Starting phenix.real_space_refine on Fri Jul 26 00:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/07_2024/7uz9_26883.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/07_2024/7uz9_26883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/07_2024/7uz9_26883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/07_2024/7uz9_26883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/07_2024/7uz9_26883.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uz9_26883/07_2024/7uz9_26883.cif" } resolution = 3.5 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= 0.023 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 19515 2.51 5 N 5040 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 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30669 Number of models: 1 Model: "" Number of chains: 12 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "M" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "P" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 961 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 3, 'TRANS': 103} Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 16.95, per 1000 atoms: 0.55 Number of scatterers: 30669 At special positions: 0 Unit cell: (158.08, 178.88, 196.352, 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 5040 7.00 C 19515 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 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 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 122 " " NAG A1314 " - " 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 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 122 " " NAG B1314 " - " 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 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 122 " " NAG C1314 " - " ASN C 282 " Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 5.6 seconds 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 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: 80 helices and 65 sheets defined 22.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 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 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.505A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.091A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.599A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.751A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.898A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.952A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.997A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.603A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.165A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.982A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.650A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1147' 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 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.634A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.703A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.616A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.640A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 884 removed outlier: 3.574A pdb=" N SER C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.730A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' 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: 3.732A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.216A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.529A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1147' Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.560A pdb=" N SER H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.813A pdb=" N VAL L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 37 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'N' and resid 95 through 99 removed outlier: 3.707A pdb=" N VAL N 99 " --> pdb=" O ALA N 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.648A pdb=" N TYR P 37 " --> pdb=" O PHE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.790A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.134A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.951A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.161A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 146 removed outlier: 7.428A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.728A 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: 5.461A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.004A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.929A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.792A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.936A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 723 removed outlier: 3.555A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 723 removed outlier: 3.555A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 3.510A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.563A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.921A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.882A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 145 removed outlier: 6.864A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.451A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.985A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.664A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.595A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.824A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 723 removed outlier: 3.789A pdb=" N VAL B1060 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 723 Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.545A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.431A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.773A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 70 removed outlier: 3.542A pdb=" N HIS C 69 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.575A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 142 through 146 removed outlier: 7.220A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.417A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.843A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.798A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.856A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.801A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.802A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.526A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.559A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 13 removed outlier: 6.459A pdb=" N ILE H 39 " --> pdb=" O ASP H 55 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG H 64 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.620A pdb=" N ILE L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 55 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.698A pdb=" N THR L 117 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.626A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP M 38 " --> pdb=" O TYR M 107 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE M 39 " --> pdb=" O ASP M 55 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP M 55 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG M 64 " --> pdb=" O TYR M 57 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 13 removed outlier: 3.626A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG M 106 " --> pdb=" O TYR M 117 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR M 117 " --> pdb=" O ARG M 106 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.746A pdb=" N ILE N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR N 55 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AG6, first strand: chain 'P' and resid 3 through 5 removed outlier: 3.513A pdb=" N SER P 26 " --> pdb=" O GLN P 3 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN P 5 " --> pdb=" O LYS P 24 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS P 24 " --> pdb=" O GLN P 5 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.545A pdb=" N GLU P 11 " --> pdb=" O THR P 125 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY P 54 " --> pdb=" O TRP P 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG P 64 " --> pdb=" O TYR P 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE Q 39 " --> pdb=" O TYR Q 55 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR Q 55 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR Q 117 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 30 through 31 1174 hydrogen bonds defined for protein. 3111 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: 15.22 Time building geometry restraints manager: 13.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9800 1.35 - 1.47: 7960 1.47 - 1.59: 13458 1.59 - 1.71: 0 1.71 - 1.83: 171 Bond restraints: 31389 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 ... (remaining 31384 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.04: 570 105.04 - 112.29: 15957 112.29 - 119.53: 9595 119.53 - 126.78: 16270 126.78 - 134.03: 355 Bond angle restraints: 42747 Sorted by residual: angle pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " pdb=" NE ARG B 273 " ideal model delta sigma weight residual 112.00 101.83 10.17 2.20e+00 2.07e-01 2.14e+01 angle pdb=" N VAL M 111A" pdb=" CA VAL M 111A" pdb=" C VAL M 111A" ideal model delta sigma weight residual 112.98 109.16 3.82 1.25e+00 6.40e-01 9.36e+00 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.71 110.93 2.78 9.50e-01 1.11e+00 8.58e+00 angle pdb=" C TYR H 112 " pdb=" CA TYR H 112 " pdb=" CB TYR H 112 " ideal model delta sigma weight residual 110.42 116.03 -5.61 1.99e+00 2.53e-01 7.94e+00 ... (remaining 42742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 18026 23.09 - 46.18: 912 46.18 - 69.27: 95 69.27 - 92.37: 43 92.37 - 115.46: 76 Dihedral angle restraints: 19152 sinusoidal: 7896 harmonic: 11256 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 7.45 85.55 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 104 " pdb=" CB CYS P 104 " ideal model delta sinusoidal sigma weight residual 93.00 36.09 56.91 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA TRP A 886 " pdb=" C TRP A 886 " pdb=" N THR A 887 " pdb=" CA THR A 887 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 19149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4703 0.099 - 0.198: 206 0.198 - 0.297: 9 0.297 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG C1313 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1313 " pdb=" O5 NAG C1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG B1314 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1314 " pdb=" O5 NAG B1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4917 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 273 " 0.398 9.50e-02 1.11e+02 1.78e-01 2.01e+01 pdb=" NE ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 273 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 273 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 273 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 579 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO C 85 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.039 5.00e-02 4.00e+02 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1267 2.72 - 3.27: 30860 3.27 - 3.81: 49793 3.81 - 4.36: 58865 4.36 - 4.90: 99897 Nonbonded interactions: 240682 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.175 2.440 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.188 2.440 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.188 2.520 nonbonded pdb=" O MET C 731 " pdb=" NE2 GLN C 774 " model vdw 2.197 2.520 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.200 2.440 ... (remaining 240677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 85.610 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.003 0.053 31389 Z= 0.224 Angle : 0.590 10.480 42747 Z= 0.306 Chirality : 0.045 0.494 4920 Planarity : 0.005 0.178 5481 Dihedral : 15.469 115.458 11820 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.31 (0.13), residues: 3825 helix: 1.26 (0.20), residues: 680 sheet: 0.57 (0.17), residues: 910 loop : -0.23 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 886 HIS 0.005 0.001 HIS B 49 PHE 0.022 0.002 PHE C 86 TYR 0.020 0.001 TYR B 904 ARG 0.014 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 894 LEU cc_start: 0.8079 (mt) cc_final: 0.7863 (mm) REVERT: B 53 ASP cc_start: 0.8113 (t0) cc_final: 0.7722 (t70) REVERT: B 54 LEU cc_start: 0.8678 (mm) cc_final: 0.8441 (mm) REVERT: B 55 PHE cc_start: 0.7374 (m-80) cc_final: 0.7095 (m-80) REVERT: B 128 ILE cc_start: 0.8956 (mm) cc_final: 0.8608 (mm) REVERT: B 170 TYR cc_start: 0.8768 (t80) cc_final: 0.8303 (t80) REVERT: B 707 TYR cc_start: 0.8054 (t80) cc_final: 0.7273 (t80) REVERT: B 1082 CYS cc_start: 0.6596 (t) cc_final: 0.6276 (t) REVERT: B 1139 ASP cc_start: 0.8241 (m-30) cc_final: 0.8032 (t0) REVERT: C 196 ASN cc_start: 0.7825 (t0) cc_final: 0.7548 (t0) REVERT: C 584 ILE cc_start: 0.7840 (mm) cc_final: 0.7429 (mm) REVERT: C 658 ASN cc_start: 0.8117 (t0) cc_final: 0.7438 (t0) REVERT: C 675 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8041 (tm-30) REVERT: C 699 LEU cc_start: 0.7858 (tp) cc_final: 0.7438 (mt) REVERT: C 755 GLN cc_start: 0.7692 (pp30) cc_final: 0.7484 (pp30) REVERT: M 38 TRP cc_start: 0.7381 (m-90) cc_final: 0.6855 (m-90) REVERT: M 110 ASN cc_start: 0.8069 (t0) cc_final: 0.7593 (t0) REVERT: P 21 MET cc_start: 0.2346 (tpt) cc_final: -0.0786 (pmm) REVERT: P 115 MET cc_start: 0.3253 (tpt) cc_final: 0.2725 (tpp) outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.3780 time to fit residues: 246.6580 Evaluate side-chains 301 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31389 Z= 0.297 Angle : 0.656 18.066 42747 Z= 0.328 Chirality : 0.048 0.351 4920 Planarity : 0.005 0.122 5481 Dihedral : 11.584 109.059 5064 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.03 % Allowed : 8.65 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.27 (0.13), residues: 3825 helix: 1.05 (0.19), residues: 694 sheet: 0.61 (0.17), residues: 952 loop : -0.26 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.012 0.001 HIS B 49 PHE 0.025 0.002 PHE C 562 TYR 0.020 0.001 TYR A 204 ARG 0.010 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 328 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7339 (t80) cc_final: 0.6930 (t80) REVERT: A 610 VAL cc_start: 0.9090 (t) cc_final: 0.8820 (p) REVERT: B 53 ASP cc_start: 0.8174 (t0) cc_final: 0.7633 (t70) REVERT: B 54 LEU cc_start: 0.8702 (mm) cc_final: 0.8341 (mm) REVERT: B 55 PHE cc_start: 0.7555 (m-80) cc_final: 0.7255 (m-80) REVERT: B 265 TYR cc_start: 0.5868 (p90) cc_final: 0.5595 (p90) REVERT: B 532 ASN cc_start: 0.8523 (t0) cc_final: 0.8205 (t0) REVERT: B 586 ASP cc_start: 0.6783 (t0) cc_final: 0.6540 (t0) REVERT: B 707 TYR cc_start: 0.8189 (t80) cc_final: 0.7286 (t80) REVERT: B 1082 CYS cc_start: 0.6463 (t) cc_final: 0.6198 (t) REVERT: C 321 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8569 (mm-40) REVERT: C 533 LEU cc_start: 0.8166 (mt) cc_final: 0.7952 (mt) REVERT: C 584 ILE cc_start: 0.8074 (mm) cc_final: 0.7555 (mm) REVERT: C 592 PHE cc_start: 0.8694 (p90) cc_final: 0.8463 (p90) REVERT: C 661 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 675 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7867 (tm-30) REVERT: C 900 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7174 (mtm) REVERT: C 1033 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8129 (p) REVERT: M 110 ASN cc_start: 0.8080 (t0) cc_final: 0.7815 (t0) REVERT: P 21 MET cc_start: 0.2297 (tpt) cc_final: 0.1703 (tpt) REVERT: P 115 MET cc_start: 0.3365 (tpt) cc_final: 0.3149 (tpp) outliers start: 34 outliers final: 27 residues processed: 349 average time/residue: 0.3687 time to fit residues: 220.5637 Evaluate side-chains 327 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 298 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1033 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 349 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 346 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31389 Z= 0.242 Angle : 0.599 17.376 42747 Z= 0.297 Chirality : 0.046 0.328 4920 Planarity : 0.004 0.098 5481 Dihedral : 8.642 114.941 5064 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.69 % Allowed : 11.62 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.28 (0.13), residues: 3825 helix: 1.19 (0.20), residues: 683 sheet: 0.52 (0.17), residues: 980 loop : -0.25 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.013 0.001 HIS B 49 PHE 0.025 0.002 PHE C 55 TYR 0.017 0.001 TYR B1067 ARG 0.008 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 315 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8549 (t80) cc_final: 0.8198 (t80) REVERT: A 610 VAL cc_start: 0.9149 (t) cc_final: 0.8881 (p) REVERT: A 699 LEU cc_start: 0.8043 (tt) cc_final: 0.7792 (tt) REVERT: A 873 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: B 53 ASP cc_start: 0.8199 (t0) cc_final: 0.7727 (t70) REVERT: B 54 LEU cc_start: 0.8700 (mm) cc_final: 0.8330 (mm) REVERT: B 55 PHE cc_start: 0.7425 (m-80) cc_final: 0.7202 (m-80) REVERT: B 168 PHE cc_start: 0.7932 (t80) cc_final: 0.7725 (t80) REVERT: B 177 MET cc_start: 0.8511 (ppp) cc_final: 0.8225 (ppp) REVERT: B 214 ARG cc_start: 0.8495 (mpp-170) cc_final: 0.7106 (ttt-90) REVERT: B 265 TYR cc_start: 0.5864 (p90) cc_final: 0.5650 (p90) REVERT: B 532 ASN cc_start: 0.8413 (t0) cc_final: 0.8130 (t0) REVERT: B 707 TYR cc_start: 0.8175 (t80) cc_final: 0.7064 (t80) REVERT: B 906 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6729 (m-10) REVERT: B 1082 CYS cc_start: 0.6267 (t) cc_final: 0.5986 (t) REVERT: C 176 LEU cc_start: 0.7062 (mm) cc_final: 0.6715 (mm) REVERT: C 196 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.7173 (t0) REVERT: C 242 LEU cc_start: 0.6869 (tt) cc_final: 0.6605 (tt) REVERT: C 584 ILE cc_start: 0.8034 (mm) cc_final: 0.7542 (mm) REVERT: C 675 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 900 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7114 (mtm) REVERT: M 110 ASN cc_start: 0.8062 (t0) cc_final: 0.7807 (t0) REVERT: P 21 MET cc_start: 0.2115 (tpt) cc_final: 0.1818 (tpt) outliers start: 56 outliers final: 35 residues processed: 349 average time/residue: 0.3665 time to fit residues: 218.7369 Evaluate side-chains 323 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 284 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1033 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 40.0000 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 20.0000 chunk 371 optimal weight: 50.0000 chunk 183 optimal weight: 0.5980 chunk 332 optimal weight: 50.0000 chunk 100 optimal weight: 1.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 31389 Z= 0.393 Angle : 0.677 18.953 42747 Z= 0.341 Chirality : 0.047 0.334 4920 Planarity : 0.005 0.110 5481 Dihedral : 7.856 106.996 5064 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.18 % Allowed : 13.13 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.06 (0.13), residues: 3825 helix: 0.91 (0.19), residues: 674 sheet: 0.40 (0.17), residues: 976 loop : -0.36 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.009 0.001 HIS B 49 PHE 0.039 0.002 PHE C 275 TYR 0.021 0.002 TYR A 279 ARG 0.010 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 291 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 VAL cc_start: 0.9193 (t) cc_final: 0.8900 (p) REVERT: A 973 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9319 (tt) REVERT: B 168 PHE cc_start: 0.8101 (t80) cc_final: 0.7896 (t80) REVERT: B 265 TYR cc_start: 0.5893 (p90) cc_final: 0.5639 (p90) REVERT: B 532 ASN cc_start: 0.8310 (t0) cc_final: 0.8047 (t0) REVERT: B 707 TYR cc_start: 0.8336 (t80) cc_final: 0.7095 (t80) REVERT: B 873 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7295 (t80) REVERT: B 901 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.6833 (tm130) REVERT: B 906 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7007 (m-10) REVERT: B 943 SER cc_start: 0.8292 (m) cc_final: 0.7980 (p) REVERT: B 1077 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8157 (t) REVERT: B 1082 CYS cc_start: 0.6302 (t) cc_final: 0.6072 (t) REVERT: C 533 LEU cc_start: 0.8258 (mt) cc_final: 0.8036 (mt) REVERT: C 584 ILE cc_start: 0.8087 (mm) cc_final: 0.7602 (mm) REVERT: C 675 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 731 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.6811 (ppp) REVERT: C 823 PHE cc_start: 0.8352 (t80) cc_final: 0.7999 (t80) REVERT: C 872 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: P 115 MET cc_start: 0.3993 (tpp) cc_final: 0.3673 (tpp) outliers start: 105 outliers final: 75 residues processed: 363 average time/residue: 0.3533 time to fit residues: 220.1854 Evaluate side-chains 365 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 283 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 5 optimal weight: 0.0870 chunk 276 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 316 optimal weight: 0.0050 chunk 256 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 333 optimal weight: 50.0000 chunk 93 optimal weight: 2.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 774 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 774 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31389 Z= 0.146 Angle : 0.558 16.225 42747 Z= 0.275 Chirality : 0.045 0.307 4920 Planarity : 0.004 0.083 5481 Dihedral : 6.988 93.725 5064 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.24 % Allowed : 14.16 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.30 (0.14), residues: 3825 helix: 1.36 (0.20), residues: 678 sheet: 0.45 (0.17), residues: 1011 loop : -0.25 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.013 0.001 HIS B 49 PHE 0.040 0.002 PHE C 275 TYR 0.021 0.001 TYR B 873 ARG 0.005 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 326 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7948 (mp10) REVERT: A 584 ILE cc_start: 0.8591 (mm) cc_final: 0.8345 (mm) REVERT: A 610 VAL cc_start: 0.9083 (t) cc_final: 0.8836 (p) REVERT: A 756 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 895 GLN cc_start: 0.7625 (pp30) cc_final: 0.7296 (pp30) REVERT: A 973 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9289 (tt) REVERT: B 177 MET cc_start: 0.8572 (ppp) cc_final: 0.8310 (ppp) REVERT: B 214 ARG cc_start: 0.8443 (mpp-170) cc_final: 0.7189 (ttt-90) REVERT: B 265 TYR cc_start: 0.5881 (p90) cc_final: 0.5597 (p90) REVERT: B 641 ASN cc_start: 0.8386 (m110) cc_final: 0.7893 (p0) REVERT: B 754 LEU cc_start: 0.8951 (tp) cc_final: 0.8626 (pp) REVERT: B 873 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7040 (t80) REVERT: B 906 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: B 943 SER cc_start: 0.8239 (m) cc_final: 0.7921 (p) REVERT: B 1082 CYS cc_start: 0.6340 (t) cc_final: 0.6023 (t) REVERT: C 196 ASN cc_start: 0.7589 (p0) cc_final: 0.6953 (t0) REVERT: C 533 LEU cc_start: 0.8178 (mt) cc_final: 0.7946 (mt) REVERT: C 584 ILE cc_start: 0.8014 (mm) cc_final: 0.7550 (mm) REVERT: C 661 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 675 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 731 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.6731 (ptp) REVERT: C 872 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: C 895 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6578 (pp30) REVERT: C 900 MET cc_start: 0.7407 (mtm) cc_final: 0.7094 (mtt) REVERT: C 962 LEU cc_start: 0.9220 (tp) cc_final: 0.8933 (tt) REVERT: C 1107 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7004 (mtp180) REVERT: M 110 ASN cc_start: 0.8105 (t0) cc_final: 0.7866 (t0) REVERT: P 115 MET cc_start: 0.4342 (tpp) cc_final: 0.4052 (tpp) outliers start: 74 outliers final: 44 residues processed: 380 average time/residue: 0.3645 time to fit residues: 235.8791 Evaluate side-chains 341 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 289 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 73 optimal weight: 0.0040 chunk 217 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31389 Z= 0.295 Angle : 0.600 16.539 42747 Z= 0.300 Chirality : 0.045 0.314 4920 Planarity : 0.004 0.085 5481 Dihedral : 6.929 89.731 5064 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 14.97 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.22 (0.14), residues: 3825 helix: 1.21 (0.20), residues: 680 sheet: 0.49 (0.17), residues: 960 loop : -0.31 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.008 0.001 HIS B 49 PHE 0.043 0.002 PHE C 275 TYR 0.026 0.001 TYR B 707 ARG 0.007 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 289 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8005 (mp10) REVERT: A 610 VAL cc_start: 0.9153 (t) cc_final: 0.8888 (p) REVERT: A 973 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9328 (tt) REVERT: B 177 MET cc_start: 0.8638 (ppp) cc_final: 0.8384 (ppp) REVERT: B 214 ARG cc_start: 0.8465 (mpp-170) cc_final: 0.7275 (ttt-90) REVERT: B 265 TYR cc_start: 0.5848 (p90) cc_final: 0.5556 (p90) REVERT: B 276 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8134 (mm) REVERT: B 532 ASN cc_start: 0.8432 (t0) cc_final: 0.8131 (t0) REVERT: B 707 TYR cc_start: 0.7934 (t80) cc_final: 0.6488 (t80) REVERT: B 730 SER cc_start: 0.8615 (t) cc_final: 0.8106 (p) REVERT: B 873 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7043 (t80) REVERT: B 906 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: B 943 SER cc_start: 0.8389 (m) cc_final: 0.8094 (p) REVERT: B 1028 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7153 (mmmt) REVERT: B 1082 CYS cc_start: 0.6314 (t) cc_final: 0.6068 (t) REVERT: C 529 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8206 (mmmt) REVERT: C 533 LEU cc_start: 0.8286 (mt) cc_final: 0.8046 (mt) REVERT: C 584 ILE cc_start: 0.8056 (mm) cc_final: 0.7571 (mm) REVERT: C 661 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 731 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.6935 (ptp) REVERT: C 823 PHE cc_start: 0.8217 (t80) cc_final: 0.7804 (t80) REVERT: C 895 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6790 (pp30) REVERT: C 962 LEU cc_start: 0.9255 (tp) cc_final: 0.8981 (tt) REVERT: P 115 MET cc_start: 0.4507 (tpp) cc_final: 0.4139 (tpp) outliers start: 93 outliers final: 75 residues processed: 355 average time/residue: 0.3919 time to fit residues: 239.5875 Evaluate side-chains 354 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 273 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 5.9990 chunk 41 optimal weight: 50.0000 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 312 optimal weight: 0.0770 chunk 207 optimal weight: 2.9990 chunk 370 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31389 Z= 0.198 Angle : 0.568 16.247 42747 Z= 0.280 Chirality : 0.045 0.318 4920 Planarity : 0.004 0.079 5481 Dihedral : 6.708 86.348 5064 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.66 % Allowed : 15.91 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.24 (0.14), residues: 3825 helix: 1.26 (0.19), residues: 680 sheet: 0.48 (0.17), residues: 974 loop : -0.29 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.010 0.001 HIS B 49 PHE 0.040 0.002 PHE C 275 TYR 0.023 0.001 TYR B 707 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 293 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8031 (mp10) REVERT: A 610 VAL cc_start: 0.9144 (t) cc_final: 0.8888 (p) REVERT: B 177 MET cc_start: 0.8671 (ppp) cc_final: 0.8438 (ppp) REVERT: B 214 ARG cc_start: 0.8462 (mpp-170) cc_final: 0.7321 (ttt-90) REVERT: B 265 TYR cc_start: 0.5838 (p90) cc_final: 0.5537 (p90) REVERT: B 275 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7157 (m-10) REVERT: B 532 ASN cc_start: 0.8386 (t0) cc_final: 0.8105 (t0) REVERT: B 587 ILE cc_start: 0.7948 (mt) cc_final: 0.7719 (mp) REVERT: B 707 TYR cc_start: 0.7867 (t80) cc_final: 0.6401 (t80) REVERT: B 754 LEU cc_start: 0.8948 (tp) cc_final: 0.8608 (pp) REVERT: B 873 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7056 (t80) REVERT: B 906 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: B 943 SER cc_start: 0.8351 (m) cc_final: 0.8061 (p) REVERT: B 1082 CYS cc_start: 0.6349 (t) cc_final: 0.6014 (t) REVERT: C 529 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8190 (mmmt) REVERT: C 584 ILE cc_start: 0.8044 (mm) cc_final: 0.7577 (mm) REVERT: C 731 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.6961 (ptp) REVERT: C 872 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: C 895 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6827 (pp30) REVERT: C 1107 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7214 (ttm170) REVERT: P 115 MET cc_start: 0.4616 (tpp) cc_final: 0.4219 (tpp) outliers start: 88 outliers final: 71 residues processed: 356 average time/residue: 0.3604 time to fit residues: 218.5315 Evaluate side-chains 351 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 274 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 0.0050 chunk 252 optimal weight: 0.5980 chunk 182 optimal weight: 0.0470 chunk 34 optimal weight: 30.0000 chunk 290 optimal weight: 0.0270 overall best weight: 0.1448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 787 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31389 Z= 0.149 Angle : 0.554 15.949 42747 Z= 0.270 Chirality : 0.045 0.314 4920 Planarity : 0.004 0.068 5481 Dihedral : 6.276 81.403 5064 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.72 % Allowed : 17.21 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.37 (0.14), residues: 3825 helix: 1.52 (0.20), residues: 672 sheet: 0.49 (0.17), residues: 988 loop : -0.24 (0.14), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.013 0.001 HIS B 49 PHE 0.053 0.002 PHE A 135 TYR 0.024 0.001 TYR B 707 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 326 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8305 (tp) cc_final: 0.8027 (mp) REVERT: A 271 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8009 (mp10) REVERT: A 610 VAL cc_start: 0.9042 (t) cc_final: 0.8794 (p) REVERT: A 756 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 869 MET cc_start: 0.7492 (mmm) cc_final: 0.6963 (mmm) REVERT: A 957 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 968 SER cc_start: 0.8658 (t) cc_final: 0.8446 (p) REVERT: B 177 MET cc_start: 0.8711 (ppp) cc_final: 0.8485 (ppp) REVERT: B 265 TYR cc_start: 0.5885 (p90) cc_final: 0.5660 (p90) REVERT: B 587 ILE cc_start: 0.7889 (mt) cc_final: 0.7646 (mp) REVERT: B 707 TYR cc_start: 0.7664 (t80) cc_final: 0.6540 (t80) REVERT: B 754 LEU cc_start: 0.8911 (tp) cc_final: 0.8574 (pp) REVERT: B 777 ASN cc_start: 0.7981 (m-40) cc_final: 0.7776 (m110) REVERT: B 856 ASN cc_start: 0.6690 (t0) cc_final: 0.6229 (m110) REVERT: B 873 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 906 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: B 943 SER cc_start: 0.8320 (m) cc_final: 0.8039 (p) REVERT: B 996 LEU cc_start: 0.8311 (tt) cc_final: 0.8063 (tt) REVERT: C 529 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8187 (mmmt) REVERT: C 584 ILE cc_start: 0.8146 (mm) cc_final: 0.7701 (mm) REVERT: C 661 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7948 (tm-30) REVERT: C 731 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: C 878 LEU cc_start: 0.8738 (tp) cc_final: 0.8531 (tp) REVERT: C 1107 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7048 (ttm170) REVERT: P 115 MET cc_start: 0.4683 (tpp) cc_final: 0.4246 (tpp) outliers start: 57 outliers final: 42 residues processed: 361 average time/residue: 0.3730 time to fit residues: 229.9254 Evaluate side-chains 347 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 300 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.5980 chunk 354 optimal weight: 20.0000 chunk 323 optimal weight: 6.9990 chunk 344 optimal weight: 40.0000 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 311 optimal weight: 0.7980 chunk 326 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 856 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31389 Z= 0.302 Angle : 0.617 17.541 42747 Z= 0.308 Chirality : 0.046 0.335 4920 Planarity : 0.005 0.079 5481 Dihedral : 6.448 81.255 5064 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.12 % Allowed : 17.48 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.25 (0.14), residues: 3825 helix: 1.36 (0.20), residues: 661 sheet: 0.48 (0.17), residues: 977 loop : -0.31 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 886 HIS 0.010 0.001 HIS B 49 PHE 0.040 0.002 PHE C 275 TYR 0.023 0.001 TYR B 160 ARG 0.008 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 280 time to evaluate : 3.242 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8046 (mp10) REVERT: A 610 VAL cc_start: 0.9149 (t) cc_final: 0.8886 (p) REVERT: B 116 SER cc_start: 0.6597 (m) cc_final: 0.6219 (p) REVERT: B 117 LEU cc_start: 0.8007 (tp) cc_final: 0.7719 (tt) REVERT: B 177 MET cc_start: 0.8733 (ppp) cc_final: 0.8485 (ppp) REVERT: B 214 ARG cc_start: 0.8552 (mpp-170) cc_final: 0.7191 (ttt-90) REVERT: B 707 TYR cc_start: 0.7972 (t80) cc_final: 0.6527 (t80) REVERT: B 873 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7128 (t80) REVERT: B 906 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: B 943 SER cc_start: 0.8328 (m) cc_final: 0.8055 (p) REVERT: B 1028 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7163 (mmmt) REVERT: B 1082 CYS cc_start: 0.6621 (t) cc_final: 0.6314 (t) REVERT: C 529 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8230 (mmmt) REVERT: C 584 ILE cc_start: 0.8175 (mm) cc_final: 0.7691 (mm) REVERT: C 731 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.6721 (ppp) REVERT: C 823 PHE cc_start: 0.8196 (t80) cc_final: 0.7811 (t80) REVERT: C 872 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: C 895 GLN cc_start: 0.7633 (pp30) cc_final: 0.6789 (pp30) REVERT: C 1107 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7255 (ttm170) REVERT: P 115 MET cc_start: 0.4723 (tpp) cc_final: 0.4264 (tpp) outliers start: 70 outliers final: 57 residues processed: 335 average time/residue: 0.3563 time to fit residues: 203.8981 Evaluate side-chains 335 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 273 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain P residue 89 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.0970 chunk 364 optimal weight: 50.0000 chunk 222 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 chunk 352 optimal weight: 50.0000 chunk 304 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31389 Z= 0.328 Angle : 0.640 18.681 42747 Z= 0.319 Chirality : 0.046 0.346 4920 Planarity : 0.005 0.086 5481 Dihedral : 6.548 81.120 5064 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.30 % Allowed : 17.82 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.10 (0.14), residues: 3825 helix: 1.16 (0.20), residues: 659 sheet: 0.43 (0.17), residues: 1003 loop : -0.41 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 886 HIS 0.010 0.001 HIS B 49 PHE 0.043 0.002 PHE C 275 TYR 0.044 0.001 TYR A 873 ARG 0.017 0.001 ARG B 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7650 Ramachandran restraints generated. 3825 Oldfield, 0 Emsley, 3825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 269 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8291 (mp10) REVERT: A 554 GLU cc_start: 0.8069 (tp30) cc_final: 0.7786 (tp30) REVERT: A 610 VAL cc_start: 0.9178 (t) cc_final: 0.8913 (p) REVERT: B 116 SER cc_start: 0.6782 (m) cc_final: 0.6404 (p) REVERT: B 177 MET cc_start: 0.8758 (ppp) cc_final: 0.8527 (ppp) REVERT: B 214 ARG cc_start: 0.8491 (mpp-170) cc_final: 0.7220 (ttt-90) REVERT: B 697 MET cc_start: 0.8881 (mmm) cc_final: 0.8662 (mmt) REVERT: B 707 TYR cc_start: 0.8018 (t80) cc_final: 0.6575 (t80) REVERT: B 754 LEU cc_start: 0.8967 (tp) cc_final: 0.8584 (pp) REVERT: B 873 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 906 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: B 943 SER cc_start: 0.8425 (m) cc_final: 0.8149 (p) REVERT: B 1028 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7172 (mmmt) REVERT: B 1082 CYS cc_start: 0.6493 (t) cc_final: 0.6165 (t) REVERT: C 529 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8233 (mmmt) REVERT: C 584 ILE cc_start: 0.8178 (mm) cc_final: 0.7693 (mm) REVERT: C 731 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.6846 (ppp) REVERT: C 823 PHE cc_start: 0.8255 (t80) cc_final: 0.7846 (t80) REVERT: C 895 GLN cc_start: 0.7560 (pp30) cc_final: 0.6667 (pp30) REVERT: C 1107 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7243 (ttm170) REVERT: P 115 MET cc_start: 0.4776 (tpp) cc_final: 0.4293 (tpp) outliers start: 76 outliers final: 69 residues processed: 328 average time/residue: 0.3550 time to fit residues: 200.8092 Evaluate side-chains 335 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 262 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1138 TYR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 44 optimal weight: 40.0000 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 313 optimal weight: 0.0170 chunk 38 optimal weight: 40.0000 chunk 56 optimal weight: 4.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.202611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107526 restraints weight = 51732.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111159 restraints weight = 22900.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113555 restraints weight = 13668.470| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31389 Z= 0.247 Angle : 0.600 18.235 42747 Z= 0.296 Chirality : 0.045 0.346 4920 Planarity : 0.005 0.084 5481 Dihedral : 6.394 79.609 5064 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.15 % Allowed : 18.24 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % 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: 0.16 (0.14), residues: 3825 helix: 1.25 (0.20), residues: 661 sheet: 0.44 (0.17), residues: 995 loop : -0.37 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.012 0.001 HIS B 49 PHE 0.041 0.002 PHE C 275 TYR 0.033 0.001 TYR A 873 ARG 0.007 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6087.88 seconds wall clock time: 110 minutes 4.65 seconds (6604.65 seconds total)