) REVERT: B 314 GLN cc_start: 0.8106 (tt0) cc_final: 0.7884 (tp40) REVERT: B 356 LYS cc_start: 0.5377 (ptpp) cc_final: 0.4834 (ttpp) REVERT: B 979 ASP cc_start: 0.7814 (t70) cc_final: 0.7608 (t0) REVERT: C 534 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8130 (m) REVERT: C 564 GLN cc_start: 0.7356 (tm-30) cc_final: 0.6628 (tm-30) REVERT: C 1130 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8263 (pt) REVERT: C 1141 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6886 (tp) outliers start: 73 outliers final: 59 residues processed: 235 average time/residue: 0.8678 time to fit residues: 251.1360 Evaluate side-chains 235 residues out of total 2582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 787 GLN A1002 GLN B 544 ASN B 992 GLN B1005 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114176 restraints weight = 29843.259| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.14 r_work: 0.3141 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 23446 Z= 0.448 Angle : 0.685 14.686 31975 Z= 0.348 Chirality : 0.050 0.250 3852 Planarity : 0.005 0.055 4075 Dihedral : 5.564 58.469 4058 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.10 % Allowed : 18.97 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2862 helix: 1.11 (0.21), residues: 699 sheet: 0.10 (0.18), residues: 679 loop : -1.05 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 353 HIS 0.004 0.001 HIS C1048 PHE 0.030 0.002 PHE C 565 TYR 0.024 0.002 TYR C 904 ARG 0.008 0.001 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6849.08 seconds wall clock time: 123 minutes 34.61 seconds (7414.61 seconds total)