Starting phenix.real_space_refine on Fri Jul 26 02:18:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz6_26880/07_2024/7uz6_26880.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz6_26880/07_2024/7uz6_26880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz6_26880/07_2024/7uz6_26880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz6_26880/07_2024/7uz6_26880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz6_26880/07_2024/7uz6_26880.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz6_26880/07_2024/7uz6_26880.cif" } resolution = 2.8 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= -0.001 sd= 0.029 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 132 5.16 5 C 19689 2.51 5 N 5106 2.21 5 O 6015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.87s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30942 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8356 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1019} Chain breaks: 4 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "P" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.17, per 1000 atoms: 0.52 Number of scatterers: 30942 At special positions: 0 Unit cell: (153.088, 151.424, 189.696, 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 132 16.00 O 6015 8.00 N 5106 7.00 C 19689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B 234 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C 234 " " NAG C1313 " - " ASN C 282 " Time building additional restraints: 11.18 Conformation dependent library (CDL) restraints added in 5.7 seconds 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7302 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 71 sheets defined 21.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.263A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.302A 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 636 through 640 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.619A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.591A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.472A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.631A pdb=" N THR B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.136A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.732A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.588A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.212A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.578A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.609A pdb=" N THR C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.131A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.667A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.876A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.096A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.499A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.461A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.090A pdb=" N TYR H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.129A pdb=" N ILE L 99 " --> pdb=" O SER L 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'N' and resid 95 through 100 removed outlier: 3.504A pdb=" N ILE N 99 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA N 100 " --> pdb=" O GLU N 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 removed outlier: 3.564A pdb=" N SER P 99 " --> pdb=" O SER P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.739A pdb=" N ILE Q 99 " --> pdb=" O SER Q 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.898A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.899A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.965A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.036A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.236A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.805A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.628A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.723A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.587A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.603A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.495A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.881A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.584A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.042A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.781A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.542A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.540A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.209A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.731A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.614A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.320A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.740A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.003A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.161A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.760A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.201A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.711A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.706A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.539A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.652A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.196A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.575A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.489A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.489A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF8, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AF9, first strand: chain 'H' and resid 64 through 67 removed outlier: 3.585A pdb=" N PHE H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 64 through 67 removed outlier: 3.585A pdb=" N PHE H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.952A pdb=" N ASP L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER L 83 " --> pdb=" O ASP L 86 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.591A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.789A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG L 51 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.613A pdb=" N THR M 77 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 65 through 67 removed outlier: 6.897A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP M 55 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE M 39 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.576A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.576A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP N 86 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 83 " --> pdb=" O ASP N 86 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'N' and resid 66 through 67 removed outlier: 6.851A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS N 55 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE N 39 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'P' and resid 64 through 67 removed outlier: 3.505A pdb=" N PHE P 64 " --> pdb=" O TYR P 57 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR P 66 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP P 41 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASP P 55 " --> pdb=" O ILE P 39 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE P 39 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL P 42 " --> pdb=" O TYR P 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.589A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 24 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.589A pdb=" N THR Q 5 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 24 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP Q 86 " --> pdb=" O SER Q 83 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Q 83 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.502A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE Q 39 " --> pdb=" O LYS Q 55 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS Q 55 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.502A pdb=" N LEU Q 11 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.83 Time building geometry restraints manager: 12.59 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: 9921 1.35 - 1.47: 8210 1.47 - 1.59: 13386 1.59 - 1.72: 1 1.72 - 1.84: 168 Bond restraints: 31686 Sorted by residual: bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" CB PRO B 230 " pdb=" CG PRO B 230 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 ... (remaining 31681 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.84: 720 105.84 - 112.88: 17098 112.88 - 119.92: 9946 119.92 - 126.96: 15065 126.96 - 134.00: 353 Bond angle restraints: 43182 Sorted by residual: angle pdb=" N VAL B 127 " pdb=" CA VAL B 127 " pdb=" C VAL B 127 " ideal model delta sigma weight residual 106.21 110.32 -4.11 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N VAL A 127 " pdb=" CA VAL A 127 " pdb=" C VAL A 127 " ideal model delta sigma weight residual 106.21 110.05 -3.84 1.07e+00 8.73e-01 1.29e+01 angle pdb=" N GLY A1124 " pdb=" CA GLY A1124 " pdb=" C GLY A1124 " ideal model delta sigma weight residual 111.21 114.92 -3.71 1.04e+00 9.25e-01 1.28e+01 angle pdb=" C ARG A 102 " pdb=" N GLY A 103 " pdb=" CA GLY A 103 " ideal model delta sigma weight residual 122.03 117.66 4.37 1.28e+00 6.10e-01 1.17e+01 angle pdb=" N GLY C1124 " pdb=" CA GLY C1124 " pdb=" C GLY C1124 " ideal model delta sigma weight residual 111.21 114.74 -3.53 1.04e+00 9.25e-01 1.15e+01 ... (remaining 43177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.76: 18175 22.76 - 45.52: 954 45.52 - 68.28: 101 68.28 - 91.04: 36 91.04 - 113.79: 3 Dihedral angle restraints: 19269 sinusoidal: 7902 harmonic: 11367 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -24.51 -61.49 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 153.52 -60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -34.74 -51.26 1 1.00e+01 1.00e-02 3.59e+01 ... (remaining 19266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4290 0.065 - 0.130: 664 0.130 - 0.195: 8 0.195 - 0.260: 3 0.260 - 0.325: 6 Chirality restraints: 4971 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4968 not shown) Planarity restraints: 5583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO L 50 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 49 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO N 50 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO N 50 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 50 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.015 2.00e-02 2.50e+03 1.52e-02 4.07e+00 pdb=" CG PHE A 906 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.002 2.00e-02 2.50e+03 ... (remaining 5580 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 315 2.62 - 3.19: 27230 3.19 - 3.76: 47629 3.76 - 4.33: 67680 4.33 - 4.90: 113970 Nonbonded interactions: 256824 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.055 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.199 2.440 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.202 2.440 nonbonded pdb=" OG SER A 155 " pdb=" NH1 ARG A 246 " model vdw 2.209 2.520 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.212 2.440 ... (remaining 256819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 2.830 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: 1.240 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 87.700 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.160 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.004 0.107 31686 Z= 0.243 Angle : 0.563 6.762 43182 Z= 0.301 Chirality : 0.045 0.325 4971 Planarity : 0.004 0.096 5544 Dihedral : 13.209 113.795 11841 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.03 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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 (0.13), residues: 3864 helix: 1.46 (0.20), residues: 731 sheet: -0.08 (0.16), residues: 1004 loop : -0.95 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 258 HIS 0.004 0.001 HIS A 625 PHE 0.035 0.001 PHE A 906 TYR 0.021 0.001 TYR B 636 ARG 0.008 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 377 time to evaluate : 3.520 Fit side-chains REVERT: A 153 MET cc_start: 0.7049 (tpt) cc_final: 0.6755 (ptt) REVERT: A 495 TYR cc_start: 0.6814 (t80) cc_final: 0.6544 (t80) REVERT: A 1123 SER cc_start: 0.8614 (m) cc_final: 0.8340 (m) REVERT: B 463 PRO cc_start: 0.8981 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: H 89 MET cc_start: 0.4529 (ppp) cc_final: 0.3804 (ppp) REVERT: M 21 MET cc_start: 0.6675 (mmt) cc_final: 0.6117 (mpt) REVERT: M 43 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6879 (ttmm) REVERT: N 91 ILE cc_start: 0.6764 (mt) cc_final: 0.6549 (pt) REVERT: P 21 MET cc_start: 0.6663 (mmt) cc_final: 0.6179 (mpt) REVERT: P 89 MET cc_start: 0.4287 (ppp) cc_final: 0.3850 (ppp) REVERT: P 108 ASP cc_start: 0.7173 (t70) cc_final: 0.6951 (t70) REVERT: P 113 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7157 (ptp-110) outliers start: 1 outliers final: 2 residues processed: 377 average time/residue: 1.2430 time to fit residues: 565.4640 Evaluate side-chains 264 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain B residue 794 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 0.0570 chunk 155 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 196 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 422 ASN B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN H 36 HIS L 108 ASN N 108 ASN P 44 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31686 Z= 0.310 Angle : 0.586 12.167 43182 Z= 0.303 Chirality : 0.047 0.327 4971 Planarity : 0.004 0.065 5544 Dihedral : 6.506 97.242 5020 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.46 % Allowed : 7.27 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.34 (0.13), residues: 3864 helix: 1.79 (0.20), residues: 682 sheet: -0.17 (0.16), residues: 997 loop : -0.92 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.005 0.001 HIS A 49 PHE 0.029 0.002 PHE A 906 TYR 0.033 0.002 TYR H 109 ARG 0.009 0.001 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 297 time to evaluate : 3.651 Fit side-chains REVERT: A 153 MET cc_start: 0.6734 (tpt) cc_final: 0.6446 (ptt) REVERT: A 564 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: B 463 PRO cc_start: 0.8945 (Cg_exo) cc_final: 0.8550 (Cg_endo) REVERT: C 153 MET cc_start: 0.5834 (pp-130) cc_final: 0.4944 (pmm) REVERT: C 309 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: H 89 MET cc_start: 0.4320 (ppp) cc_final: 0.3869 (ppp) REVERT: M 21 MET cc_start: 0.6476 (mmt) cc_final: 0.6040 (mpt) REVERT: M 40 SER cc_start: 0.8523 (t) cc_final: 0.8280 (p) REVERT: M 113 ARG cc_start: 0.7874 (mpp-170) cc_final: 0.7229 (ptp-110) REVERT: P 21 MET cc_start: 0.6430 (mmt) cc_final: 0.5640 (mmm) REVERT: P 41 TRP cc_start: 0.5772 (m100) cc_final: 0.5522 (m100) REVERT: P 89 MET cc_start: 0.4566 (ppp) cc_final: 0.4218 (ppp) outliers start: 49 outliers final: 24 residues processed: 323 average time/residue: 1.0893 time to fit residues: 433.4529 Evaluate side-chains 297 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 271 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 56 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 349 optimal weight: 20.0000 chunk 377 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 50.0000 chunk 280 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN H 36 HIS N 108 ASN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 31686 Z= 0.394 Angle : 0.603 11.427 43182 Z= 0.311 Chirality : 0.048 0.331 4971 Planarity : 0.004 0.054 5544 Dihedral : 6.311 95.552 5016 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.50 % Allowed : 10.10 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.47 (0.13), residues: 3864 helix: 1.70 (0.20), residues: 681 sheet: -0.37 (0.15), residues: 1034 loop : -0.93 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 38 HIS 0.007 0.001 HIS A 625 PHE 0.031 0.002 PHE A 906 TYR 0.026 0.002 TYR H 109 ARG 0.012 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 286 time to evaluate : 3.358 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6712 (tpt) cc_final: 0.6443 (ptt) REVERT: A 564 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: A 756 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: A 902 MET cc_start: 0.8261 (tpt) cc_final: 0.8032 (mmt) REVERT: C 153 MET cc_start: 0.6178 (pp-130) cc_final: 0.5188 (pmm) REVERT: C 309 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: C 495 TYR cc_start: 0.7079 (t80) cc_final: 0.6811 (t80) REVERT: H 21 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5464 (mpt) REVERT: H 89 MET cc_start: 0.4437 (ppp) cc_final: 0.3597 (ppp) REVERT: M 21 MET cc_start: 0.6443 (mmt) cc_final: 0.6048 (mpt) REVERT: M 43 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7283 (ttmm) REVERT: M 113 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7139 (ptp-110) REVERT: P 21 MET cc_start: 0.6344 (mmt) cc_final: 0.5663 (mmm) REVERT: P 41 TRP cc_start: 0.5862 (m100) cc_final: 0.5608 (m100) REVERT: P 89 MET cc_start: 0.4333 (ppp) cc_final: 0.4058 (ppp) REVERT: P 108 ASP cc_start: 0.7005 (t70) cc_final: 0.6801 (t70) REVERT: P 113 ARG cc_start: 0.7841 (mtm110) cc_final: 0.6945 (ptp-110) outliers start: 84 outliers final: 41 residues processed: 332 average time/residue: 1.1002 time to fit residues: 453.0912 Evaluate side-chains 317 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 271 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 371 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 332 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS N 108 ASN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31686 Z= 0.185 Angle : 0.536 11.604 43182 Z= 0.275 Chirality : 0.045 0.326 4971 Planarity : 0.004 0.053 5544 Dihedral : 5.958 92.130 5016 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.03 % Allowed : 11.56 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 3864 helix: 2.06 (0.20), residues: 681 sheet: -0.30 (0.15), residues: 1047 loop : -0.92 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 38 HIS 0.005 0.001 HIS A 49 PHE 0.020 0.001 PHE H 64 TYR 0.026 0.001 TYR H 109 ARG 0.009 0.001 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 287 time to evaluate : 3.345 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6041 (ppp) cc_final: 0.5178 (ppp) REVERT: A 357 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7818 (ptm160) REVERT: A 558 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8473 (mptp) REVERT: A 574 ASP cc_start: 0.7815 (t0) cc_final: 0.7497 (t0) REVERT: A 756 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: A 902 MET cc_start: 0.8193 (tpt) cc_final: 0.7992 (mmt) REVERT: B 646 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7463 (ttp80) REVERT: C 153 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5037 (pmm) REVERT: C 495 TYR cc_start: 0.7018 (t80) cc_final: 0.6794 (t80) REVERT: C 1092 GLU cc_start: 0.8010 (tp30) cc_final: 0.7692 (pt0) REVERT: H 21 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5505 (mpt) REVERT: H 43 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7590 (ttmm) REVERT: H 89 MET cc_start: 0.4412 (ppp) cc_final: 0.3606 (ppp) REVERT: H 107 TRP cc_start: 0.8388 (t60) cc_final: 0.8172 (t60) REVERT: L 108 ASN cc_start: 0.8240 (t0) cc_final: 0.8034 (t0) REVERT: M 21 MET cc_start: 0.6463 (mmt) cc_final: 0.6090 (mpt) REVERT: M 43 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7207 (ttmm) REVERT: M 64 PHE cc_start: 0.8202 (t80) cc_final: 0.7638 (t80) REVERT: M 113 ARG cc_start: 0.7851 (mpp-170) cc_final: 0.6960 (ptp-110) REVERT: N 27 GLN cc_start: 0.8002 (mp-120) cc_final: 0.7694 (mm-40) REVERT: P 21 MET cc_start: 0.6257 (mmt) cc_final: 0.5501 (mmm) REVERT: P 41 TRP cc_start: 0.5913 (m100) cc_final: 0.5652 (m100) REVERT: P 89 MET cc_start: 0.4389 (ppp) cc_final: 0.4063 (ppp) REVERT: P 113 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7034 (ptp-110) outliers start: 68 outliers final: 27 residues processed: 327 average time/residue: 1.1558 time to fit residues: 467.1015 Evaluate side-chains 308 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 277 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 276 optimal weight: 0.9980 chunk 153 optimal weight: 0.0670 chunk 316 optimal weight: 0.7980 chunk 256 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 333 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 354 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 675 GLN H 36 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31686 Z= 0.159 Angle : 0.517 11.368 43182 Z= 0.263 Chirality : 0.045 0.326 4971 Planarity : 0.004 0.050 5544 Dihedral : 5.582 85.891 5016 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 2.17 % Allowed : 12.39 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.18 (0.13), residues: 3864 helix: 2.26 (0.20), residues: 686 sheet: -0.23 (0.16), residues: 1023 loop : -0.85 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 38 HIS 0.005 0.001 HIS A 625 PHE 0.025 0.001 PHE H 64 TYR 0.026 0.001 TYR A 453 ARG 0.011 0.001 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 299 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6946 (tmtt) cc_final: 0.6459 (tptp) REVERT: A 177 MET cc_start: 0.5941 (ppp) cc_final: 0.4824 (ppp) REVERT: A 237 ARG cc_start: 0.6996 (mtm-85) cc_final: 0.6790 (mtm-85) REVERT: A 467 ASP cc_start: 0.7559 (t70) cc_final: 0.7305 (t0) REVERT: A 558 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8432 (mptp) REVERT: A 564 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: A 574 ASP cc_start: 0.7732 (t0) cc_final: 0.7414 (t0) REVERT: A 756 TYR cc_start: 0.7358 (t80) cc_final: 0.6945 (m-80) REVERT: A 902 MET cc_start: 0.8226 (tpt) cc_final: 0.8002 (mmt) REVERT: A 1092 GLU cc_start: 0.7911 (tp30) cc_final: 0.7445 (pt0) REVERT: B 240 THR cc_start: 0.7723 (p) cc_final: 0.7338 (p) REVERT: B 346 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8017 (ttm110) REVERT: B 646 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7443 (ttp80) REVERT: C 153 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.5010 (pmm) REVERT: C 1092 GLU cc_start: 0.7959 (tp30) cc_final: 0.7706 (pt0) REVERT: H 21 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5713 (mmm) REVERT: H 43 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7577 (ttmm) REVERT: H 89 MET cc_start: 0.4448 (ppp) cc_final: 0.4173 (ppp) REVERT: L 66 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8071 (mt-10) REVERT: M 21 MET cc_start: 0.6483 (mmt) cc_final: 0.6092 (mpt) REVERT: M 43 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7208 (ttmm) REVERT: M 64 PHE cc_start: 0.8253 (t80) cc_final: 0.7608 (t80) REVERT: M 113 ARG cc_start: 0.7782 (mpp-170) cc_final: 0.7088 (ptp-110) REVERT: N 27 GLN cc_start: 0.8050 (mp-120) cc_final: 0.7699 (mm-40) REVERT: P 21 MET cc_start: 0.6216 (mmt) cc_final: 0.5634 (mmm) REVERT: P 89 MET cc_start: 0.4383 (ppp) cc_final: 0.4000 (ppp) REVERT: P 113 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7056 (ptp-110) outliers start: 73 outliers final: 30 residues processed: 345 average time/residue: 1.1165 time to fit residues: 474.9678 Evaluate side-chains 315 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 280 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.0980 chunk 334 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS L 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31686 Z= 0.172 Angle : 0.518 11.109 43182 Z= 0.263 Chirality : 0.044 0.325 4971 Planarity : 0.004 0.050 5544 Dihedral : 5.189 57.620 5016 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 2.29 % Allowed : 13.40 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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 (0.13), residues: 3864 helix: 2.33 (0.20), residues: 686 sheet: -0.12 (0.16), residues: 1007 loop : -0.85 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 107 HIS 0.005 0.001 HIS A 207 PHE 0.018 0.001 PHE M 71 TYR 0.023 0.001 TYR A 453 ARG 0.013 0.001 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 297 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7437 (m-80) cc_final: 0.6849 (m-80) REVERT: A 153 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.4629 (tpt) REVERT: A 177 MET cc_start: 0.5975 (ppp) cc_final: 0.4860 (ppp) REVERT: A 233 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5898 (mt) REVERT: A 237 ARG cc_start: 0.7004 (mtm-85) cc_final: 0.6799 (mtm-85) REVERT: A 558 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8402 (mptp) REVERT: A 564 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: A 574 ASP cc_start: 0.7771 (t0) cc_final: 0.7447 (t0) REVERT: A 756 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: A 902 MET cc_start: 0.8150 (tpt) cc_final: 0.7944 (mmt) REVERT: A 1092 GLU cc_start: 0.7876 (tp30) cc_final: 0.7480 (pt0) REVERT: B 346 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7999 (ttm110) REVERT: B 646 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7460 (ttp80) REVERT: B 1106 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: C 153 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5006 (pmm) REVERT: C 309 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: C 495 TYR cc_start: 0.6630 (t80) cc_final: 0.6422 (t80) REVERT: C 900 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7494 (mtp) REVERT: C 1092 GLU cc_start: 0.7929 (tp30) cc_final: 0.7695 (pt0) REVERT: C 1144 GLU cc_start: 0.8752 (mp0) cc_final: 0.8518 (mp0) REVERT: H 21 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5911 (mmm) REVERT: H 39 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8022 (tp) REVERT: H 43 LYS cc_start: 0.7937 (ttpp) cc_final: 0.7238 (ttmm) REVERT: H 89 MET cc_start: 0.4330 (ppp) cc_final: 0.4018 (ppp) REVERT: L 66 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8058 (mt-10) REVERT: M 21 MET cc_start: 0.6486 (mmt) cc_final: 0.6141 (mpt) REVERT: M 45 ARG cc_start: 0.8781 (mtp-110) cc_final: 0.8493 (mtp-110) REVERT: M 113 ARG cc_start: 0.7784 (mpp-170) cc_final: 0.7126 (ptp-110) REVERT: P 43 LYS cc_start: 0.7593 (tttt) cc_final: 0.6970 (tmtt) REVERT: P 89 MET cc_start: 0.4407 (ppp) cc_final: 0.3776 (ppp) REVERT: P 113 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7061 (ptp-110) outliers start: 77 outliers final: 30 residues processed: 342 average time/residue: 1.1299 time to fit residues: 477.2435 Evaluate side-chains 320 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 312 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 chunk 370 optimal weight: 0.3980 chunk 231 optimal weight: 0.8980 chunk 225 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1010 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31686 Z= 0.227 Angle : 0.534 11.176 43182 Z= 0.271 Chirality : 0.045 0.325 4971 Planarity : 0.004 0.050 5544 Dihedral : 5.111 57.824 5016 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.53 % Allowed : 13.79 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.16 (0.13), residues: 3864 helix: 2.28 (0.20), residues: 680 sheet: -0.18 (0.16), residues: 1030 loop : -0.85 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 107 HIS 0.005 0.001 HIS A 207 PHE 0.017 0.001 PHE H 71 TYR 0.025 0.001 TYR A 170 ARG 0.011 0.001 ARG M 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 287 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7104 (tmtt) cc_final: 0.6586 (tptp) REVERT: A 153 MET cc_start: 0.5424 (OUTLIER) cc_final: 0.4647 (tpt) REVERT: A 177 MET cc_start: 0.5991 (ppp) cc_final: 0.4760 (ppp) REVERT: A 233 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5975 (mt) REVERT: A 467 ASP cc_start: 0.7546 (t70) cc_final: 0.7248 (t0) REVERT: A 558 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8388 (mptp) REVERT: A 564 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: A 574 ASP cc_start: 0.7813 (t0) cc_final: 0.7452 (t0) REVERT: A 756 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: A 902 MET cc_start: 0.8191 (tpt) cc_final: 0.7972 (mmt) REVERT: A 1092 GLU cc_start: 0.7922 (tp30) cc_final: 0.7521 (pt0) REVERT: B 346 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7994 (ttm110) REVERT: B 646 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7564 (ttp80) REVERT: C 153 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5011 (pmm) REVERT: C 309 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: C 495 TYR cc_start: 0.6761 (t80) cc_final: 0.6513 (t80) REVERT: C 1092 GLU cc_start: 0.7992 (tp30) cc_final: 0.7703 (pt0) REVERT: C 1144 GLU cc_start: 0.8757 (mp0) cc_final: 0.8509 (mp0) REVERT: H 21 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5871 (mmm) REVERT: H 43 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7450 (ttmm) REVERT: H 53 ILE cc_start: 0.6902 (mm) cc_final: 0.6458 (mp) REVERT: H 89 MET cc_start: 0.4428 (ppp) cc_final: 0.4204 (ppp) REVERT: L 66 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8095 (mt-10) REVERT: M 21 MET cc_start: 0.6547 (mmt) cc_final: 0.6175 (mpt) REVERT: M 43 LYS cc_start: 0.7640 (ttpp) cc_final: 0.7226 (ttmm) REVERT: M 64 PHE cc_start: 0.8151 (t80) cc_final: 0.7529 (t80) REVERT: M 113 ARG cc_start: 0.7770 (mpp-170) cc_final: 0.7121 (ptp-110) REVERT: N 26 SER cc_start: 0.8829 (t) cc_final: 0.8622 (m) REVERT: N 27 GLN cc_start: 0.8019 (mp10) cc_final: 0.7805 (mm110) REVERT: P 89 MET cc_start: 0.4369 (ppp) cc_final: 0.3781 (ppp) outliers start: 85 outliers final: 42 residues processed: 335 average time/residue: 1.1288 time to fit residues: 470.5240 Evaluate side-chains 326 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 275 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 787 GLN A1010 GLN B 437 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN H 36 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31686 Z= 0.348 Angle : 0.579 11.385 43182 Z= 0.295 Chirality : 0.047 0.329 4971 Planarity : 0.004 0.051 5544 Dihedral : 5.223 58.020 5016 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 2.20 % Allowed : 14.24 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.30 (0.13), residues: 3864 helix: 2.14 (0.21), residues: 669 sheet: -0.32 (0.16), residues: 1043 loop : -0.88 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 107 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.002 PHE B1121 TYR 0.022 0.002 TYR A1067 ARG 0.013 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 273 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7048 (tmtt) cc_final: 0.6477 (tptp) REVERT: A 153 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.4580 (tpt) REVERT: A 177 MET cc_start: 0.6065 (ppp) cc_final: 0.4862 (ppp) REVERT: A 233 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6210 (mt) REVERT: A 467 ASP cc_start: 0.7598 (t70) cc_final: 0.7263 (t0) REVERT: A 558 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8421 (mptp) REVERT: A 564 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: A 574 ASP cc_start: 0.7816 (t0) cc_final: 0.7503 (t0) REVERT: A 756 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7284 (m-80) REVERT: A 902 MET cc_start: 0.8244 (tpt) cc_final: 0.7983 (mmt) REVERT: B 153 MET cc_start: 0.6839 (mmm) cc_final: 0.6442 (mmm) REVERT: B 346 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8111 (ttm110) REVERT: B 646 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7561 (ttp80) REVERT: C 153 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5136 (pmm) REVERT: C 309 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: C 495 TYR cc_start: 0.6856 (t80) cc_final: 0.6581 (t80) REVERT: H 21 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5852 (mmm) REVERT: H 43 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7272 (ttmm) REVERT: H 53 ILE cc_start: 0.6808 (mm) cc_final: 0.6403 (mt) REVERT: H 89 MET cc_start: 0.4444 (ppp) cc_final: 0.4147 (ppp) REVERT: H 107 TRP cc_start: 0.8337 (t60) cc_final: 0.7742 (t60) REVERT: L 66 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8088 (mt-10) REVERT: M 21 MET cc_start: 0.6534 (mmt) cc_final: 0.6178 (mpt) REVERT: M 43 LYS cc_start: 0.7692 (ttpp) cc_final: 0.7273 (ttmm) REVERT: M 64 PHE cc_start: 0.8078 (t80) cc_final: 0.7549 (t80) REVERT: M 113 ARG cc_start: 0.7768 (mpp-170) cc_final: 0.6889 (ptp-110) REVERT: N 26 SER cc_start: 0.8774 (t) cc_final: 0.8565 (m) REVERT: N 27 GLN cc_start: 0.7969 (mp10) cc_final: 0.7732 (mm110) REVERT: P 89 MET cc_start: 0.4176 (ppp) cc_final: 0.3621 (ppp) outliers start: 74 outliers final: 46 residues processed: 314 average time/residue: 1.0901 time to fit residues: 423.3609 Evaluate side-chains 322 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 267 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 7.9990 chunk 354 optimal weight: 40.0000 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 270 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 311 optimal weight: 0.7980 chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS L 108 ASN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31686 Z= 0.398 Angle : 0.607 10.703 43182 Z= 0.310 Chirality : 0.047 0.329 4971 Planarity : 0.004 0.048 5544 Dihedral : 5.335 57.776 5016 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.63 % Rotamer: Outliers : 2.38 % Allowed : 14.24 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.48 (0.13), residues: 3864 helix: 1.80 (0.20), residues: 683 sheet: -0.42 (0.16), residues: 1044 loop : -0.97 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.006 0.001 HIS A 625 PHE 0.018 0.002 PHE B 238 TYR 0.029 0.002 TYR A 453 ARG 0.012 0.001 ARG M 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 272 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7099 (tmtt) cc_final: 0.6447 (tptp) REVERT: A 153 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.4619 (tpt) REVERT: A 177 MET cc_start: 0.6097 (ppp) cc_final: 0.4950 (ppp) REVERT: A 467 ASP cc_start: 0.7658 (t70) cc_final: 0.7268 (t0) REVERT: A 558 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8435 (mptp) REVERT: A 564 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 574 ASP cc_start: 0.7897 (t0) cc_final: 0.7600 (t0) REVERT: A 756 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: B 346 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8091 (ttm110) REVERT: B 646 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7520 (ttp80) REVERT: B 1029 MET cc_start: 0.8656 (tpp) cc_final: 0.8398 (tpp) REVERT: C 153 MET cc_start: 0.6291 (OUTLIER) cc_final: 0.5245 (pmm) REVERT: C 495 TYR cc_start: 0.6944 (t80) cc_final: 0.6736 (t80) REVERT: C 675 GLN cc_start: 0.7683 (mt0) cc_final: 0.7041 (pt0) REVERT: H 21 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5914 (mmm) REVERT: H 89 MET cc_start: 0.4533 (ppp) cc_final: 0.4161 (ppp) REVERT: H 107 TRP cc_start: 0.8385 (t60) cc_final: 0.7624 (t60) REVERT: L 66 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8080 (mt-10) REVERT: M 21 MET cc_start: 0.6477 (mmt) cc_final: 0.6090 (mpt) REVERT: M 43 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7298 (ttmm) REVERT: M 64 PHE cc_start: 0.8190 (t80) cc_final: 0.7583 (t80) REVERT: M 113 ARG cc_start: 0.7740 (mpp-170) cc_final: 0.7306 (ptp-110) REVERT: N 52 LEU cc_start: 0.7575 (tp) cc_final: 0.7279 (tp) REVERT: N 103 TYR cc_start: 0.6468 (m-10) cc_final: 0.5902 (m-10) REVERT: P 89 MET cc_start: 0.4381 (ppp) cc_final: 0.3771 (ppp) outliers start: 80 outliers final: 43 residues processed: 319 average time/residue: 1.0652 time to fit residues: 421.4375 Evaluate side-chains 315 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 607 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 20.0000 chunk 364 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 253 optimal weight: 0.9980 chunk 382 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31686 Z= 0.195 Angle : 0.542 12.601 43182 Z= 0.277 Chirality : 0.045 0.326 4971 Planarity : 0.004 0.056 5544 Dihedral : 5.080 57.049 5016 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.64 % Allowed : 15.22 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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 (0.13), residues: 3864 helix: 2.15 (0.20), residues: 680 sheet: -0.40 (0.16), residues: 1056 loop : -0.89 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 107 HIS 0.005 0.001 HIS A 207 PHE 0.023 0.001 PHE P 71 TYR 0.029 0.001 TYR A 453 ARG 0.013 0.001 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4599 (tpt) REVERT: A 177 MET cc_start: 0.6099 (ppp) cc_final: 0.4893 (ppp) REVERT: A 467 ASP cc_start: 0.7601 (t70) cc_final: 0.7236 (t0) REVERT: A 558 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8454 (mptp) REVERT: A 756 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7182 (m-80) REVERT: A 1092 GLU cc_start: 0.7965 (tp30) cc_final: 0.7520 (pt0) REVERT: B 34 ARG cc_start: 0.6074 (mmt180) cc_final: 0.5808 (mmt180) REVERT: B 153 MET cc_start: 0.6792 (mmm) cc_final: 0.6387 (mmm) REVERT: B 237 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.6294 (mpp80) REVERT: B 646 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7523 (ttp80) REVERT: C 153 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5272 (pmm) REVERT: C 284 THR cc_start: 0.8530 (p) cc_final: 0.8303 (t) REVERT: H 21 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5851 (mmm) REVERT: H 53 ILE cc_start: 0.6862 (mm) cc_final: 0.6429 (mt) REVERT: H 89 MET cc_start: 0.4590 (ppp) cc_final: 0.4235 (ppp) REVERT: H 107 TRP cc_start: 0.8368 (t60) cc_final: 0.7664 (t60) REVERT: M 21 MET cc_start: 0.6489 (mmt) cc_final: 0.6095 (mpt) REVERT: M 43 LYS cc_start: 0.7727 (ttpp) cc_final: 0.6879 (ttmm) REVERT: M 64 PHE cc_start: 0.8164 (t80) cc_final: 0.7577 (t80) REVERT: M 113 ARG cc_start: 0.7721 (mpp-170) cc_final: 0.7256 (ptp-110) REVERT: N 27 GLN cc_start: 0.8010 (mp10) cc_final: 0.7672 (mm-40) REVERT: P 53 ILE cc_start: 0.7420 (mm) cc_final: 0.7052 (mt) REVERT: P 89 MET cc_start: 0.4594 (ppp) cc_final: 0.3908 (ppp) outliers start: 55 outliers final: 37 residues processed: 300 average time/residue: 1.0965 time to fit residues: 407.7392 Evaluate side-chains 300 residues out of total 3417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 258 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain Q residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 44 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 108 ASN N 44 GLN ** N 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.197129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120381 restraints weight = 38460.263| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.71 r_work: 0.3361 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31686 Z= 0.175 Angle : 0.531 12.005 43182 Z= 0.270 Chirality : 0.044 0.324 4971 Planarity : 0.004 0.055 5544 Dihedral : 4.878 56.906 5016 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 1.40 % Allowed : 15.61 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.18 (0.14), residues: 3864 helix: 2.43 (0.20), residues: 668 sheet: -0.33 (0.16), residues: 1046 loop : -0.83 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 38 HIS 0.006 0.001 HIS A 207 PHE 0.036 0.001 PHE P 64 TYR 0.038 0.001 TYR A 170 ARG 0.016 0.001 ARG M 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9770.26 seconds wall clock time: 173 minutes 26.20 seconds (10406.20 seconds total)