Starting phenix.real_space_refine on Wed Jul 24 22:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uza_26884/07_2024/7uza_26884.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uza_26884/07_2024/7uza_26884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uza_26884/07_2024/7uza_26884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uza_26884/07_2024/7uza_26884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uza_26884/07_2024/7uza_26884.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uza_26884/07_2024/7uza_26884.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 120 5.16 5 C 17180 2.51 5 N 4438 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26992 Number of models: 1 Model: "" Number of chains: 10 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: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.28, per 1000 atoms: 0.57 Number of scatterers: 26992 At special positions: 0 Unit cell: (158.912, 164.736, 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 120 16.00 O 5254 8.00 N 4438 7.00 C 17180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.04 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=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 282 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " Time building additional restraints: 11.21 Conformation dependent library (CDL) restraints added in 4.7 seconds 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6372 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 56 sheets defined 22.9% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 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 498 through 502 removed outlier: 3.676A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 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 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.615A 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 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.501A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.691A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.204A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.020A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.782A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.923A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.586A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.630A 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: 3.658A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.216A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.140A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.913A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.153A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.810A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.866A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.363A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 86 removed outlier: 3.924A pdb=" N THR H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.030A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.256A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.738A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.128A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.998A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 14.677A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 14.644A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.224A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.548A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.122A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.693A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.703A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.496A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.331A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.354A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.562A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.001A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.479A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 90 through 94 removed outlier: 5.885A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 121 removed outlier: 5.577A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 142 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU B 154 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B 144 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP B 152 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 121 removed outlier: 7.251A pdb=" N LEU B 244 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N TYR B 145 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.341A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.709A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.717A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.571A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 727 removed outlier: 6.688A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 727 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.928A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.309A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.019A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.736A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.119A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.544A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.433A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.759A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.386A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.634A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 6.781A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.581A pdb=" N GLN H 5 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS H 24 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.050A pdb=" N MET H 39 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 54 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TRP H 41 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TRP H 52 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS H 43 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU H 50 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG H 45 " --> pdb=" O GLN H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.674A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE L 21 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS L 23 " --> pdb=" O PHE L 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.116A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'L' and resid 51 through 54 removed outlier: 6.642A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 103 " --> pdb=" O TYR L 42 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2838 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: 12.00 Time building geometry restraints manager: 12.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8509 1.34 - 1.46: 5878 1.46 - 1.58: 13083 1.58 - 1.70: 0 1.70 - 1.82: 155 Bond restraints: 27625 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.509 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" N VAL C 705 " pdb=" CA VAL C 705 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.27e-02 6.20e+03 7.74e+00 bond pdb=" N GLU C1072 " pdb=" CA GLU C1072 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.21e-02 6.83e+03 6.55e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27620 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.87: 495 104.87 - 112.15: 14041 112.15 - 119.44: 8359 119.44 - 126.72: 14409 126.72 - 134.00: 327 Bond angle restraints: 37631 Sorted by residual: angle pdb=" C ASN C1074 " pdb=" CA ASN C1074 " pdb=" CB ASN C1074 " ideal model delta sigma weight residual 109.48 116.83 -7.35 1.68e+00 3.54e-01 1.91e+01 angle pdb=" C ALA L 9 " pdb=" CA ALA L 9 " pdb=" CB ALA L 9 " ideal model delta sigma weight residual 116.34 110.89 5.45 1.40e+00 5.10e-01 1.52e+01 angle pdb=" C SER A1030 " pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta sigma weight residual 122.67 116.61 6.06 1.59e+00 3.96e-01 1.45e+01 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 111.36 115.10 -3.74 1.17e+00 7.31e-01 1.02e+01 angle pdb=" N ASP L 114 " pdb=" CA ASP L 114 " pdb=" C ASP L 114 " ideal model delta sigma weight residual 109.81 116.51 -6.70 2.21e+00 2.05e-01 9.18e+00 ... (remaining 37626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 16061 24.32 - 48.65: 717 48.65 - 72.97: 83 72.97 - 97.30: 18 97.30 - 121.62: 20 Dihedral angle restraints: 16899 sinusoidal: 6979 harmonic: 9920 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.21 64.21 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 141.58 -48.58 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.63 46.63 1 1.00e+01 1.00e-02 3.01e+01 ... (remaining 16896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4161 0.099 - 0.199: 190 0.199 - 0.298: 7 0.298 - 0.397: 2 0.397 - 0.496: 1 Chirality restraints: 4361 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 4358 not shown) Planarity restraints: 4869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.205 2.00e-02 2.50e+03 1.70e-01 3.61e+02 pdb=" C7 NAG C1308 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.006 2.00e-02 2.50e+03 3.30e-02 1.36e+01 pdb=" CG ASN C 801 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 41 " 0.016 2.00e-02 2.50e+03 1.63e-02 6.65e+00 pdb=" CG TRP L 41 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP L 41 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 41 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 41 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 41 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 41 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP L 41 " -0.005 2.00e-02 2.50e+03 ... (remaining 4866 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 650 2.69 - 3.24: 27182 3.24 - 3.80: 43547 3.80 - 4.35: 57861 4.35 - 4.90: 95394 Nonbonded interactions: 224634 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.139 2.520 nonbonded pdb=" OE1 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.170 2.440 nonbonded pdb=" O GLU C 780 " pdb=" NE2 GLN C 784 " model vdw 2.193 2.520 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASN C 801 " pdb=" ND2 ASN C 928 " model vdw 2.201 2.520 ... (remaining 224629 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' and (resid 26 through 1147 or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 73.500 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 27625 Z= 0.267 Angle : 0.624 9.077 37631 Z= 0.336 Chirality : 0.046 0.496 4361 Planarity : 0.004 0.170 4833 Dihedral : 13.777 121.624 10413 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3369 helix: 1.38 (0.19), residues: 673 sheet: 0.00 (0.19), residues: 710 loop : -0.64 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 41 HIS 0.006 0.001 HIS H 57 PHE 0.029 0.002 PHE C 802 TYR 0.021 0.002 TYR C1138 ARG 0.007 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8408 (pp30) cc_final: 0.8022 (pp30) REVERT: A 351 TYR cc_start: 0.8347 (p90) cc_final: 0.7914 (p90) REVERT: A 584 ILE cc_start: 0.8987 (mm) cc_final: 0.8559 (tp) REVERT: A 663 ASP cc_start: 0.8009 (m-30) cc_final: 0.7411 (m-30) REVERT: B 106 PHE cc_start: 0.6849 (p90) cc_final: 0.6599 (p90) REVERT: B 229 LEU cc_start: 0.8528 (mt) cc_final: 0.8161 (tt) REVERT: B 313 TYR cc_start: 0.7685 (m-80) cc_final: 0.7316 (m-80) REVERT: B 420 ASP cc_start: 0.8199 (t70) cc_final: 0.7771 (t0) REVERT: B 501 ASN cc_start: 0.8262 (m110) cc_final: 0.7928 (m-40) REVERT: B 697 MET cc_start: 0.7325 (ptm) cc_final: 0.7067 (ptm) REVERT: B 900 MET cc_start: 0.6906 (mtm) cc_final: 0.6595 (mtp) REVERT: B 1141 LEU cc_start: 0.8652 (mm) cc_final: 0.8317 (tp) REVERT: H 40 HIS cc_start: 0.9306 (m170) cc_final: 0.8987 (m170) REVERT: H 51 GLU cc_start: 0.8448 (pp20) cc_final: 0.7894 (pp20) REVERT: H 88 TYR cc_start: 0.8881 (m-80) cc_final: 0.8140 (m-80) REVERT: H 89 MET cc_start: 0.7326 (ppp) cc_final: 0.7098 (ppp) REVERT: H 113 ASP cc_start: 0.7780 (m-30) cc_final: 0.7168 (m-30) REVERT: L 24 ARG cc_start: 0.8805 (ptp-110) cc_final: 0.7844 (ttm110) REVERT: L 85 THR cc_start: 0.8694 (t) cc_final: 0.8124 (t) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.3492 time to fit residues: 182.8897 Evaluate side-chains 242 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 218 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 907 ASN B 913 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 872 GLN C 969 ASN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27625 Z= 0.255 Angle : 0.605 10.829 37631 Z= 0.306 Chirality : 0.047 0.475 4361 Planarity : 0.004 0.039 4833 Dihedral : 9.126 109.965 4455 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.82 % Allowed : 6.32 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.17 (0.14), residues: 3369 helix: 1.34 (0.19), residues: 699 sheet: -0.04 (0.18), residues: 779 loop : -0.68 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 41 HIS 0.004 0.001 HIS C1048 PHE 0.028 0.002 PHE A 168 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 263 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8433 (pp30) cc_final: 0.7917 (pp30) REVERT: A 86 PHE cc_start: 0.4859 (t80) cc_final: 0.4246 (t80) REVERT: A 390 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.4001 (pp) REVERT: A 400 PHE cc_start: 0.7187 (p90) cc_final: 0.6973 (p90) REVERT: A 508 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8377 (t80) REVERT: B 55 PHE cc_start: 0.7149 (m-10) cc_final: 0.6599 (m-10) REVERT: B 313 TYR cc_start: 0.7530 (m-80) cc_final: 0.7165 (m-80) REVERT: B 403 ARG cc_start: 0.6987 (ttp80) cc_final: 0.6139 (ttp80) REVERT: B 449 TYR cc_start: 0.7397 (m-80) cc_final: 0.7058 (m-80) REVERT: B 501 ASN cc_start: 0.8214 (m110) cc_final: 0.7864 (m110) REVERT: B 697 MET cc_start: 0.7421 (ptm) cc_final: 0.7147 (ptm) REVERT: B 740 MET cc_start: 0.8516 (tpp) cc_final: 0.8217 (tpt) REVERT: B 1141 LEU cc_start: 0.8629 (mm) cc_final: 0.8256 (tp) REVERT: H 6 GLN cc_start: 0.3994 (mm-40) cc_final: 0.3678 (mm-40) REVERT: H 51 GLU cc_start: 0.7882 (pp20) cc_final: 0.7564 (pp20) REVERT: H 88 TYR cc_start: 0.8876 (m-80) cc_final: 0.8404 (m-80) REVERT: H 113 ASP cc_start: 0.7348 (m-30) cc_final: 0.7135 (m-30) REVERT: L 24 ARG cc_start: 0.8422 (ptp-110) cc_final: 0.7905 (mtp-110) REVERT: L 51 LYS cc_start: 0.8723 (tppt) cc_final: 0.8342 (tttm) REVERT: L 53 LEU cc_start: 0.7966 (mp) cc_final: 0.7688 (mp) REVERT: L 116 PHE cc_start: 0.8966 (m-80) cc_final: 0.8268 (m-80) outliers start: 24 outliers final: 10 residues processed: 277 average time/residue: 0.3356 time to fit residues: 156.0493 Evaluate side-chains 247 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 332 optimal weight: 30.0000 chunk 273 optimal weight: 7.9990 chunk 304 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 246 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27625 Z= 0.243 Angle : 0.574 9.205 37631 Z= 0.289 Chirality : 0.046 0.460 4361 Planarity : 0.004 0.044 4833 Dihedral : 7.821 106.651 4455 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.13 % Allowed : 8.89 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.17 (0.14), residues: 3369 helix: 1.43 (0.19), residues: 692 sheet: -0.06 (0.18), residues: 764 loop : -0.69 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 353 HIS 0.005 0.001 HIS H 40 PHE 0.023 0.002 PHE L 118 TYR 0.026 0.001 TYR A 91 ARG 0.007 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8464 (pp30) cc_final: 0.7918 (pp30) REVERT: A 160 TYR cc_start: 0.7614 (p90) cc_final: 0.7361 (p90) REVERT: A 740 MET cc_start: 0.7590 (tpt) cc_final: 0.6649 (mmt) REVERT: B 55 PHE cc_start: 0.7154 (m-10) cc_final: 0.6669 (m-10) REVERT: B 313 TYR cc_start: 0.7654 (m-80) cc_final: 0.7221 (m-80) REVERT: B 347 PHE cc_start: 0.6584 (m-80) cc_final: 0.6351 (m-80) REVERT: B 354 ASN cc_start: 0.7512 (m110) cc_final: 0.7156 (m-40) REVERT: B 420 ASP cc_start: 0.8239 (t0) cc_final: 0.7871 (t0) REVERT: B 449 TYR cc_start: 0.7449 (m-80) cc_final: 0.7040 (m-80) REVERT: B 501 ASN cc_start: 0.8179 (m110) cc_final: 0.7776 (m110) REVERT: B 697 MET cc_start: 0.7419 (ptm) cc_final: 0.7123 (ptm) REVERT: B 1141 LEU cc_start: 0.8660 (mm) cc_final: 0.8286 (tp) REVERT: H 41 TRP cc_start: 0.6603 (m100) cc_final: 0.6344 (m100) REVERT: H 50 LEU cc_start: 0.8329 (mm) cc_final: 0.8125 (mm) REVERT: H 55 MET cc_start: 0.7142 (tmm) cc_final: 0.6755 (ppp) REVERT: H 67 TYR cc_start: 0.5747 (m-80) cc_final: 0.5342 (m-80) REVERT: H 88 TYR cc_start: 0.8869 (m-80) cc_final: 0.8139 (m-80) REVERT: H 113 ASP cc_start: 0.7420 (m-30) cc_final: 0.7153 (m-30) REVERT: L 24 ARG cc_start: 0.8781 (ptp-110) cc_final: 0.7705 (mtp-110) REVERT: L 51 LYS cc_start: 0.8868 (tppt) cc_final: 0.8375 (tttm) outliers start: 33 outliers final: 15 residues processed: 280 average time/residue: 0.3412 time to fit residues: 159.6850 Evaluate side-chains 247 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 4.9990 chunk 231 optimal weight: 50.0000 chunk 159 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 308 optimal weight: 0.0570 chunk 326 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 907 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27625 Z= 0.329 Angle : 0.600 9.451 37631 Z= 0.302 Chirality : 0.047 0.458 4361 Planarity : 0.004 0.042 4833 Dihedral : 7.223 100.414 4455 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.02 % Allowed : 10.39 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.33 (0.14), residues: 3369 helix: 1.24 (0.19), residues: 686 sheet: -0.18 (0.18), residues: 772 loop : -0.76 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 353 HIS 0.014 0.001 HIS A 519 PHE 0.035 0.002 PHE A 65 TYR 0.025 0.002 TYR C1067 ARG 0.013 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 250 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8577 (pp30) cc_final: 0.7959 (pp30) REVERT: A 104 TRP cc_start: 0.6469 (m-90) cc_final: 0.6063 (m-10) REVERT: A 160 TYR cc_start: 0.7688 (p90) cc_final: 0.7311 (p90) REVERT: A 368 LEU cc_start: 0.8178 (mm) cc_final: 0.7943 (tp) REVERT: A 386 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8647 (mmmm) REVERT: A 400 PHE cc_start: 0.8594 (p90) cc_final: 0.7986 (p90) REVERT: A 641 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6482 (t0) REVERT: A 740 MET cc_start: 0.7661 (tpt) cc_final: 0.6659 (mmt) REVERT: A 1089 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: B 313 TYR cc_start: 0.7852 (m-80) cc_final: 0.7326 (m-80) REVERT: B 354 ASN cc_start: 0.7519 (m110) cc_final: 0.7130 (m-40) REVERT: B 420 ASP cc_start: 0.8277 (t0) cc_final: 0.7920 (t0) REVERT: B 501 ASN cc_start: 0.8198 (m110) cc_final: 0.7803 (m110) REVERT: B 697 MET cc_start: 0.7507 (ptm) cc_final: 0.7128 (ptm) REVERT: B 823 PHE cc_start: 0.7267 (m-80) cc_final: 0.6867 (m-80) REVERT: B 1141 LEU cc_start: 0.8653 (mm) cc_final: 0.8273 (tp) REVERT: H 5 GLN cc_start: 0.7711 (mp10) cc_final: 0.7471 (mp10) REVERT: H 41 TRP cc_start: 0.6809 (m100) cc_final: 0.6329 (m100) REVERT: H 67 TYR cc_start: 0.5807 (m-80) cc_final: 0.5410 (m-80) REVERT: H 88 TYR cc_start: 0.8865 (m-80) cc_final: 0.8164 (m-80) REVERT: H 113 ASP cc_start: 0.7480 (m-30) cc_final: 0.7242 (m-30) REVERT: L 24 ARG cc_start: 0.8774 (ptp-110) cc_final: 0.8267 (ttm110) REVERT: L 51 LYS cc_start: 0.8966 (tppt) cc_final: 0.8398 (tttm) outliers start: 59 outliers final: 36 residues processed: 296 average time/residue: 0.3360 time to fit residues: 166.0708 Evaluate side-chains 269 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 243 optimal weight: 50.0000 chunk 134 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 122 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27625 Z= 0.259 Angle : 0.577 11.543 37631 Z= 0.288 Chirality : 0.046 0.452 4361 Planarity : 0.004 0.040 4833 Dihedral : 6.933 97.906 4455 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 11.62 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.33 (0.14), residues: 3369 helix: 1.37 (0.19), residues: 686 sheet: -0.18 (0.19), residues: 754 loop : -0.82 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 353 HIS 0.004 0.001 HIS C1048 PHE 0.033 0.002 PHE A 65 TYR 0.022 0.001 TYR C1067 ARG 0.008 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8582 (pp30) cc_final: 0.7974 (pp30) REVERT: A 104 TRP cc_start: 0.6467 (m-90) cc_final: 0.6053 (m-10) REVERT: A 160 TYR cc_start: 0.7720 (p90) cc_final: 0.7324 (p90) REVERT: A 368 LEU cc_start: 0.8153 (mm) cc_final: 0.7924 (tp) REVERT: A 386 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8652 (mmmm) REVERT: A 740 MET cc_start: 0.7668 (tpt) cc_final: 0.6644 (mmt) REVERT: B 55 PHE cc_start: 0.7748 (m-10) cc_final: 0.6980 (m-10) REVERT: B 354 ASN cc_start: 0.7446 (m110) cc_final: 0.7057 (m-40) REVERT: B 420 ASP cc_start: 0.8265 (t0) cc_final: 0.7917 (t0) REVERT: B 449 TYR cc_start: 0.7615 (m-80) cc_final: 0.7196 (m-80) REVERT: B 501 ASN cc_start: 0.8250 (m110) cc_final: 0.7849 (m110) REVERT: B 697 MET cc_start: 0.7526 (ptm) cc_final: 0.7154 (ptm) REVERT: B 823 PHE cc_start: 0.7307 (m-80) cc_final: 0.6888 (m-80) REVERT: B 900 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7394 (mtm) REVERT: B 983 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8347 (ttm110) REVERT: B 1141 LEU cc_start: 0.8653 (mm) cc_final: 0.8273 (tp) REVERT: C 1082 CYS cc_start: 0.5927 (t) cc_final: 0.5670 (t) REVERT: C 1127 ASP cc_start: 0.7989 (t0) cc_final: 0.7522 (m-30) REVERT: H 6 GLN cc_start: 0.4079 (mm-40) cc_final: 0.3565 (mm-40) REVERT: H 41 TRP cc_start: 0.6896 (m100) cc_final: 0.6516 (m100) REVERT: H 67 TYR cc_start: 0.5777 (m-80) cc_final: 0.5541 (m-80) REVERT: H 88 TYR cc_start: 0.8847 (m-80) cc_final: 0.8136 (m-80) REVERT: H 113 ASP cc_start: 0.7393 (m-30) cc_final: 0.7098 (m-30) REVERT: L 24 ARG cc_start: 0.8769 (ptp-110) cc_final: 0.7713 (mtp-110) REVERT: L 51 LYS cc_start: 0.8989 (tppt) cc_final: 0.8450 (tttm) outliers start: 55 outliers final: 40 residues processed: 286 average time/residue: 0.3337 time to fit residues: 159.5772 Evaluate side-chains 266 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27625 Z= 0.223 Angle : 0.561 11.757 37631 Z= 0.280 Chirality : 0.045 0.442 4361 Planarity : 0.004 0.041 4833 Dihedral : 6.659 93.610 4455 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.95 % Allowed : 12.27 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3369 helix: 1.50 (0.19), residues: 682 sheet: -0.16 (0.19), residues: 732 loop : -0.82 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 353 HIS 0.004 0.001 HIS C1048 PHE 0.029 0.002 PHE A 65 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 253 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8564 (pp30) cc_final: 0.7975 (pp30) REVERT: A 104 TRP cc_start: 0.6462 (m-90) cc_final: 0.6150 (m-10) REVERT: A 160 TYR cc_start: 0.7716 (p90) cc_final: 0.7306 (p90) REVERT: A 273 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7864 (ttm-80) REVERT: A 368 LEU cc_start: 0.8143 (mm) cc_final: 0.7931 (tp) REVERT: A 386 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8620 (mmmm) REVERT: A 641 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.6579 (t0) REVERT: A 1031 GLU cc_start: 0.7465 (pm20) cc_final: 0.7257 (pt0) REVERT: B 55 PHE cc_start: 0.7916 (m-10) cc_final: 0.7143 (m-10) REVERT: B 354 ASN cc_start: 0.7333 (m110) cc_final: 0.6906 (m-40) REVERT: B 403 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6606 (ttp80) REVERT: B 420 ASP cc_start: 0.8272 (t0) cc_final: 0.7939 (t0) REVERT: B 449 TYR cc_start: 0.7601 (m-80) cc_final: 0.6971 (m-80) REVERT: B 501 ASN cc_start: 0.8248 (m110) cc_final: 0.7846 (m110) REVERT: B 697 MET cc_start: 0.7513 (ptm) cc_final: 0.7154 (ptm) REVERT: B 823 PHE cc_start: 0.7303 (m-80) cc_final: 0.6876 (m-80) REVERT: B 1141 LEU cc_start: 0.8649 (mm) cc_final: 0.8272 (tp) REVERT: C 856 ASN cc_start: 0.7767 (m-40) cc_final: 0.7030 (t0) REVERT: C 1082 CYS cc_start: 0.5870 (t) cc_final: 0.5638 (t) REVERT: H 41 TRP cc_start: 0.6965 (m100) cc_final: 0.6012 (m100) REVERT: H 67 TYR cc_start: 0.5374 (m-80) cc_final: 0.5111 (m-80) REVERT: H 88 TYR cc_start: 0.8812 (m-80) cc_final: 0.8109 (m-80) REVERT: H 89 MET cc_start: 0.6624 (ppp) cc_final: 0.6399 (ppp) REVERT: H 113 ASP cc_start: 0.7386 (m-30) cc_final: 0.7113 (m-30) REVERT: L 24 ARG cc_start: 0.8781 (ptp-110) cc_final: 0.7678 (mtp-110) REVERT: L 51 LYS cc_start: 0.9001 (tppt) cc_final: 0.8447 (tttm) outliers start: 57 outliers final: 43 residues processed: 296 average time/residue: 0.3500 time to fit residues: 173.6720 Evaluate side-chains 275 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 325 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27625 Z= 0.204 Angle : 0.557 11.089 37631 Z= 0.278 Chirality : 0.045 0.432 4361 Planarity : 0.004 0.041 4833 Dihedral : 6.584 101.979 4455 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.85 % Allowed : 13.44 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.26 (0.14), residues: 3369 helix: 1.59 (0.19), residues: 683 sheet: -0.16 (0.19), residues: 722 loop : -0.81 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 353 HIS 0.005 0.001 HIS L 105 PHE 0.029 0.001 PHE B 347 TYR 0.019 0.001 TYR C 248 ARG 0.010 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8494 (pp30) cc_final: 0.7950 (pp30) REVERT: A 104 TRP cc_start: 0.6448 (m-90) cc_final: 0.6030 (m-10) REVERT: A 160 TYR cc_start: 0.7673 (p90) cc_final: 0.7315 (p90) REVERT: A 273 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7903 (ttm-80) REVERT: A 428 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7421 (p0) REVERT: A 641 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6587 (t0) REVERT: A 740 MET cc_start: 0.7319 (tpt) cc_final: 0.6485 (mmt) REVERT: B 55 PHE cc_start: 0.7915 (m-10) cc_final: 0.7161 (m-10) REVERT: B 354 ASN cc_start: 0.7259 (m110) cc_final: 0.6627 (m-40) REVERT: B 420 ASP cc_start: 0.8235 (t0) cc_final: 0.7934 (t0) REVERT: B 449 TYR cc_start: 0.7585 (m-80) cc_final: 0.6955 (m-80) REVERT: B 501 ASN cc_start: 0.8191 (m110) cc_final: 0.7788 (m110) REVERT: B 697 MET cc_start: 0.7531 (ptm) cc_final: 0.7175 (ptm) REVERT: C 856 ASN cc_start: 0.7695 (m-40) cc_final: 0.6979 (t0) REVERT: C 1082 CYS cc_start: 0.5941 (t) cc_final: 0.5730 (t) REVERT: C 1127 ASP cc_start: 0.7960 (t0) cc_final: 0.7549 (m-30) REVERT: H 41 TRP cc_start: 0.6493 (m100) cc_final: 0.6133 (m100) REVERT: H 88 TYR cc_start: 0.8776 (m-80) cc_final: 0.8116 (m-80) REVERT: H 113 ASP cc_start: 0.7402 (m-30) cc_final: 0.7106 (m-30) REVERT: H 115 PHE cc_start: 0.7193 (m-80) cc_final: 0.6772 (m-10) REVERT: L 24 ARG cc_start: 0.8773 (ptp-110) cc_final: 0.7483 (mtp-110) REVERT: L 51 LYS cc_start: 0.9026 (tppt) cc_final: 0.8462 (tttm) outliers start: 54 outliers final: 44 residues processed: 289 average time/residue: 0.3414 time to fit residues: 165.3698 Evaluate side-chains 277 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 57 HIS Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 207 optimal weight: 0.0970 chunk 221 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN H 59 ASN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27625 Z= 0.229 Angle : 0.572 10.485 37631 Z= 0.284 Chirality : 0.045 0.426 4361 Planarity : 0.004 0.041 4833 Dihedral : 6.474 98.441 4455 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.98 % Allowed : 13.61 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3369 helix: 1.56 (0.19), residues: 683 sheet: -0.20 (0.19), residues: 727 loop : -0.83 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP L 41 HIS 0.004 0.001 HIS C1048 PHE 0.021 0.001 PHE C 65 TYR 0.022 0.001 TYR C 248 ARG 0.008 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 243 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8537 (pp30) cc_final: 0.7939 (pp30) REVERT: A 104 TRP cc_start: 0.6431 (m-90) cc_final: 0.5978 (m-10) REVERT: A 160 TYR cc_start: 0.7677 (p90) cc_final: 0.7315 (p90) REVERT: A 641 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.6712 (t0) REVERT: A 740 MET cc_start: 0.7405 (tpt) cc_final: 0.6445 (mmt) REVERT: B 237 ARG cc_start: 0.7361 (mmm-85) cc_final: 0.6913 (mmm-85) REVERT: B 354 ASN cc_start: 0.7176 (m110) cc_final: 0.6525 (m-40) REVERT: B 403 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6672 (ttp80) REVERT: B 420 ASP cc_start: 0.8223 (t0) cc_final: 0.7922 (t0) REVERT: B 449 TYR cc_start: 0.7625 (m-80) cc_final: 0.7212 (m-80) REVERT: B 501 ASN cc_start: 0.8194 (m110) cc_final: 0.7788 (m110) REVERT: B 641 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6869 (t0) REVERT: B 697 MET cc_start: 0.7546 (ptm) cc_final: 0.7201 (ptm) REVERT: B 823 PHE cc_start: 0.7201 (m-80) cc_final: 0.6844 (m-80) REVERT: B 858 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8592 (pp) REVERT: C 1082 CYS cc_start: 0.5942 (t) cc_final: 0.5698 (t) REVERT: C 1127 ASP cc_start: 0.7973 (t0) cc_final: 0.7565 (m-30) REVERT: H 88 TYR cc_start: 0.8763 (m-80) cc_final: 0.7935 (m-80) REVERT: H 89 MET cc_start: 0.6701 (ppp) cc_final: 0.6090 (ppp) REVERT: H 113 ASP cc_start: 0.7439 (m-30) cc_final: 0.7166 (m-30) REVERT: H 115 PHE cc_start: 0.7213 (m-80) cc_final: 0.6785 (m-10) REVERT: L 24 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.7475 (mtp-110) REVERT: L 51 LYS cc_start: 0.9038 (tppt) cc_final: 0.8504 (tttm) outliers start: 58 outliers final: 47 residues processed: 287 average time/residue: 0.3398 time to fit residues: 164.3551 Evaluate side-chains 279 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 114 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 284 optimal weight: 0.7980 chunk 303 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN H 59 ASN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27625 Z= 0.190 Angle : 0.568 12.144 37631 Z= 0.280 Chirality : 0.045 0.422 4361 Planarity : 0.003 0.040 4833 Dihedral : 6.318 95.403 4455 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 14.02 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.26 (0.14), residues: 3369 helix: 1.67 (0.19), residues: 683 sheet: -0.23 (0.19), residues: 727 loop : -0.82 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP L 41 HIS 0.005 0.001 HIS C1048 PHE 0.025 0.001 PHE C 65 TYR 0.023 0.001 TYR C 248 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 240 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8512 (pp30) cc_final: 0.7910 (pp30) REVERT: A 160 TYR cc_start: 0.7671 (p90) cc_final: 0.7329 (p90) REVERT: A 273 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7891 (mtm-85) REVERT: A 641 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6711 (t0) REVERT: A 740 MET cc_start: 0.7432 (tpt) cc_final: 0.6488 (mmt) REVERT: B 237 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.6931 (mmm-85) REVERT: B 354 ASN cc_start: 0.7114 (m110) cc_final: 0.6460 (m-40) REVERT: B 403 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6633 (ttp80) REVERT: B 420 ASP cc_start: 0.8210 (t0) cc_final: 0.7824 (t0) REVERT: B 449 TYR cc_start: 0.7614 (m-80) cc_final: 0.7066 (m-80) REVERT: B 501 ASN cc_start: 0.8160 (m110) cc_final: 0.7753 (m110) REVERT: B 641 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6847 (t0) REVERT: B 697 MET cc_start: 0.7535 (ptm) cc_final: 0.7191 (ptm) REVERT: B 858 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8622 (pp) REVERT: C 1127 ASP cc_start: 0.7969 (t0) cc_final: 0.7567 (m-30) REVERT: H 88 TYR cc_start: 0.8569 (m-80) cc_final: 0.7922 (m-80) REVERT: H 89 MET cc_start: 0.6240 (ppp) cc_final: 0.5960 (ppp) REVERT: H 113 ASP cc_start: 0.7489 (m-30) cc_final: 0.7195 (m-30) REVERT: L 24 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.7412 (mtp-110) REVERT: L 51 LYS cc_start: 0.9038 (tppt) cc_final: 0.8528 (tttm) outliers start: 55 outliers final: 46 residues processed: 281 average time/residue: 0.3487 time to fit residues: 166.0339 Evaluate side-chains 280 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 41 TRP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 114 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 0.8980 chunk 321 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 309 optimal weight: 0.5980 chunk 268 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN H 59 ASN L 44 GLN ** L 66 ASN ** 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: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27625 Z= 0.189 Angle : 0.568 12.506 37631 Z= 0.280 Chirality : 0.045 0.417 4361 Planarity : 0.003 0.039 4833 Dihedral : 6.191 92.621 4455 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.81 % Allowed : 14.15 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.26 (0.14), residues: 3369 helix: 1.69 (0.19), residues: 687 sheet: -0.23 (0.19), residues: 725 loop : -0.84 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP L 41 HIS 0.004 0.001 HIS H 57 PHE 0.025 0.001 PHE C 65 TYR 0.021 0.001 TYR C 248 ARG 0.008 0.000 ARG L 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6738 Ramachandran restraints generated. 3369 Oldfield, 0 Emsley, 3369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 235 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8502 (pp30) cc_final: 0.7925 (pp30) REVERT: A 160 TYR cc_start: 0.7688 (p90) cc_final: 0.7342 (p90) REVERT: A 201 PHE cc_start: 0.8170 (t80) cc_final: 0.7691 (t80) REVERT: A 273 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7889 (mtm-85) REVERT: A 641 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.6721 (t0) REVERT: A 740 MET cc_start: 0.7419 (tpt) cc_final: 0.6463 (mmt) REVERT: B 55 PHE cc_start: 0.7870 (m-10) cc_final: 0.7148 (m-10) REVERT: B 354 ASN cc_start: 0.7098 (m110) cc_final: 0.6434 (m-40) REVERT: B 403 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6636 (ttp80) REVERT: B 420 ASP cc_start: 0.8196 (t0) cc_final: 0.7816 (t0) REVERT: B 449 TYR cc_start: 0.7612 (m-80) cc_final: 0.7240 (m-80) REVERT: B 501 ASN cc_start: 0.8157 (m110) cc_final: 0.7746 (m110) REVERT: B 641 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6726 (t0) REVERT: B 697 MET cc_start: 0.7528 (ptm) cc_final: 0.7193 (ptm) REVERT: B 858 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8649 (pp) REVERT: C 1127 ASP cc_start: 0.7929 (t0) cc_final: 0.7524 (m-30) REVERT: H 88 TYR cc_start: 0.8550 (m-80) cc_final: 0.7935 (m-80) REVERT: H 89 MET cc_start: 0.6161 (ppp) cc_final: 0.5933 (ppp) REVERT: H 113 ASP cc_start: 0.7456 (m-30) cc_final: 0.7139 (m-30) REVERT: H 115 PHE cc_start: 0.7339 (m-10) cc_final: 0.7049 (m-10) REVERT: L 24 ARG cc_start: 0.8743 (ptp-110) cc_final: 0.7505 (mtp-110) REVERT: L 51 LYS cc_start: 0.9052 (tppt) cc_final: 0.8539 (tttm) outliers start: 53 outliers final: 46 residues processed: 275 average time/residue: 0.3328 time to fit residues: 155.0164 Evaluate side-chains 278 residues out of total 2985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 HIS Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain L residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 268 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 275 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN L 44 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.160600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100643 restraints weight = 47558.194| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.76 r_work: 0.3366 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27625 Z= 0.204 Angle : 0.572 11.539 37631 Z= 0.281 Chirality : 0.045 0.414 4361 Planarity : 0.003 0.039 4833 Dihedral : 6.085 85.993 4455 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.74 % Allowed : 14.53 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % 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: -0.28 (0.14), residues: 3369 helix: 1.66 (0.19), residues: 687 sheet: -0.23 (0.19), residues: 730 loop : -0.85 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 41 HIS 0.006 0.001 HIS H 57 PHE 0.024 0.001 PHE C 65 TYR 0.020 0.001 TYR C 248 ARG 0.006 0.000 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6495.41 seconds wall clock time: 116 minutes 28.39 seconds (6988.39 seconds total)