Starting phenix.real_space_refine on Thu Mar 21 16:07:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/03_2024/7uz7_26881.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/03_2024/7uz7_26881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/03_2024/7uz7_26881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/03_2024/7uz7_26881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/03_2024/7uz7_26881.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz7_26881/03_2024/7uz7_26881.pdb" } resolution = 2.9 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= 0.025 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 19419 2.51 5 N 5019 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 68": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30552 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 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: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 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: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8216 Classifications: {'peptide': 1059} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 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: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "N" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 16.25, per 1000 atoms: 0.53 Number of scatterers: 30552 At special positions: 0 Unit cell: (164.736, 161.408, 188.032, 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 5982 8.00 N 5019 7.00 C 19419 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 122 " " NAG C1313 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 12.32 Conformation dependent library (CDL) restraints added in 5.4 seconds 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 60 sheets defined 19.9% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.725A 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 384 through 388 removed outlier: 4.069A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.813A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.667A 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 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.579A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 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 removed outlier: 3.596A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.730A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.055A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.808A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.796A 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 886 through 890 removed outlier: 3.570A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.664A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 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 984 removed outlier: 3.625A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.794A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.548A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.720A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.065A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.809A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.569A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.790A 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 908 removed outlier: 3.655A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 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 984 removed outlier: 3.619A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.679A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.582A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.754A pdb=" N ASN H 36 " --> pdb=" O ASN H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'M' and resid 29 through 37 removed outlier: 3.789A pdb=" N ASN M 36 " --> pdb=" O ASN M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.742A pdb=" N ASN P 36 " --> pdb=" O ASN P 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.697A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.894A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A 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 removed outlier: 3.792A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.194A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 435 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.854A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.682A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.647A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.633A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.642A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.906A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.615A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.948A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.692A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.069A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 12.652A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.723A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.100A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.638A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.661A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.187A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.720A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.735A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.517A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.111A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.858A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.637A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.561A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.735A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.970A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 19 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 66 through 67 removed outlier: 5.082A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.031A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.169A pdb=" N GLU L 125 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.975A pdb=" N GLN M 3 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL M 19 " --> pdb=" O LEU M 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 66 through 67 removed outlier: 5.087A pdb=" N TRP M 52 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS M 43 " --> pdb=" O TRP M 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 54 " --> pdb=" O TRP M 41 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.801A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.670A pdb=" N GLU N 125 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR N 122 " --> pdb=" O TYR N 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.984A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL P 19 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 66 through 67 removed outlier: 5.048A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR P 122 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.846A pdb=" N THR Q 5 " --> pdb=" O LYS Q 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS Q 23 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE Q 87 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Q 122 " --> pdb=" O TYR Q 102 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE Q 54 " --> pdb=" O TRP Q 41 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN Q 43 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU Q 52 " --> pdb=" O GLN Q 43 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.63 Time building geometry restraints manager: 13.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 4372 1.25 - 1.39: 8349 1.39 - 1.54: 17592 1.54 - 1.68: 773 1.68 - 1.82: 171 Bond restraints: 31257 Sorted by residual: bond pdb=" CG PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.503 1.100 0.403 3.40e-02 8.65e+02 1.40e+02 bond pdb=" CG PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N ASN C 801 " pdb=" CA ASN C 801 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 5.98e+00 ... (remaining 31252 not shown) Histogram of bond angle deviations from ideal: 80.75 - 91.41: 4 91.41 - 102.06: 50 102.06 - 112.72: 17377 112.72 - 123.38: 24280 123.38 - 134.04: 871 Bond angle restraints: 42582 Sorted by residual: angle pdb=" N PRO A1079 " pdb=" CD PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 103.20 80.75 22.45 1.50e+00 4.44e-01 2.24e+02 angle pdb=" N PRO B1079 " pdb=" CD PRO B1079 " pdb=" CG PRO B1079 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO B1079 " pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 112.00 97.65 14.35 1.40e+00 5.10e-01 1.05e+02 angle pdb=" CA PRO A1079 " pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 112.00 98.42 13.58 1.40e+00 5.10e-01 9.41e+01 angle pdb=" CA PRO A1079 " pdb=" CB PRO A1079 " pdb=" CG PRO A1079 " ideal model delta sigma weight residual 104.50 89.34 15.16 1.90e+00 2.77e-01 6.37e+01 ... (remaining 42577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 17978 21.67 - 43.35: 968 43.35 - 65.02: 139 65.02 - 86.69: 47 86.69 - 108.36: 11 Dihedral angle restraints: 19143 sinusoidal: 7920 harmonic: 11223 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 167.97 -74.97 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 104 " pdb=" CB CYS N 104 " ideal model delta sinusoidal sigma weight residual 93.00 163.23 -70.23 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS Q 23 " pdb=" SG CYS Q 23 " pdb=" SG CYS Q 104 " pdb=" CB CYS Q 104 " ideal model delta sinusoidal sigma weight residual 93.00 154.84 -61.84 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 19140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4130 0.058 - 0.115: 747 0.115 - 0.173: 63 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 4941 not shown) Planarity restraints: 5499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.228 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" C7 NAG A1307 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.226 2.00e-02 2.50e+03 1.93e-01 4.65e+02 pdb=" C7 NAG B1307 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " -0.222 2.00e-02 2.50e+03 1.89e-01 4.49e+02 pdb=" C7 NAG C1307 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.008 2.00e-02 2.50e+03 ... (remaining 5496 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 521 2.68 - 3.23: 29270 3.23 - 3.79: 47533 3.79 - 4.34: 65317 4.34 - 4.90: 107380 Nonbonded interactions: 250021 Sorted by model distance: nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.121 2.440 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.195 2.440 nonbonded pdb=" OE1 GLN B 804 " pdb=" NE2 GLN B 935 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.209 2.440 ... (remaining 250016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.900 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: 11.280 Check model and map are aligned: 0.520 Set scattering table: 0.340 Process input model: 85.250 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.005 0.403 31257 Z= 0.277 Angle : 0.607 22.452 42582 Z= 0.327 Chirality : 0.044 0.289 4944 Planarity : 0.006 0.195 5457 Dihedral : 13.463 108.363 11811 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.04 (0.14), residues: 3813 helix: 1.79 (0.21), residues: 672 sheet: 0.32 (0.17), residues: 888 loop : -0.64 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.002 0.001 HIS B 655 PHE 0.023 0.001 PHE A 906 TYR 0.025 0.001 TYR B 248 ARG 0.005 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6905 (m-90) cc_final: 0.6613 (m-90) REVERT: A 120 VAL cc_start: 0.7684 (t) cc_final: 0.7455 (m) REVERT: B 104 TRP cc_start: 0.7650 (m-90) cc_final: 0.7262 (m-90) REVERT: B 265 TYR cc_start: 0.7589 (p90) cc_final: 0.7309 (p90) REVERT: N 4 MET cc_start: 0.2404 (tpt) cc_final: 0.2153 (tpt) REVERT: N 122 THR cc_start: 0.1325 (p) cc_final: 0.0575 (p) REVERT: Q 4 MET cc_start: 0.2405 (tpp) cc_final: 0.2165 (tpp) outliers start: 0 outliers final: 1 residues processed: 244 average time/residue: 1.1664 time to fit residues: 347.9975 Evaluate side-chains 153 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 702 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 0.0040 chunk 288 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 345 optimal weight: 50.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 913 GLN A1010 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31257 Z= 0.326 Angle : 0.612 10.786 42582 Z= 0.311 Chirality : 0.046 0.309 4944 Planarity : 0.004 0.051 5457 Dihedral : 7.937 81.630 5085 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.76 % Allowed : 8.63 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.05 (0.13), residues: 3813 helix: 1.55 (0.21), residues: 660 sheet: 0.45 (0.18), residues: 846 loop : -0.70 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.005 0.001 HIS C1088 PHE 0.026 0.002 PHE A 906 TYR 0.026 0.002 TYR B1067 ARG 0.008 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 265 TYR cc_start: 0.7256 (p90) cc_final: 0.6910 (p90) REVERT: C 177 MET cc_start: 0.6931 (mpt) cc_final: 0.6559 (tpt) REVERT: Q 4 MET cc_start: 0.2668 (tpp) cc_final: 0.2246 (tpp) outliers start: 25 outliers final: 10 residues processed: 186 average time/residue: 1.1033 time to fit residues: 256.4477 Evaluate side-chains 150 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 346 optimal weight: 20.0000 chunk 374 optimal weight: 50.0000 chunk 308 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 278 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 207 HIS ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31257 Z= 0.320 Angle : 0.598 10.914 42582 Z= 0.303 Chirality : 0.046 0.319 4944 Planarity : 0.004 0.043 5457 Dihedral : 6.939 59.792 5082 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.79 % Allowed : 11.17 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3813 helix: 1.47 (0.20), residues: 660 sheet: 0.42 (0.17), residues: 873 loop : -0.73 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.006 0.001 HIS C1088 PHE 0.026 0.002 PHE C1121 TYR 0.024 0.001 TYR B1067 ARG 0.007 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.5756 (p0) cc_final: 0.5461 (p0) REVERT: C 177 MET cc_start: 0.7027 (mpt) cc_final: 0.6786 (tpt) REVERT: C 178 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.6798 (t70) REVERT: Q 4 MET cc_start: 0.2949 (tpp) cc_final: 0.2621 (tpp) outliers start: 59 outliers final: 27 residues processed: 205 average time/residue: 1.0832 time to fit residues: 276.9312 Evaluate side-chains 170 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain L residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 30.0000 chunk 260 optimal weight: 7.9990 chunk 179 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 347 optimal weight: 50.0000 chunk 368 optimal weight: 50.0000 chunk 181 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A1011 GLN A1106 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN B1023 ASN B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31257 Z= 0.329 Angle : 0.598 11.746 42582 Z= 0.302 Chirality : 0.046 0.321 4944 Planarity : 0.004 0.046 5457 Dihedral : 6.492 56.760 5082 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.24 % Allowed : 13.14 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 3813 helix: 1.46 (0.20), residues: 660 sheet: 0.31 (0.17), residues: 909 loop : -0.79 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.005 0.001 HIS C1088 PHE 0.026 0.002 PHE C1121 TYR 0.024 0.001 TYR C 170 ARG 0.011 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 152 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.6785 (m-30) cc_final: 0.6579 (m-30) REVERT: B 122 ASN cc_start: 0.5829 (p0) cc_final: 0.5537 (p0) REVERT: B 235 ILE cc_start: 0.6342 (tp) cc_final: 0.6132 (tt) REVERT: C 177 MET cc_start: 0.6991 (mpt) cc_final: 0.6715 (tpt) REVERT: H 122 THR cc_start: 0.2460 (OUTLIER) cc_final: 0.2193 (t) outliers start: 74 outliers final: 40 residues processed: 213 average time/residue: 1.0334 time to fit residues: 275.3786 Evaluate side-chains 182 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 0.1980 chunk 209 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 151 optimal weight: 30.0000 chunk 314 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 330 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN A1106 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31257 Z= 0.267 Angle : 0.572 10.933 42582 Z= 0.288 Chirality : 0.045 0.321 4944 Planarity : 0.004 0.050 5457 Dihedral : 6.196 56.223 5082 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.51 % Allowed : 14.26 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.14 (0.13), residues: 3813 helix: 1.60 (0.20), residues: 660 sheet: 0.39 (0.17), residues: 885 loop : -0.82 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.022 0.001 PHE C1121 TYR 0.027 0.001 TYR C 170 ARG 0.008 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 152 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.6784 (m-30) cc_final: 0.6559 (m-30) REVERT: B 122 ASN cc_start: 0.6035 (p0) cc_final: 0.5737 (p0) REVERT: C 177 MET cc_start: 0.7086 (mpt) cc_final: 0.6841 (tpt) REVERT: C 178 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6996 (t70) REVERT: C 675 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7481 (tm-30) REVERT: H 122 THR cc_start: 0.2677 (OUTLIER) cc_final: 0.2404 (t) REVERT: M 122 THR cc_start: 0.2479 (OUTLIER) cc_final: 0.2249 (t) REVERT: N 74 ASP cc_start: 0.4417 (OUTLIER) cc_final: 0.4201 (m-30) REVERT: Q 4 MET cc_start: 0.2739 (OUTLIER) cc_final: 0.1965 (tpp) outliers start: 83 outliers final: 41 residues processed: 222 average time/residue: 1.0323 time to fit residues: 288.8744 Evaluate side-chains 188 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 72 optimal weight: 0.0980 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 368 optimal weight: 50.0000 chunk 306 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31257 Z= 0.305 Angle : 0.583 10.076 42582 Z= 0.294 Chirality : 0.046 0.328 4944 Planarity : 0.004 0.048 5457 Dihedral : 6.019 58.026 5082 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.60 % Allowed : 14.93 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.19 (0.13), residues: 3813 helix: 1.54 (0.20), residues: 660 sheet: 0.25 (0.16), residues: 930 loop : -0.82 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS C1088 PHE 0.029 0.002 PHE B1121 TYR 0.027 0.001 TYR C 170 ARG 0.007 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 147 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7949 (p0) REVERT: A 820 ASP cc_start: 0.6812 (m-30) cc_final: 0.6555 (m-30) REVERT: B 122 ASN cc_start: 0.6038 (p0) cc_final: 0.5745 (p0) REVERT: C 84 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5930 (mm) REVERT: C 177 MET cc_start: 0.7145 (mpt) cc_final: 0.6904 (tpt) REVERT: C 178 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7037 (t70) REVERT: C 675 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7486 (tm-30) REVERT: H 122 THR cc_start: 0.2874 (OUTLIER) cc_final: 0.2624 (t) REVERT: M 122 THR cc_start: 0.2352 (OUTLIER) cc_final: 0.2125 (t) REVERT: Q 4 MET cc_start: 0.2693 (OUTLIER) cc_final: 0.1960 (tpp) outliers start: 86 outliers final: 44 residues processed: 222 average time/residue: 1.0251 time to fit residues: 286.6909 Evaluate side-chains 191 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 40.0000 chunk 41 optimal weight: 50.0000 chunk 210 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 chunk 310 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 367 optimal weight: 50.0000 chunk 229 optimal weight: 0.0670 chunk 223 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1106 GLN B 196 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 31257 Z= 0.160 Angle : 0.536 10.843 42582 Z= 0.270 Chirality : 0.044 0.328 4944 Planarity : 0.003 0.040 5457 Dihedral : 5.567 54.930 5082 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.88 % Allowed : 16.23 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.06 (0.13), residues: 3813 helix: 1.91 (0.21), residues: 660 sheet: 0.53 (0.17), residues: 867 loop : -0.74 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.000 HIS A 207 PHE 0.016 0.001 PHE A1121 TYR 0.024 0.001 TYR C 170 ARG 0.011 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 159 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7247 (mtm-85) REVERT: A 558 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7652 (mmtm) REVERT: A 745 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7851 (p0) REVERT: B 122 ASN cc_start: 0.6091 (p0) cc_final: 0.5833 (p0) REVERT: C 177 MET cc_start: 0.7228 (mpt) cc_final: 0.6883 (tpt) REVERT: C 574 ASP cc_start: 0.7301 (t0) cc_final: 0.6900 (t0) REVERT: C 675 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7463 (tm-30) REVERT: H 122 THR cc_start: 0.2877 (OUTLIER) cc_final: 0.2630 (t) REVERT: L 4 MET cc_start: 0.1850 (tpt) cc_final: 0.1094 (tpp) REVERT: M 122 THR cc_start: 0.2331 (OUTLIER) cc_final: 0.2107 (t) REVERT: Q 4 MET cc_start: 0.2463 (OUTLIER) cc_final: 0.1698 (tpp) outliers start: 62 outliers final: 31 residues processed: 212 average time/residue: 1.0128 time to fit residues: 272.2371 Evaluate side-chains 176 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 5.9990 chunk 146 optimal weight: 50.0000 chunk 219 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 250 optimal weight: 50.0000 chunk 181 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31257 Z= 0.207 Angle : 0.549 11.455 42582 Z= 0.275 Chirality : 0.044 0.332 4944 Planarity : 0.004 0.048 5457 Dihedral : 5.476 55.511 5082 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 2.18 % Allowed : 16.14 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.09 (0.13), residues: 3813 helix: 1.92 (0.20), residues: 660 sheet: 0.54 (0.17), residues: 858 loop : -0.70 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.003 0.000 HIS C1088 PHE 0.018 0.001 PHE A1121 TYR 0.021 0.001 TYR B 170 ARG 0.013 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 145 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 122 ASN cc_start: 0.6152 (p0) cc_final: 0.5899 (p0) REVERT: C 177 MET cc_start: 0.7260 (mpt) cc_final: 0.7009 (tpt) REVERT: C 675 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7444 (tm-30) REVERT: H 122 THR cc_start: 0.2868 (OUTLIER) cc_final: 0.2620 (t) REVERT: L 4 MET cc_start: 0.1857 (OUTLIER) cc_final: 0.1094 (tpp) REVERT: M 122 THR cc_start: 0.2269 (OUTLIER) cc_final: 0.2044 (t) REVERT: Q 4 MET cc_start: 0.2326 (OUTLIER) cc_final: 0.1581 (tpp) outliers start: 72 outliers final: 40 residues processed: 206 average time/residue: 0.9702 time to fit residues: 255.9357 Evaluate side-chains 182 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 0.8980 chunk 351 optimal weight: 30.0000 chunk 320 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 149 optimal weight: 20.0000 chunk 268 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 chunk 341 optimal weight: 0.4980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN M 117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31257 Z= 0.295 Angle : 0.582 12.772 42582 Z= 0.292 Chirality : 0.046 0.344 4944 Planarity : 0.004 0.057 5457 Dihedral : 5.550 55.927 5082 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 1.79 % Allowed : 16.53 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.01 (0.13), residues: 3813 helix: 1.76 (0.21), residues: 660 sheet: 0.41 (0.17), residues: 882 loop : -0.72 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS C1088 PHE 0.025 0.002 PHE B1121 TYR 0.024 0.001 TYR C 170 ARG 0.015 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 144 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7926 (p0) REVERT: B 122 ASN cc_start: 0.6181 (p0) cc_final: 0.5953 (p0) REVERT: C 177 MET cc_start: 0.7246 (mpt) cc_final: 0.6990 (tpt) REVERT: C 675 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 745 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7860 (p0) REVERT: H 122 THR cc_start: 0.2888 (OUTLIER) cc_final: 0.2658 (t) REVERT: L 4 MET cc_start: 0.1929 (OUTLIER) cc_final: 0.1150 (tpp) REVERT: M 122 THR cc_start: 0.2256 (OUTLIER) cc_final: 0.2022 (t) REVERT: P 39 MET cc_start: 0.4024 (ptm) cc_final: 0.3594 (ttp) REVERT: Q 4 MET cc_start: 0.2366 (tpt) cc_final: 0.1612 (tpp) outliers start: 59 outliers final: 38 residues processed: 196 average time/residue: 0.9986 time to fit residues: 247.2704 Evaluate side-chains 178 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 6.9990 chunk 361 optimal weight: 30.0000 chunk 220 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 251 optimal weight: 50.0000 chunk 379 optimal weight: 8.9990 chunk 349 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 233 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN Q 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31257 Z= 0.235 Angle : 0.565 13.196 42582 Z= 0.283 Chirality : 0.045 0.350 4944 Planarity : 0.004 0.041 5457 Dihedral : 5.429 55.450 5082 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.57 % Allowed : 16.83 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.01 (0.13), residues: 3813 helix: 1.80 (0.20), residues: 660 sheet: 0.45 (0.17), residues: 861 loop : -0.72 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.019 0.001 PHE A1121 TYR 0.022 0.001 TYR B 170 ARG 0.018 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7626 Ramachandran restraints generated. 3813 Oldfield, 0 Emsley, 3813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 140 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7914 (p0) REVERT: B 122 ASN cc_start: 0.6276 (p0) cc_final: 0.6011 (p0) REVERT: C 177 MET cc_start: 0.7199 (mpt) cc_final: 0.6984 (tpt) REVERT: C 675 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7484 (tm-30) REVERT: C 745 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7849 (p0) REVERT: H 122 THR cc_start: 0.2877 (OUTLIER) cc_final: 0.2648 (t) REVERT: L 4 MET cc_start: 0.1986 (OUTLIER) cc_final: 0.1275 (tpp) REVERT: M 122 THR cc_start: 0.2205 (OUTLIER) cc_final: 0.1970 (t) REVERT: P 39 MET cc_start: 0.4055 (ptm) cc_final: 0.3590 (ttp) REVERT: Q 4 MET cc_start: 0.2397 (OUTLIER) cc_final: 0.1646 (tpp) outliers start: 52 outliers final: 40 residues processed: 185 average time/residue: 0.9661 time to fit residues: 230.5474 Evaluate side-chains 178 residues out of total 3363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain Q residue 4 MET Chi-restraints excluded: chain Q residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 126 optimal weight: 40.0000 chunk 310 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.221146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.133548 restraints weight = 42795.532| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.73 r_work: 0.3320 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31257 Z= 0.222 Angle : 0.562 13.250 42582 Z= 0.281 Chirality : 0.045 0.347 4944 Planarity : 0.004 0.045 5457 Dihedral : 5.365 55.360 5082 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.57 % Allowed : 16.89 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.03 (0.13), residues: 3813 helix: 1.80 (0.20), residues: 678 sheet: 0.46 (0.17), residues: 861 loop : -0.72 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.019 0.001 PHE A1121 TYR 0.024 0.001 TYR C 170 ARG 0.015 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8632.78 seconds wall clock time: 155 minutes 24.70 seconds (9324.70 seconds total)