Starting phenix.real_space_refine on Fri Mar 22 06:32:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t20_40976/03_2024/8t20_40976.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t20_40976/03_2024/8t20_40976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t20_40976/03_2024/8t20_40976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t20_40976/03_2024/8t20_40976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t20_40976/03_2024/8t20_40976.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t20_40976/03_2024/8t20_40976.pdb" } resolution = 3.36 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= 0.062 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 161 5.16 5 C 20836 2.51 5 N 5431 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 431": "OD1" <-> "OD2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 398": "OE1" <-> "OE2" Residue "E ASP 435": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32612 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "B" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7497 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 51, 'TRANS': 910} Chain breaks: 10 Chain: "C" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7497 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 51, 'TRANS': 910} Chain breaks: 10 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain: "E" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Time building chain proxies: 15.91, per 1000 atoms: 0.49 Number of scatterers: 32612 At special positions: 0 Unit cell: (132.09, 166.5, 249.75, 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 161 16.00 O 6184 8.00 N 5431 7.00 C 20836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.00 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 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 Time building additional restraints: 12.29 Conformation dependent library (CDL) restraints added in 5.7 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7730 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 36.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.587A pdb=" N TYR A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.022A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.540A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.666A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.663A 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 945 through 968 removed outlier: 3.945A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.424A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.589A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.920A pdb=" N TYR B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.518A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.948A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.697A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.939A 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 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.114A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.155A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.918A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.653A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 4.107A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.821A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.309A pdb=" N TYR D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.609A pdb=" N THR D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 83 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.932A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.754A pdb=" N LEU D 278 " --> pdb=" O TRP D 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 279' Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.908A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.545A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 449 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.529A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 600 Proline residue: D 590 - end of helix Processing helix chain 'E' and resid 20 through 53 Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 109 through 130 removed outlier: 4.572A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.952A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 172 through 193 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 220 through 252 removed outlier: 4.464A pdb=" N GLN E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 292 through 300 removed outlier: 4.145A pdb=" N ALA E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 4.279A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU E 312 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL E 316 " --> pdb=" O GLU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 Processing helix chain 'E' and resid 365 through 385 Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.628A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 442 Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.400A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR E 453 " --> pdb=" O THR E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 534 removed outlier: 3.606A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 Processing helix chain 'E' and resid 565 through 575 removed outlier: 4.426A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.713A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'A' and resid 539 through 540 Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.623A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.697A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.697A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.668A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.625A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.208A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.106A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.891A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.937A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 575 through 577 removed outlier: 3.940A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.522A pdb=" N VAL B 656 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.824A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.619A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.504A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.699A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.573A pdb=" N LEU C 189 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 318 removed outlier: 7.150A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 355 through 356 removed outlier: 4.218A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.645A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.776A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.859A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.859A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1122 1246 hydrogen bonds defined for protein. 3588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.00 Time building geometry restraints manager: 13.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 1 1.05 - 1.25: 4698 1.25 - 1.45: 10146 1.45 - 1.65: 18338 1.65 - 1.85: 229 Bond restraints: 33412 Sorted by residual: bond pdb=" CG PRO D 583 " pdb=" CD PRO D 583 " ideal model delta sigma weight residual 1.503 0.845 0.658 3.40e-02 8.65e+02 3.74e+02 bond pdb=" CG PRO D 289 " pdb=" CD PRO D 289 " ideal model delta sigma weight residual 1.503 1.223 0.280 3.40e-02 8.65e+02 6.81e+01 bond pdb=" CG PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" N PRO D 583 " pdb=" CD PRO D 583 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.20e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.34e+01 ... (remaining 33407 not shown) Histogram of bond angle deviations from ideal: 73.99 - 87.08: 3 87.08 - 100.17: 27 100.17 - 113.27: 18390 113.27 - 126.36: 26481 126.36 - 139.45: 540 Bond angle restraints: 45441 Sorted by residual: angle pdb=" N PRO D 583 " pdb=" CD PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 103.20 73.99 29.21 1.50e+00 4.44e-01 3.79e+02 angle pdb=" CA PRO D 426 " pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 112.00 93.72 18.28 1.40e+00 5.10e-01 1.71e+02 angle pdb=" CA PRO D 289 " pdb=" N PRO D 289 " pdb=" CD PRO D 289 " ideal model delta sigma weight residual 112.00 95.29 16.71 1.40e+00 5.10e-01 1.43e+02 angle pdb=" N THR D 608 " pdb=" CA THR D 608 " pdb=" C THR D 608 " ideal model delta sigma weight residual 111.17 127.46 -16.29 1.41e+00 5.03e-01 1.33e+02 angle pdb=" CA PRO D 583 " pdb=" CB PRO D 583 " pdb=" CG PRO D 583 " ideal model delta sigma weight residual 104.50 83.27 21.23 1.90e+00 2.77e-01 1.25e+02 ... (remaining 45436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16565 17.92 - 35.84: 2496 35.84 - 53.75: 653 53.75 - 71.67: 122 71.67 - 89.59: 53 Dihedral angle restraints: 19889 sinusoidal: 7890 harmonic: 11999 Sorted by residual: dihedral pdb=" CA PHE A 55 " pdb=" C PHE A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta harmonic sigma weight residual 180.00 129.95 50.05 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA PHE A 220 " pdb=" C PHE A 220 " pdb=" N SER A 221 " pdb=" CA SER A 221 " ideal model delta harmonic sigma weight residual 180.00 132.59 47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 178.36 -85.36 1 1.00e+01 1.00e-02 8.82e+01 ... (remaining 19886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4387 0.081 - 0.163: 579 0.163 - 0.244: 45 0.244 - 0.326: 11 0.326 - 0.407: 5 Chirality restraints: 5027 Sorted by residual: chirality pdb=" CG LEU A 962 " pdb=" CB LEU A 962 " pdb=" CD1 LEU A 962 " pdb=" CD2 LEU A 962 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA PRO A 986 " pdb=" N PRO A 986 " pdb=" C PRO A 986 " pdb=" CB PRO A 986 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA PRO A 561 " pdb=" N PRO A 561 " pdb=" C PRO A 561 " pdb=" CB PRO A 561 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 5024 not shown) Planarity restraints: 5898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 489 " -0.091 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO D 490 " 0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 490 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 490 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 986 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 288 " -0.082 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO D 289 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " -0.058 5.00e-02 4.00e+02 ... (remaining 5895 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 196 2.45 - 3.06: 22173 3.06 - 3.67: 50154 3.67 - 4.29: 69131 4.29 - 4.90: 112406 Nonbonded interactions: 254060 Sorted by model distance: nonbonded pdb=" N ILE D 484 " pdb=" O ASN D 607 " model vdw 1.836 2.520 nonbonded pdb=" O GLN C1002 " pdb=" OG1 THR C1006 " model vdw 1.893 2.440 nonbonded pdb=" O SER A 46 " pdb=" N ASN A 282 " model vdw 1.935 2.520 nonbonded pdb=" O ASP D 225 " pdb=" OG1 THR D 229 " model vdw 1.970 2.440 nonbonded pdb=" O GLN A1005 " pdb=" OG1 THR A1009 " model vdw 1.971 2.440 ... (remaining 254055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 320 or resid 335 through 366 or resid 376 throu \ gh 527 or resid 544 through 1147)) selection = chain 'B' selection = chain 'C' } 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: 0.010 Normalize map: mean=0, sd=1: 10.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 30.080 Check model and map are aligned: 0.430 Set scattering table: 0.300 Process input model: 79.500 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 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 : 0.007 0.658 33412 Z= 0.488 Angle : 1.055 29.211 45441 Z= 0.585 Chirality : 0.055 0.407 5027 Planarity : 0.008 0.130 5898 Dihedral : 18.406 89.590 12036 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.88 % Favored : 86.92 % Rotamer: Outliers : 0.67 % Allowed : 29.50 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.36 % 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: -2.81 (0.12), residues: 4053 helix: -0.09 (0.14), residues: 1325 sheet: -1.47 (0.25), residues: 372 loop : -3.19 (0.11), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 349 HIS 0.015 0.002 HIS D 535 PHE 0.063 0.003 PHE A 275 TYR 0.049 0.002 TYR A 279 ARG 0.011 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 485 time to evaluate : 3.594 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 116 SER cc_start: 0.5841 (p) cc_final: 0.5351 (t) REVERT: B 200 TYR cc_start: 0.2415 (OUTLIER) cc_final: 0.2002 (m-80) REVERT: B 237 ARG cc_start: 0.4922 (mmm160) cc_final: 0.4658 (mmp-170) REVERT: C 237 ARG cc_start: 0.4916 (ptm160) cc_final: 0.4619 (ppt170) REVERT: C 355 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.4368 (ttm170) REVERT: C 1077 THR cc_start: 0.5046 (t) cc_final: 0.4473 (m) REVERT: D 48 TRP cc_start: 0.1286 (t-100) cc_final: 0.0759 (t-100) REVERT: D 152 MET cc_start: -0.1122 (mmt) cc_final: -0.3592 (ptm) REVERT: D 376 MET cc_start: 0.0469 (tpt) cc_final: 0.0107 (ptm) REVERT: D 400 PHE cc_start: 0.2778 (t80) cc_final: 0.2102 (m-10) REVERT: E 62 MET cc_start: 0.2118 (tmm) cc_final: 0.1592 (tmm) REVERT: E 123 MET cc_start: 0.1290 (tmm) cc_final: 0.0388 (tmm) REVERT: E 190 MET cc_start: 0.3774 (tmm) cc_final: 0.3454 (ptt) REVERT: E 474 MET cc_start: 0.0114 (tmm) cc_final: -0.1133 (mmt) REVERT: E 480 MET cc_start: 0.1229 (mmp) cc_final: 0.0387 (tpp) REVERT: E 557 MET cc_start: -0.1441 (OUTLIER) cc_final: -0.1916 (mtm) outliers start: 24 outliers final: 5 residues processed: 504 average time/residue: 0.4320 time to fit residues: 357.6762 Evaluate side-chains 300 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 292 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 124 optimal weight: 0.0370 chunk 195 optimal weight: 0.3980 chunk 239 optimal weight: 0.8980 chunk 372 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 955 ASN A1106 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 690 GLN B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1106 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 232 GLN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 33412 Z= 0.282 Angle : 0.845 15.383 45441 Z= 0.446 Chirality : 0.051 0.344 5027 Planarity : 0.006 0.084 5898 Dihedral : 7.217 51.485 4435 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.71 % Favored : 89.19 % Rotamer: Outliers : 5.05 % Allowed : 26.62 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.79 % Twisted General : 0.23 % 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: -2.47 (0.13), residues: 4053 helix: 0.08 (0.14), residues: 1344 sheet: -1.19 (0.24), residues: 400 loop : -2.96 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 168 HIS 0.009 0.001 HIS E 373 PHE 0.033 0.002 PHE A 562 TYR 0.031 0.002 TYR A 279 ARG 0.009 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 309 time to evaluate : 3.681 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 37 TYR cc_start: 0.0748 (OUTLIER) cc_final: -0.0211 (m-80) REVERT: A 492 LEU cc_start: -0.1395 (OUTLIER) cc_final: -0.1694 (mt) REVERT: A 996 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7148 (tt) REVERT: A 998 THR cc_start: 0.8265 (t) cc_final: 0.8052 (p) REVERT: A 1009 THR cc_start: 0.0881 (OUTLIER) cc_final: 0.0615 (m) REVERT: B 237 ARG cc_start: 0.4915 (mmm160) cc_final: 0.4624 (mmp-170) REVERT: B 740 MET cc_start: 0.6922 (tpt) cc_final: 0.6476 (tpp) REVERT: B 898 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.5973 (m-80) REVERT: C 97 LYS cc_start: 0.4791 (tptp) cc_final: 0.3983 (mmmt) REVERT: C 130 VAL cc_start: 0.2258 (OUTLIER) cc_final: 0.2028 (t) REVERT: C 188 ASN cc_start: 0.5714 (OUTLIER) cc_final: 0.5498 (m-40) REVERT: C 355 ARG cc_start: 0.5420 (OUTLIER) cc_final: 0.3787 (ttm170) REVERT: D 131 LYS cc_start: -0.0249 (OUTLIER) cc_final: -0.0504 (pttt) REVERT: D 376 MET cc_start: 0.1242 (tpt) cc_final: 0.0220 (ttm) REVERT: D 400 PHE cc_start: 0.3081 (t80) cc_final: 0.2136 (m-10) REVERT: D 523 PHE cc_start: -0.0189 (OUTLIER) cc_final: -0.0449 (t80) REVERT: E 62 MET cc_start: 0.1631 (tmm) cc_final: 0.1106 (tmm) REVERT: E 123 MET cc_start: 0.0736 (tmm) cc_final: -0.0150 (tmm) REVERT: E 176 LEU cc_start: 0.1446 (OUTLIER) cc_final: 0.1245 (mm) REVERT: E 190 MET cc_start: 0.3969 (OUTLIER) cc_final: 0.3417 (ptt) REVERT: E 285 PHE cc_start: -0.0290 (OUTLIER) cc_final: -0.1320 (p90) REVERT: E 480 MET cc_start: 0.1569 (mmp) cc_final: 0.0940 (tpt) outliers start: 182 outliers final: 82 residues processed: 464 average time/residue: 0.4010 time to fit residues: 308.8941 Evaluate side-chains 339 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 244 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 372 optimal weight: 4.9990 chunk 402 optimal weight: 0.0970 chunk 332 optimal weight: 9.9990 chunk 369 optimal weight: 0.9990 chunk 127 optimal weight: 0.0570 chunk 299 optimal weight: 1.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 117 ASN D 228 HIS D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN E 58 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 33412 Z= 0.275 Angle : 0.809 15.197 45441 Z= 0.431 Chirality : 0.049 0.332 5027 Planarity : 0.006 0.077 5898 Dihedral : 6.794 45.100 4427 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.81 % Favored : 89.09 % Rotamer: Outliers : 5.72 % Allowed : 26.23 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.16 % 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: -2.34 (0.13), residues: 4053 helix: 0.18 (0.14), residues: 1339 sheet: -0.81 (0.25), residues: 402 loop : -2.94 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 478 HIS 0.034 0.001 HIS D 228 PHE 0.028 0.002 PHE B 106 TYR 0.030 0.002 TYR A 279 ARG 0.010 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 269 time to evaluate : 3.150 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.0911 (OUTLIER) cc_final: -0.0041 (m-80) REVERT: A 241 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5880 (tt) REVERT: A 316 SER cc_start: 0.7745 (OUTLIER) cc_final: 0.7491 (m) REVERT: A 492 LEU cc_start: -0.1128 (OUTLIER) cc_final: -0.1425 (mt) REVERT: A 693 ILE cc_start: 0.5628 (OUTLIER) cc_final: 0.5416 (pt) REVERT: A 962 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8588 (pt) REVERT: A 996 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7370 (tt) REVERT: B 210 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5271 (mm) REVERT: B 237 ARG cc_start: 0.5098 (mmm160) cc_final: 0.4697 (mmp-170) REVERT: B 402 ILE cc_start: 0.2770 (OUTLIER) cc_final: 0.2378 (pt) REVERT: B 740 MET cc_start: 0.7522 (tpt) cc_final: 0.6935 (tpp) REVERT: B 898 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: B 918 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: B 935 GLN cc_start: 0.4701 (OUTLIER) cc_final: 0.3970 (tp40) REVERT: B 981 LEU cc_start: 0.8229 (tp) cc_final: 0.8020 (tt) REVERT: B 994 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7324 (p0) REVERT: B 1000 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7823 (ptm-80) REVERT: B 1005 GLN cc_start: 0.6107 (mm-40) cc_final: 0.5742 (tm-30) REVERT: C 97 LYS cc_start: 0.4994 (tptp) cc_final: 0.4125 (mmmt) REVERT: C 204 TYR cc_start: 0.5691 (m-80) cc_final: 0.5226 (m-80) REVERT: C 355 ARG cc_start: 0.5154 (OUTLIER) cc_final: 0.4505 (tpp-160) REVERT: D 174 LYS cc_start: 0.0387 (mmtt) cc_final: -0.0416 (pttp) REVERT: D 376 MET cc_start: 0.1363 (tpt) cc_final: 0.1071 (ttm) REVERT: D 400 PHE cc_start: 0.3060 (t80) cc_final: 0.2072 (m-10) REVERT: D 408 MET cc_start: -0.1119 (ptp) cc_final: -0.2132 (mmm) REVERT: E 62 MET cc_start: 0.1661 (tmm) cc_final: 0.1128 (tmm) REVERT: E 123 MET cc_start: 0.0705 (tmm) cc_final: 0.0034 (tmm) REVERT: E 176 LEU cc_start: 0.1340 (OUTLIER) cc_final: 0.0799 (mm) REVERT: E 190 MET cc_start: 0.3955 (OUTLIER) cc_final: 0.3368 (ptt) REVERT: E 285 PHE cc_start: 0.0017 (OUTLIER) cc_final: -0.1258 (p90) REVERT: E 310 GLU cc_start: 0.1789 (OUTLIER) cc_final: 0.1185 (tp30) REVERT: E 462 MET cc_start: 0.5423 (tmm) cc_final: 0.5128 (ttt) REVERT: E 480 MET cc_start: 0.1768 (mmp) cc_final: 0.0751 (tpp) REVERT: E 498 CYS cc_start: 0.5140 (OUTLIER) cc_final: 0.3846 (m) REVERT: E 536 GLU cc_start: -0.0176 (OUTLIER) cc_final: -0.1822 (mp0) outliers start: 206 outliers final: 96 residues processed: 446 average time/residue: 0.4154 time to fit residues: 309.0945 Evaluate side-chains 357 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 240 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 9.9990 chunk 280 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 374 optimal weight: 3.9990 chunk 396 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 564 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 957 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C1002 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS E 188 ASN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 526 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33412 Z= 0.388 Angle : 0.907 15.889 45441 Z= 0.480 Chirality : 0.053 0.332 5027 Planarity : 0.007 0.095 5898 Dihedral : 7.109 50.360 4427 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.99 % Favored : 87.86 % Rotamer: Outliers : 7.52 % Allowed : 25.01 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.12), residues: 4053 helix: -0.10 (0.14), residues: 1360 sheet: -1.00 (0.25), residues: 389 loop : -3.02 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 594 HIS 0.016 0.002 HIS D 228 PHE 0.049 0.003 PHE A 562 TYR 0.035 0.002 TYR A 279 ARG 0.015 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 242 time to evaluate : 3.514 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 37 TYR cc_start: 0.2059 (OUTLIER) cc_final: 0.0377 (m-80) REVERT: A 354 ASN cc_start: 0.4058 (OUTLIER) cc_final: 0.3552 (p0) REVERT: A 492 LEU cc_start: -0.1083 (OUTLIER) cc_final: -0.1401 (mt) REVERT: A 996 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 1009 THR cc_start: 0.2629 (OUTLIER) cc_final: 0.2396 (m) REVERT: B 191 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5404 (mp0) REVERT: B 210 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5477 (mm) REVERT: B 237 ARG cc_start: 0.5024 (mmm160) cc_final: 0.3937 (mmp-170) REVERT: B 402 ILE cc_start: 0.2967 (OUTLIER) cc_final: 0.2570 (pt) REVERT: B 740 MET cc_start: 0.8164 (tpt) cc_final: 0.7703 (tpp) REVERT: B 966 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.5100 (mt) REVERT: B 1000 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8237 (ptm-80) REVERT: B 1004 LEU cc_start: 0.6307 (tp) cc_final: 0.5746 (tp) REVERT: C 115 GLN cc_start: 0.2229 (OUTLIER) cc_final: 0.1643 (tp40) REVERT: C 191 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6339 (mm-30) REVERT: C 740 MET cc_start: 0.8027 (tpp) cc_final: 0.7771 (ttt) REVERT: D 90 ASP cc_start: 0.2822 (OUTLIER) cc_final: 0.2541 (p0) REVERT: D 297 MET cc_start: 0.1978 (mmm) cc_final: 0.1583 (mmm) REVERT: D 400 PHE cc_start: 0.3388 (t80) cc_final: 0.2195 (m-10) REVERT: D 408 MET cc_start: -0.0766 (ptp) cc_final: -0.2568 (mtm) REVERT: D 543 ASP cc_start: 0.2668 (OUTLIER) cc_final: 0.2401 (m-30) REVERT: D 579 MET cc_start: -0.0774 (OUTLIER) cc_final: -0.2186 (tmm) REVERT: E 62 MET cc_start: 0.1945 (tmm) cc_final: 0.1310 (tmm) REVERT: E 123 MET cc_start: 0.0585 (tmm) cc_final: -0.0029 (tmm) REVERT: E 176 LEU cc_start: 0.1297 (OUTLIER) cc_final: 0.0385 (mp) REVERT: E 285 PHE cc_start: 0.0833 (OUTLIER) cc_final: -0.0395 (p90) REVERT: E 310 GLU cc_start: 0.2029 (OUTLIER) cc_final: 0.1409 (tp30) REVERT: E 350 ASP cc_start: 0.4309 (OUTLIER) cc_final: 0.2673 (t70) REVERT: E 383 MET cc_start: 0.0204 (OUTLIER) cc_final: -0.0004 (mmt) REVERT: E 446 ILE cc_start: 0.2928 (OUTLIER) cc_final: 0.2329 (mp) REVERT: E 480 MET cc_start: 0.1943 (mmp) cc_final: 0.0673 (tpt) REVERT: E 536 GLU cc_start: 0.0032 (OUTLIER) cc_final: -0.1982 (mp0) outliers start: 271 outliers final: 149 residues processed: 482 average time/residue: 0.4090 time to fit residues: 331.4542 Evaluate side-chains 373 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 203 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 350 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 338 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 0.5980 chunk 355 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 804 GLN C 122 ASN C 804 GLN D 33 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 228 HIS D 322 ASN D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 380 GLN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33412 Z= 0.240 Angle : 0.781 15.779 45441 Z= 0.409 Chirality : 0.049 0.312 5027 Planarity : 0.006 0.068 5898 Dihedral : 6.679 50.547 4423 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.41 % Favored : 89.49 % Rotamer: Outliers : 5.75 % Allowed : 26.51 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.13), residues: 4053 helix: 0.20 (0.14), residues: 1332 sheet: -0.78 (0.26), residues: 384 loop : -2.96 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 594 HIS 0.005 0.001 HIS D 555 PHE 0.033 0.002 PHE B 106 TYR 0.035 0.002 TYR A 279 ARG 0.008 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 218 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1356 (OUTLIER) cc_final: -0.0137 (m-80) REVERT: A 492 LEU cc_start: -0.0766 (OUTLIER) cc_final: -0.1065 (mt) REVERT: A 980 ILE cc_start: 0.3839 (mm) cc_final: 0.3472 (mm) REVERT: A 996 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7748 (tt) REVERT: A 1002 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6332 (tt0) REVERT: B 106 PHE cc_start: 0.1955 (OUTLIER) cc_final: 0.1623 (m-80) REVERT: B 191 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5202 (mp0) REVERT: B 210 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.5387 (mm) REVERT: B 237 ARG cc_start: 0.4967 (mmm160) cc_final: 0.4178 (mmp-170) REVERT: B 402 ILE cc_start: 0.3087 (OUTLIER) cc_final: 0.2698 (pt) REVERT: B 740 MET cc_start: 0.8177 (tpt) cc_final: 0.7738 (tpp) REVERT: B 918 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: B 1000 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8061 (ptm-80) REVERT: C 191 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6235 (mm-30) REVERT: C 740 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7749 (ttt) REVERT: D 32 PHE cc_start: 0.1883 (OUTLIER) cc_final: -0.2024 (t80) REVERT: D 297 MET cc_start: 0.1981 (mmm) cc_final: 0.1683 (mmm) REVERT: D 332 MET cc_start: 0.2507 (tmm) cc_final: 0.1709 (tmm) REVERT: D 367 ASP cc_start: 0.3053 (OUTLIER) cc_final: 0.2602 (p0) REVERT: D 400 PHE cc_start: 0.3279 (t80) cc_final: 0.2310 (m-10) REVERT: D 408 MET cc_start: -0.1544 (ptp) cc_final: -0.2632 (mtm) REVERT: D 579 MET cc_start: -0.2521 (mtm) cc_final: -0.3166 (tmm) REVERT: E 61 LYS cc_start: 0.2314 (OUTLIER) cc_final: 0.1696 (tptp) REVERT: E 62 MET cc_start: 0.1826 (tmm) cc_final: 0.1236 (tmm) REVERT: E 89 GLN cc_start: 0.3644 (tp40) cc_final: 0.2069 (mt0) REVERT: E 94 LYS cc_start: 0.1167 (OUTLIER) cc_final: 0.0861 (ptpt) REVERT: E 190 MET cc_start: 0.4178 (OUTLIER) cc_final: 0.3099 (ptt) REVERT: E 285 PHE cc_start: 0.0318 (OUTLIER) cc_final: -0.1062 (p90) REVERT: E 306 ARG cc_start: 0.1996 (OUTLIER) cc_final: 0.0786 (ttm-80) REVERT: E 310 GLU cc_start: 0.1786 (OUTLIER) cc_final: 0.0527 (tp30) REVERT: E 480 MET cc_start: 0.1825 (mmp) cc_final: 0.0553 (tpt) REVERT: E 536 GLU cc_start: -0.0171 (OUTLIER) cc_final: -0.2036 (mp0) REVERT: E 600 ARG cc_start: 0.2659 (OUTLIER) cc_final: 0.2206 (tpp-160) outliers start: 207 outliers final: 113 residues processed: 402 average time/residue: 0.4067 time to fit residues: 271.9815 Evaluate side-chains 333 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 199 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 78 optimal weight: 0.0050 chunk 232 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 396 optimal weight: 7.9990 chunk 329 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 388 GLN D 493 HIS ** D 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33412 Z= 0.243 Angle : 0.770 16.482 45441 Z= 0.402 Chirality : 0.048 0.311 5027 Planarity : 0.006 0.064 5898 Dihedral : 6.483 54.184 4423 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.81 % Favored : 89.09 % Rotamer: Outliers : 5.63 % Allowed : 26.70 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % 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: -2.25 (0.13), residues: 4053 helix: 0.35 (0.14), residues: 1335 sheet: -0.65 (0.26), residues: 370 loop : -2.93 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 594 HIS 0.007 0.001 HIS D 555 PHE 0.026 0.002 PHE B 106 TYR 0.029 0.001 TYR B 279 ARG 0.011 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 210 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.1440 (OUTLIER) cc_final: 0.0701 (m-80) REVERT: A 279 TYR cc_start: 0.1721 (m-80) cc_final: 0.1245 (m-80) REVERT: A 492 LEU cc_start: -0.0519 (OUTLIER) cc_final: -0.0839 (mt) REVERT: A 996 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 1138 TYR cc_start: 0.7229 (t80) cc_final: 0.6862 (t80) REVERT: B 210 ILE cc_start: 0.5780 (OUTLIER) cc_final: 0.5323 (mm) REVERT: B 237 ARG cc_start: 0.5015 (mmm160) cc_final: 0.4066 (mmp-170) REVERT: B 740 MET cc_start: 0.8134 (tpt) cc_final: 0.7924 (ttm) REVERT: B 918 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: B 1000 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8060 (ptm-80) REVERT: C 115 GLN cc_start: 0.3020 (OUTLIER) cc_final: 0.2553 (tm-30) REVERT: C 191 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6375 (mm-30) REVERT: C 1060 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8920 (p) REVERT: C 1145 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4672 (mp) REVERT: D 32 PHE cc_start: 0.2047 (OUTLIER) cc_final: -0.1748 (t80) REVERT: D 270 MET cc_start: 0.1482 (ttm) cc_final: 0.1027 (ttm) REVERT: D 332 MET cc_start: 0.2338 (tmm) cc_final: 0.1633 (tmm) REVERT: D 367 ASP cc_start: 0.3075 (OUTLIER) cc_final: 0.2709 (p0) REVERT: D 400 PHE cc_start: 0.3209 (t80) cc_final: 0.2219 (m-10) REVERT: D 408 MET cc_start: -0.1379 (ptp) cc_final: -0.2177 (mtm) REVERT: D 474 MET cc_start: 0.1613 (tpt) cc_final: 0.0919 (tpp) REVERT: D 478 TRP cc_start: -0.0281 (OUTLIER) cc_final: -0.1901 (m100) REVERT: E 61 LYS cc_start: 0.2189 (OUTLIER) cc_final: 0.1594 (tptp) REVERT: E 62 MET cc_start: 0.1693 (tmm) cc_final: 0.1165 (tmm) REVERT: E 89 GLN cc_start: 0.3791 (tp40) cc_final: 0.2050 (mt0) REVERT: E 94 LYS cc_start: 0.1263 (OUTLIER) cc_final: 0.0929 (ptpt) REVERT: E 176 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0423 (mp) REVERT: E 190 MET cc_start: 0.4102 (OUTLIER) cc_final: 0.3015 (ptt) REVERT: E 285 PHE cc_start: 0.0601 (OUTLIER) cc_final: -0.0576 (p90) REVERT: E 306 ARG cc_start: 0.2021 (OUTLIER) cc_final: 0.0813 (ttm-80) REVERT: E 310 GLU cc_start: 0.1671 (OUTLIER) cc_final: 0.0402 (tp30) REVERT: E 431 ASP cc_start: 0.0649 (OUTLIER) cc_final: 0.0442 (m-30) REVERT: E 446 ILE cc_start: 0.2641 (OUTLIER) cc_final: 0.1962 (mp) REVERT: E 480 MET cc_start: 0.1866 (mmp) cc_final: 0.0626 (tpt) REVERT: E 536 GLU cc_start: -0.0068 (OUTLIER) cc_final: -0.1929 (mp0) REVERT: E 600 ARG cc_start: 0.2695 (OUTLIER) cc_final: 0.2475 (tpp-160) outliers start: 203 outliers final: 135 residues processed: 388 average time/residue: 0.3845 time to fit residues: 249.8995 Evaluate side-chains 352 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 193 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 226 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 333 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 395 optimal weight: 8.9990 chunk 247 optimal weight: 0.3980 chunk 240 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 965 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33412 Z= 0.317 Angle : 0.824 16.377 45441 Z= 0.433 Chirality : 0.050 0.314 5027 Planarity : 0.006 0.067 5898 Dihedral : 6.675 57.210 4423 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.50 % Favored : 88.40 % Rotamer: Outliers : 5.77 % Allowed : 26.62 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.13 % 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: -2.34 (0.13), residues: 4053 helix: 0.27 (0.14), residues: 1331 sheet: -0.64 (0.26), residues: 364 loop : -2.99 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 594 HIS 0.012 0.001 HIS D 555 PHE 0.042 0.002 PHE B 106 TYR 0.036 0.002 TYR B 279 ARG 0.013 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 208 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: -0.0385 (OUTLIER) cc_final: -0.0727 (mt) REVERT: A 996 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7728 (tt) REVERT: A 1138 TYR cc_start: 0.7319 (t80) cc_final: 0.6903 (t80) REVERT: B 92 PHE cc_start: 0.4194 (m-10) cc_final: 0.3924 (m-10) REVERT: B 106 PHE cc_start: 0.2328 (OUTLIER) cc_final: 0.1735 (m-80) REVERT: B 210 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5046 (mm) REVERT: B 825 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8195 (tttp) REVERT: B 918 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: B 966 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5700 (mt) REVERT: B 1000 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8226 (ptm-80) REVERT: C 191 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6472 (mm-30) REVERT: C 215 ASP cc_start: 0.3877 (OUTLIER) cc_final: 0.3481 (t0) REVERT: C 1060 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 1145 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5062 (mp) REVERT: D 32 PHE cc_start: 0.1941 (OUTLIER) cc_final: -0.1903 (t80) REVERT: D 270 MET cc_start: 0.1564 (ttm) cc_final: 0.0653 (ttm) REVERT: D 297 MET cc_start: 0.2002 (mmm) cc_final: 0.1714 (mmm) REVERT: D 367 ASP cc_start: 0.2783 (OUTLIER) cc_final: 0.2578 (p0) REVERT: D 400 PHE cc_start: 0.3177 (t80) cc_final: 0.2211 (m-10) REVERT: D 408 MET cc_start: -0.1545 (ptp) cc_final: -0.2540 (mtt) REVERT: D 474 MET cc_start: 0.1892 (tpt) cc_final: 0.0043 (ttm) REVERT: D 579 MET cc_start: -0.3271 (mtm) cc_final: -0.3952 (tmm) REVERT: E 61 LYS cc_start: 0.2395 (OUTLIER) cc_final: 0.1864 (tptp) REVERT: E 62 MET cc_start: 0.1014 (tmm) cc_final: 0.0443 (tmm) REVERT: E 89 GLN cc_start: 0.3489 (tp40) cc_final: 0.1541 (pt0) REVERT: E 94 LYS cc_start: 0.1255 (OUTLIER) cc_final: 0.0974 (pttt) REVERT: E 176 LEU cc_start: 0.1626 (OUTLIER) cc_final: 0.0845 (mp) REVERT: E 282 MET cc_start: 0.3147 (ptp) cc_final: 0.2770 (ppp) REVERT: E 285 PHE cc_start: 0.0831 (OUTLIER) cc_final: -0.0361 (p90) REVERT: E 306 ARG cc_start: 0.2286 (OUTLIER) cc_final: 0.0685 (ttm-80) REVERT: E 310 GLU cc_start: 0.2018 (OUTLIER) cc_final: 0.0639 (tp30) REVERT: E 431 ASP cc_start: 0.0775 (OUTLIER) cc_final: 0.0474 (m-30) REVERT: E 446 ILE cc_start: 0.2732 (OUTLIER) cc_final: 0.2100 (mp) REVERT: E 480 MET cc_start: 0.2145 (mmp) cc_final: 0.0605 (tpt) REVERT: E 536 GLU cc_start: 0.0104 (OUTLIER) cc_final: -0.1949 (mp0) outliers start: 208 outliers final: 144 residues processed: 392 average time/residue: 0.3928 time to fit residues: 258.6998 Evaluate side-chains 358 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 191 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 926 GLN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 251 optimal weight: 0.9990 chunk 269 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 607 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.7731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 33412 Z= 0.226 Angle : 0.764 15.141 45441 Z= 0.399 Chirality : 0.048 0.329 5027 Planarity : 0.006 0.069 5898 Dihedral : 6.406 59.458 4423 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.07 % Favored : 89.83 % Rotamer: Outliers : 4.41 % Allowed : 28.25 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.10 % 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: -2.21 (0.13), residues: 4053 helix: 0.43 (0.14), residues: 1323 sheet: -0.55 (0.26), residues: 362 loop : -2.94 (0.11), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 594 HIS 0.005 0.001 HIS D 555 PHE 0.030 0.002 PHE B 92 TYR 0.028 0.001 TYR A 279 ARG 0.009 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 208 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.7685 (t) cc_final: 0.7466 (t) REVERT: A 492 LEU cc_start: -0.0538 (OUTLIER) cc_final: -0.0860 (mp) REVERT: A 996 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7554 (tt) REVERT: A 1138 TYR cc_start: 0.7268 (t80) cc_final: 0.6885 (t80) REVERT: B 92 PHE cc_start: 0.4359 (m-10) cc_final: 0.4079 (m-10) REVERT: B 106 PHE cc_start: 0.1985 (OUTLIER) cc_final: 0.1481 (m-80) REVERT: B 210 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.4897 (mm) REVERT: B 237 ARG cc_start: 0.4655 (mmm160) cc_final: 0.3581 (mmp-170) REVERT: B 565 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7062 (p90) REVERT: B 918 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: B 966 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.5349 (mt) REVERT: B 1000 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7858 (ptm-80) REVERT: C 191 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6393 (mm-30) REVERT: C 215 ASP cc_start: 0.3877 (OUTLIER) cc_final: 0.3513 (t0) REVERT: C 1145 LEU cc_start: 0.5130 (OUTLIER) cc_final: 0.4890 (mp) REVERT: D 32 PHE cc_start: 0.1877 (OUTLIER) cc_final: -0.1982 (t80) REVERT: D 152 MET cc_start: -0.2192 (mmm) cc_final: -0.2434 (mmp) REVERT: D 270 MET cc_start: 0.1446 (ttm) cc_final: 0.1131 (ttm) REVERT: D 366 MET cc_start: 0.1559 (pmm) cc_final: -0.1186 (mmm) REVERT: D 400 PHE cc_start: 0.3180 (t80) cc_final: 0.2282 (m-10) REVERT: D 408 MET cc_start: -0.1703 (ptp) cc_final: -0.2452 (mtt) REVERT: D 474 MET cc_start: 0.1832 (tpt) cc_final: -0.0675 (ttm) REVERT: D 478 TRP cc_start: -0.0688 (OUTLIER) cc_final: -0.1854 (m100) REVERT: D 514 ARG cc_start: 0.3734 (ptm-80) cc_final: 0.3471 (ptm-80) REVERT: D 579 MET cc_start: -0.2846 (mtm) cc_final: -0.3646 (tmm) REVERT: E 61 LYS cc_start: 0.2499 (OUTLIER) cc_final: 0.1941 (tptp) REVERT: E 62 MET cc_start: 0.1380 (tmm) cc_final: 0.0827 (tmm) REVERT: E 89 GLN cc_start: 0.3573 (tp40) cc_final: 0.1575 (pt0) REVERT: E 94 LYS cc_start: 0.1341 (OUTLIER) cc_final: 0.1029 (pttt) REVERT: E 282 MET cc_start: 0.2980 (ptp) cc_final: 0.2728 (ppp) REVERT: E 285 PHE cc_start: 0.0573 (OUTLIER) cc_final: -0.0525 (p90) REVERT: E 306 ARG cc_start: 0.1915 (OUTLIER) cc_final: 0.0645 (ttm-80) REVERT: E 310 GLU cc_start: 0.1756 (OUTLIER) cc_final: 0.0754 (tp30) REVERT: E 446 ILE cc_start: 0.2988 (OUTLIER) cc_final: 0.2360 (mp) REVERT: E 480 MET cc_start: 0.1940 (mmp) cc_final: 0.0573 (tpt) REVERT: E 536 GLU cc_start: 0.0234 (OUTLIER) cc_final: -0.1840 (mp0) REVERT: E 600 ARG cc_start: 0.2702 (OUTLIER) cc_final: 0.2290 (tpp-160) outliers start: 159 outliers final: 112 residues processed: 346 average time/residue: 0.4075 time to fit residues: 234.5617 Evaluate side-chains 333 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 200 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 8.9990 chunk 378 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 366 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 955 ASN C 422 ASN C 487 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 221 GLN D 374 HIS D 526 GLN D 607 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.8302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 33412 Z= 0.492 Angle : 0.912 16.267 45441 Z= 0.483 Chirality : 0.054 0.384 5027 Planarity : 0.007 0.076 5898 Dihedral : 6.868 55.316 4420 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.90 % Favored : 86.97 % Rotamer: Outliers : 5.41 % Allowed : 27.42 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.16 % 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: -2.56 (0.12), residues: 4053 helix: 0.08 (0.14), residues: 1322 sheet: -1.01 (0.25), residues: 381 loop : -3.07 (0.11), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 594 HIS 0.011 0.002 HIS E 265 PHE 0.038 0.003 PHE B 106 TYR 0.050 0.003 TYR A 279 ARG 0.012 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 204 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.2862 (OUTLIER) cc_final: 0.2267 (mt) REVERT: A 492 LEU cc_start: -0.0505 (OUTLIER) cc_final: -0.0988 (mt) REVERT: A 996 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7697 (tt) REVERT: B 106 PHE cc_start: 0.2448 (OUTLIER) cc_final: 0.1981 (m-80) REVERT: B 210 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5108 (mm) REVERT: B 265 TYR cc_start: 0.4943 (OUTLIER) cc_final: 0.3588 (p90) REVERT: B 565 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7101 (p90) REVERT: B 918 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: B 966 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6229 (mt) REVERT: B 1000 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8462 (ptm-80) REVERT: C 215 ASP cc_start: 0.4089 (OUTLIER) cc_final: 0.3810 (t0) REVERT: C 1145 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5401 (mp) REVERT: D 177 ARG cc_start: 0.0074 (OUTLIER) cc_final: -0.2729 (mtt-85) REVERT: D 270 MET cc_start: 0.1903 (ttm) cc_final: 0.1587 (ttm) REVERT: D 349 TRP cc_start: 0.1706 (OUTLIER) cc_final: 0.1071 (m-10) REVERT: D 400 PHE cc_start: 0.3333 (t80) cc_final: 0.2215 (m-10) REVERT: D 408 MET cc_start: -0.1378 (ptp) cc_final: -0.2491 (mtt) REVERT: D 474 MET cc_start: 0.2059 (tpt) cc_final: 0.0184 (ttm) REVERT: D 514 ARG cc_start: 0.3899 (ptm-80) cc_final: 0.3547 (ptm-80) REVERT: D 579 MET cc_start: -0.3107 (mtm) cc_final: -0.3916 (tmm) REVERT: E 61 LYS cc_start: 0.2486 (OUTLIER) cc_final: 0.1996 (tptp) REVERT: E 62 MET cc_start: 0.1129 (tmm) cc_final: 0.0637 (tmm) REVERT: E 89 GLN cc_start: 0.4151 (tp40) cc_final: 0.1641 (pt0) REVERT: E 94 LYS cc_start: 0.1154 (OUTLIER) cc_final: 0.0700 (ptpt) REVERT: E 152 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.4368 (mpp) REVERT: E 176 LEU cc_start: 0.1708 (OUTLIER) cc_final: 0.0856 (mp) REVERT: E 282 MET cc_start: 0.3232 (ptp) cc_final: 0.2795 (ppp) REVERT: E 285 PHE cc_start: 0.1421 (OUTLIER) cc_final: 0.0239 (p90) REVERT: E 306 ARG cc_start: 0.2395 (OUTLIER) cc_final: 0.0354 (ttm-80) REVERT: E 310 GLU cc_start: 0.1722 (OUTLIER) cc_final: 0.0515 (tp30) REVERT: E 446 ILE cc_start: 0.3342 (OUTLIER) cc_final: 0.2754 (mp) REVERT: E 480 MET cc_start: 0.2135 (mmp) cc_final: 0.0544 (tpt) REVERT: E 536 GLU cc_start: 0.0546 (OUTLIER) cc_final: -0.1820 (mp0) REVERT: E 588 PHE cc_start: 0.2880 (OUTLIER) cc_final: 0.2538 (m-80) REVERT: E 600 ARG cc_start: 0.2890 (OUTLIER) cc_final: 0.2214 (tpp-160) outliers start: 195 outliers final: 140 residues processed: 378 average time/residue: 0.4100 time to fit residues: 256.6130 Evaluate side-chains 354 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 189 time to evaluate : 3.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 2.9990 chunk 389 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 184 optimal weight: 0.5980 chunk 270 optimal weight: 0.9990 chunk 408 optimal weight: 0.9980 chunk 375 optimal weight: 0.6980 chunk 325 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 251 optimal weight: 0.6980 chunk 199 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.8339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 33412 Z= 0.365 Angle : 1.014 59.195 45441 Z= 0.565 Chirality : 0.053 0.559 5027 Planarity : 0.007 0.152 5898 Dihedral : 6.883 54.895 4420 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.05 % Favored : 86.87 % Rotamer: Outliers : 4.80 % Allowed : 28.39 % Favored : 66.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4053 helix: 0.03 (0.14), residues: 1323 sheet: -1.02 (0.25), residues: 381 loop : -3.07 (0.11), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP D 594 HIS 0.008 0.002 HIS E 265 PHE 0.059 0.003 PHE B 106 TYR 0.038 0.002 TYR B 279 ARG 0.013 0.001 ARG A1000 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 191 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.2815 (OUTLIER) cc_final: 0.2203 (mt) REVERT: A 492 LEU cc_start: -0.0513 (OUTLIER) cc_final: -0.0997 (mt) REVERT: A 996 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7669 (tt) REVERT: B 106 PHE cc_start: 0.2202 (OUTLIER) cc_final: 0.1813 (m-80) REVERT: B 210 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.5092 (mm) REVERT: B 265 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.3494 (p90) REVERT: B 565 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7157 (p90) REVERT: B 918 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: B 966 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6177 (mt) REVERT: B 1000 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8391 (ptm-80) REVERT: C 215 ASP cc_start: 0.4088 (OUTLIER) cc_final: 0.3808 (t0) REVERT: C 1145 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5396 (mp) REVERT: D 177 ARG cc_start: 0.0022 (OUTLIER) cc_final: -0.2751 (mtt-85) REVERT: D 270 MET cc_start: 0.1803 (ttm) cc_final: 0.1502 (ttm) REVERT: D 349 TRP cc_start: 0.1673 (OUTLIER) cc_final: 0.1020 (m-10) REVERT: D 400 PHE cc_start: 0.3311 (t80) cc_final: 0.2207 (m-10) REVERT: D 408 MET cc_start: -0.1507 (ptp) cc_final: -0.2581 (mtt) REVERT: D 474 MET cc_start: 0.2040 (tpt) cc_final: 0.0172 (ttm) REVERT: D 514 ARG cc_start: 0.3877 (ptm-80) cc_final: 0.3535 (ptm-80) REVERT: D 579 MET cc_start: -0.3110 (mtm) cc_final: -0.3920 (tmm) REVERT: E 61 LYS cc_start: 0.2466 (OUTLIER) cc_final: 0.1980 (tptp) REVERT: E 62 MET cc_start: 0.1091 (tmm) cc_final: 0.0600 (tmm) REVERT: E 89 GLN cc_start: 0.4134 (tp40) cc_final: 0.1636 (pt0) REVERT: E 94 LYS cc_start: 0.1143 (OUTLIER) cc_final: 0.0691 (ptpt) REVERT: E 152 MET cc_start: 0.5334 (OUTLIER) cc_final: 0.4329 (mpp) REVERT: E 176 LEU cc_start: 0.1674 (OUTLIER) cc_final: 0.0824 (mp) REVERT: E 282 MET cc_start: 0.3183 (ptp) cc_final: 0.2770 (ppp) REVERT: E 285 PHE cc_start: 0.1370 (OUTLIER) cc_final: 0.0190 (p90) REVERT: E 306 ARG cc_start: 0.2365 (OUTLIER) cc_final: 0.0348 (ttm-80) REVERT: E 310 GLU cc_start: 0.1682 (OUTLIER) cc_final: 0.0497 (tp30) REVERT: E 446 ILE cc_start: 0.3322 (OUTLIER) cc_final: 0.2725 (mp) REVERT: E 480 MET cc_start: 0.2095 (mmp) cc_final: 0.0570 (tpt) REVERT: E 536 GLU cc_start: 0.0521 (OUTLIER) cc_final: -0.1828 (mp0) REVERT: E 588 PHE cc_start: 0.3085 (OUTLIER) cc_final: 0.2717 (m-80) REVERT: E 600 ARG cc_start: 0.2867 (OUTLIER) cc_final: 0.2202 (tpp-160) outliers start: 173 outliers final: 142 residues processed: 347 average time/residue: 0.4280 time to fit residues: 246.4350 Evaluate side-chains 358 residues out of total 3603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 191 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 349 TRP Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 50 TYR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 73 TYR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 285 PHE Chi-restraints excluded: chain E residue 306 ARG Chi-restraints excluded: chain E residue 310 GLU Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 516 TYR Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 542 CYS Chi-restraints excluded: chain E residue 588 PHE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain E residue 606 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 0.5980 chunk 346 optimal weight: 0.3980 chunk 99 optimal weight: 0.0570 chunk 299 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 325 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 334 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 955 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 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 = 0.4797 r_free = 0.4797 target = 0.234206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.196285 restraints weight = 62242.941| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.41 r_work: 0.3965 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.8343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 33412 Z= 0.365 Angle : 1.014 59.195 45441 Z= 0.565 Chirality : 0.053 0.559 5027 Planarity : 0.007 0.152 5898 Dihedral : 6.883 54.895 4420 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.05 % Favored : 86.87 % Rotamer: Outliers : 4.64 % Allowed : 28.50 % Favored : 66.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.12), residues: 4053 helix: 0.03 (0.14), residues: 1323 sheet: -1.02 (0.25), residues: 381 loop : -3.07 (0.11), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP D 594 HIS 0.008 0.002 HIS E 265 PHE 0.059 0.003 PHE B 106 TYR 0.038 0.002 TYR B 279 ARG 0.013 0.001 ARG A1000 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7200.75 seconds wall clock time: 131 minutes 17.77 seconds (7877.77 seconds total)