Starting phenix.real_space_refine on Wed Mar 20 19:02:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8taz_41143/03_2024/8taz_41143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8taz_41143/03_2024/8taz_41143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8taz_41143/03_2024/8taz_41143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8taz_41143/03_2024/8taz_41143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8taz_41143/03_2024/8taz_41143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8taz_41143/03_2024/8taz_41143.pdb" } resolution = 3.75 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= 0.049 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 135 5.16 5 C 18042 2.51 5 N 4722 2.21 5 O 5370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D ASP 435": "OD1" <-> "OD2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D ASP 494": "OD1" <-> "OD2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 28269 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8291 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 58, 'TRANS': 1003} Chain breaks: 7 Chain: "B" Number of atoms: 8312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8312 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 58, 'TRANS': 1006} Chain breaks: 7 Chain: "C" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6755 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 47, 'TRANS': 820} Chain breaks: 8 Chain: "D" Number of atoms: 4911 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Conformer: "B" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} bond proxies already assigned to first conformer: 5038 Time building chain proxies: 17.06, per 1000 atoms: 0.60 Number of scatterers: 28269 At special positions: 0 Unit cell: (142.08, 155.4, 246.42, 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 135 16.00 O 5370 8.00 N 4722 7.00 C 18042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.07 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 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: 12.23 Conformation dependent library (CDL) restraints added in 6.3 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6752 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 43 sheets defined 30.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.284A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.274A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.539A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.725A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.331A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.631A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.505A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.223A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.671A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.504A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 757 removed outlier: 3.613A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.664A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.538A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.874A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.201A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.083A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 4.067A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.094A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.042A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.817A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.353A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.881A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.134A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (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 removed outlier: 3.736A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.289A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.820A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 4.492A pdb=" N LEU D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 68 through 83 removed outlier: 4.422A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.613A pdb=" N GLN D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 171 Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.879A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.682A pdb=" N ASP D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.740A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 249 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.415A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.742A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 406 through 414 removed outlier: 3.696A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.772A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.798A pdb=" N GLU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.222A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'D' and resid 550 through 555 Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.544A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.520A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.115A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.004A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 67 removed outlier: 3.929A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 67 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.769A pdb=" N LEU A 82 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 238 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.769A pdb=" N LEU A 82 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 238 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.246A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 3.519A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.724A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.991A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.587A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.372A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.126A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.551A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.926A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.926A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.228A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.561A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.751A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.268A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 192 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE B 194 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 88 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.232A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.525A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.405A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.609A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.314A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.002A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.002A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.577A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.995A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 194 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 88 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.943A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.098A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.375A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.882A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.882A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.664A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 348 removed outlier: 3.545A pdb=" N LYS D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3035 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: 11.44 Time building geometry restraints manager: 13.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.31: 4678 1.31 - 1.84: 24258 1.84 - 2.36: 10 2.36 - 2.88: 0 2.88 - 3.40: 1 Bond restraints: 28947 Sorted by residual: bond pdb=" CB ARG D 245 " pdb=" CG ARG D 245 " ideal model delta sigma weight residual 1.520 3.403 -1.883 3.00e-02 1.11e+03 3.94e+03 bond pdb=" CB LEU D 444 " pdb=" CG LEU D 444 " ideal model delta sigma weight residual 1.530 2.294 -0.764 2.00e-02 2.50e+03 1.46e+03 bond pdb=" CD1 TYR D 279 " pdb=" CE1 TYR D 279 " ideal model delta sigma weight residual 1.382 2.342 -0.960 3.00e-02 1.11e+03 1.02e+03 bond pdb=" CD2 TYR D 279 " pdb=" CE2 TYR D 279 " ideal model delta sigma weight residual 1.382 2.326 -0.944 3.00e-02 1.11e+03 9.90e+02 bond pdb=" CE1 TYR D 279 " pdb=" CZ TYR D 279 " ideal model delta sigma weight residual 1.378 1.953 -0.575 2.40e-02 1.74e+03 5.73e+02 ... (remaining 28942 not shown) Histogram of bond angle deviations from ideal: 81.98 - 97.90: 11 97.90 - 113.81: 16786 113.81 - 129.73: 22443 129.73 - 145.64: 156 145.64 - 161.55: 1 Bond angle restraints: 39397 Sorted by residual: angle pdb=" CA PRO D 590 " pdb=" N PRO D 590 " pdb=" CD PRO D 590 " ideal model delta sigma weight residual 112.00 91.99 20.01 1.40e+00 5.10e-01 2.04e+02 angle pdb=" N PRO D 590 " pdb=" CD PRO D 590 " pdb=" CG PRO D 590 " ideal model delta sigma weight residual 103.20 81.98 21.22 1.50e+00 4.44e-01 2.00e+02 angle pdb=" CA LEU D 444 " pdb=" CB LEU D 444 " pdb=" CG LEU D 444 " ideal model delta sigma weight residual 116.30 161.55 -45.25 3.50e+00 8.16e-02 1.67e+02 angle pdb=" CA PRO D 469 " pdb=" N PRO D 469 " pdb=" CD PRO D 469 " ideal model delta sigma weight residual 112.00 97.73 14.27 1.40e+00 5.10e-01 1.04e+02 angle pdb=" N PRO D 590 " pdb=" CA PRO D 590 " pdb=" CB PRO D 590 " ideal model delta sigma weight residual 103.25 92.85 10.40 1.05e+00 9.07e-01 9.81e+01 ... (remaining 39392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 15139 17.61 - 35.23: 1719 35.23 - 52.84: 325 52.84 - 70.45: 66 70.45 - 88.07: 36 Dihedral angle restraints: 17285 sinusoidal: 6818 harmonic: 10467 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual -86.00 1.42 -87.42 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CA TYR D 497 " pdb=" C TYR D 497 " pdb=" N CYS D 498 " pdb=" CA CYS D 498 " ideal model delta harmonic sigma weight residual -180.00 -133.48 -46.52 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.39 -76.61 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 17282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 4419 0.202 - 0.405: 2 0.405 - 0.607: 1 0.607 - 0.809: 0 0.809 - 1.011: 1 Chirality restraints: 4423 Sorted by residual: chirality pdb=" CG LEU D 444 " pdb=" CB LEU D 444 " pdb=" CD1 LEU D 444 " pdb=" CD2 LEU D 444 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA PRO D 590 " pdb=" N PRO D 590 " pdb=" C PRO D 590 " pdb=" CB PRO D 590 " both_signs ideal model delta sigma weight residual False 2.72 2.22 0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CB ILE D 119 " pdb=" CA ILE D 119 " pdb=" CG1 ILE D 119 " pdb=" CG2 ILE D 119 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 4420 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.102 5.00e-02 4.00e+02 1.56e-01 3.87e+01 pdb=" N PRO D 500 " 0.269 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 589 " 0.103 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO D 590 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO D 590 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 590 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 468 " -0.084 5.00e-02 4.00e+02 1.16e-01 2.17e+01 pdb=" N PRO D 469 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.063 5.00e-02 4.00e+02 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 679 2.67 - 3.23: 27616 3.23 - 3.79: 42580 3.79 - 4.34: 54492 4.34 - 4.90: 88436 Nonbonded interactions: 213803 Sorted by model distance: nonbonded pdb=" O PHE D 588 " pdb=" N PHE D 592 " model vdw 2.119 2.520 nonbonded pdb=" O ILE A 197 " pdb=" NZ LYS A 202 " model vdw 2.132 2.520 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.154 2.440 nonbonded pdb=" CE2 TYR D 279 " pdb=" CB LEU D 444 " model vdw 2.170 3.740 nonbonded pdb=" CD2 TYR D 279 " pdb=" CB LEU D 444 " model vdw 2.171 3.740 ... (remaining 213798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 827 or resid 848 through 1147)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 29.460 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 80.020 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 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 : 0.017 1.883 28947 Z= 1.282 Angle : 0.938 45.254 39397 Z= 0.510 Chirality : 0.050 1.011 4423 Planarity : 0.007 0.156 5115 Dihedral : 15.305 88.066 10410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 16.47 % Favored : 83.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.61 (0.14), residues: 3540 helix: 0.83 (0.18), residues: 925 sheet: -0.64 (0.22), residues: 529 loop : -2.20 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP D 165 HIS 0.010 0.001 HIS D 493 PHE 0.055 0.002 PHE D 464 TYR 0.032 0.002 TYR D 279 ARG 0.012 0.001 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7010 (t80) cc_final: 0.6687 (t80) REVERT: A 190 ARG cc_start: 0.7307 (mpt-90) cc_final: 0.6812 (mtm180) REVERT: A 204 TYR cc_start: 0.7518 (m-10) cc_final: 0.7155 (m-10) REVERT: A 298 GLU cc_start: 0.8927 (tt0) cc_final: 0.8727 (tm-30) REVERT: A 394 ASN cc_start: 0.7342 (m-40) cc_final: 0.6933 (m-40) REVERT: A 641 ASN cc_start: 0.7737 (m110) cc_final: 0.7053 (t0) REVERT: A 740 MET cc_start: 0.8189 (tmm) cc_final: 0.7604 (tmm) REVERT: B 99 ASN cc_start: 0.8313 (m-40) cc_final: 0.7652 (t0) REVERT: B 159 VAL cc_start: 0.7193 (t) cc_final: 0.6683 (t) REVERT: B 202 LYS cc_start: 0.8010 (mttp) cc_final: 0.7691 (mppt) REVERT: B 226 LEU cc_start: 0.8039 (tt) cc_final: 0.7532 (tp) REVERT: B 229 LEU cc_start: 0.7914 (tp) cc_final: 0.6947 (mp) REVERT: B 321 GLN cc_start: 0.8672 (mm110) cc_final: 0.8225 (mp10) REVERT: B 787 GLN cc_start: 0.9054 (mp10) cc_final: 0.8773 (mm110) REVERT: B 902 MET cc_start: 0.8461 (tpp) cc_final: 0.8214 (tpt) REVERT: C 14 GLN cc_start: 0.6541 (mt0) cc_final: 0.5576 (tp40) REVERT: C 133 PHE cc_start: 0.8292 (m-80) cc_final: 0.8084 (m-10) REVERT: C 190 ARG cc_start: 0.6580 (mtt180) cc_final: 0.6044 (mpt-90) REVERT: C 984 LEU cc_start: 0.7164 (mm) cc_final: 0.6907 (mm) REVERT: D 85 LEU cc_start: 0.3459 (mm) cc_final: 0.3038 (tp) REVERT: D 306 ARG cc_start: 0.4085 (tpt90) cc_final: 0.3252 (tpt170) REVERT: D 360 MET cc_start: -0.1694 (pmm) cc_final: -0.3079 (ttm) REVERT: D 455 MET cc_start: -0.4098 (tmm) cc_final: -0.4568 (tmm) REVERT: D 483 ASP cc_start: 0.5453 (m-30) cc_final: 0.5140 (t0) REVERT: D 608 THR cc_start: 0.7478 (m) cc_final: 0.6944 (p) outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.3995 time to fit residues: 264.1693 Evaluate side-chains 214 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 324 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 487 ASN A 675 GLN A 762 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 613 GLN B 644 GLN C 17 ASN C 121 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 53 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 607 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.893 28947 Z= 1.232 Angle : 0.808 45.776 39397 Z= 0.403 Chirality : 0.049 0.930 4423 Planarity : 0.006 0.121 5115 Dihedral : 5.661 42.343 3842 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.94 % Favored : 91.83 % Rotamer: Outliers : 3.05 % Allowed : 16.53 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3540 helix: 0.76 (0.17), residues: 947 sheet: -0.53 (0.22), residues: 557 loop : -2.28 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 165 HIS 0.009 0.001 HIS D 493 PHE 0.035 0.002 PHE D 464 TYR 0.029 0.002 TYR D 279 ARG 0.010 0.001 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 237 time to evaluate : 3.090 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 32 PHE cc_start: 0.2315 (m-80) cc_final: 0.2109 (m-80) REVERT: A 77 PHE cc_start: 0.7162 (t80) cc_final: 0.6953 (t80) REVERT: A 131 CYS cc_start: -0.2902 (OUTLIER) cc_final: -0.3359 (p) REVERT: A 139 PRO cc_start: 0.5717 (Cg_endo) cc_final: 0.5507 (Cg_exo) REVERT: A 190 ARG cc_start: 0.7351 (mpt-90) cc_final: 0.6811 (mtm180) REVERT: A 200 TYR cc_start: 0.8555 (m-80) cc_final: 0.8285 (t80) REVERT: A 223 LEU cc_start: 0.8022 (mp) cc_final: 0.7188 (tt) REVERT: A 641 ASN cc_start: 0.7739 (m110) cc_final: 0.6910 (t0) REVERT: A 740 MET cc_start: 0.8387 (tmm) cc_final: 0.7213 (tmm) REVERT: B 36 VAL cc_start: 0.8924 (t) cc_final: 0.8712 (p) REVERT: B 65 PHE cc_start: 0.7385 (t80) cc_final: 0.6836 (t80) REVERT: B 153 MET cc_start: 0.5152 (pmm) cc_final: 0.4951 (pmm) REVERT: B 226 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6810 (tp) REVERT: B 227 VAL cc_start: 0.5307 (OUTLIER) cc_final: 0.4844 (t) REVERT: B 229 LEU cc_start: 0.8008 (tp) cc_final: 0.7387 (mp) REVERT: B 321 GLN cc_start: 0.8669 (mm110) cc_final: 0.8253 (mp10) REVERT: B 787 GLN cc_start: 0.9115 (mp10) cc_final: 0.8661 (mm110) REVERT: C 14 GLN cc_start: 0.6139 (mp10) cc_final: 0.5222 (tp40) REVERT: C 15 CYS cc_start: -0.1839 (OUTLIER) cc_final: -0.2307 (t) REVERT: C 64 TRP cc_start: 0.7147 (t60) cc_final: 0.6312 (t60) REVERT: C 118 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 133 PHE cc_start: 0.8252 (m-80) cc_final: 0.7907 (m-10) REVERT: C 135 PHE cc_start: 0.6508 (m-80) cc_final: 0.6067 (m-80) REVERT: C 190 ARG cc_start: 0.6475 (mtt180) cc_final: 0.5815 (mmt180) REVERT: D 190 MET cc_start: 0.4124 (OUTLIER) cc_final: 0.3833 (ptp) REVERT: D 266 LEU cc_start: 0.3931 (mm) cc_final: 0.3224 (tp) REVERT: D 335 GLU cc_start: 0.3241 (mt-10) cc_final: 0.1838 (pp20) REVERT: D 360 MET cc_start: -0.1690 (pmm) cc_final: -0.3626 (ttm) REVERT: D 381 TYR cc_start: 0.2354 (OUTLIER) cc_final: 0.1586 (t80) REVERT: D 455 MET cc_start: -0.4085 (tmm) cc_final: -0.4527 (tmm) REVERT: D 462 MET cc_start: 0.3679 (mmt) cc_final: 0.2399 (mmt) REVERT: D 516 TYR cc_start: -0.0781 (t80) cc_final: -0.1409 (t80) REVERT: D 608 THR cc_start: 0.7555 (m) cc_final: 0.7120 (p) outliers start: 96 outliers final: 47 residues processed: 315 average time/residue: 0.3691 time to fit residues: 189.8797 Evaluate side-chains 243 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 189 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 381 TYR Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 0.0170 chunk 324 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 564 GLN A1135 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN B 493 GLN B 613 GLN B 804 GLN B 901 GLN B 935 GLN C 52 GLN C 185 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.985 28947 Z= 0.893 Angle : 0.882 45.977 39397 Z= 0.453 Chirality : 0.052 0.887 4423 Planarity : 0.006 0.089 5115 Dihedral : 6.015 29.326 3842 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.95 % Favored : 89.86 % Rotamer: Outliers : 5.24 % Allowed : 17.39 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 3540 helix: 0.20 (0.16), residues: 972 sheet: -0.75 (0.21), residues: 567 loop : -2.41 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 165 HIS 0.016 0.002 HIS D 493 PHE 0.032 0.002 PHE B1089 TYR 0.028 0.003 TYR B 741 ARG 0.023 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 190 time to evaluate : 3.590 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 77 PHE cc_start: 0.7138 (t80) cc_final: 0.6900 (t80) REVERT: A 104 TRP cc_start: 0.6541 (OUTLIER) cc_final: 0.5894 (m-10) REVERT: A 131 CYS cc_start: -0.2975 (OUTLIER) cc_final: -0.3374 (p) REVERT: A 200 TYR cc_start: 0.8565 (m-80) cc_final: 0.8174 (t80) REVERT: A 779 GLN cc_start: 0.8548 (mm110) cc_final: 0.8168 (tm-30) REVERT: A 1043 CYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6797 (m) REVERT: B 115 GLN cc_start: 0.5511 (OUTLIER) cc_final: 0.4879 (mm-40) REVERT: B 226 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6906 (tp) REVERT: B 374 PHE cc_start: 0.7420 (p90) cc_final: 0.6970 (p90) REVERT: B 759 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8289 (t80) REVERT: C 14 GLN cc_start: 0.5923 (mp10) cc_final: 0.4896 (tp40) REVERT: C 47 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (m) REVERT: C 66 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6377 (t70) REVERT: C 126 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8305 (t) REVERT: C 190 ARG cc_start: 0.6599 (mtt180) cc_final: 0.5991 (mmt180) REVERT: C 224 GLU cc_start: 0.7998 (mp0) cc_final: 0.7744 (mp0) REVERT: C 780 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8647 (tm-30) REVERT: C 1029 MET cc_start: 0.8582 (tpp) cc_final: 0.8216 (tmm) REVERT: C 1031 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 305 ARG cc_start: 0.4498 (OUTLIER) cc_final: 0.2666 (tpt170) REVERT: D 310 GLU cc_start: 0.5529 (mt-10) cc_final: 0.4124 (mm-30) REVERT: D 335 GLU cc_start: 0.2917 (mt-10) cc_final: 0.1462 (pp20) REVERT: D 347 THR cc_start: 0.5604 (OUTLIER) cc_final: 0.4932 (p) REVERT: D 360 MET cc_start: -0.1299 (pmm) cc_final: -0.4585 (ttm) REVERT: D 381 TYR cc_start: 0.3325 (OUTLIER) cc_final: 0.1755 (t80) REVERT: D 449 THR cc_start: 0.3832 (OUTLIER) cc_final: 0.3377 (m) REVERT: D 512 PHE cc_start: 0.2431 (OUTLIER) cc_final: 0.2211 (m-80) REVERT: D 608 THR cc_start: 0.7473 (m) cc_final: 0.7019 (p) outliers start: 165 outliers final: 95 residues processed: 330 average time/residue: 0.3437 time to fit residues: 193.0603 Evaluate side-chains 274 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 165 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 381 TYR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 154 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.982 28947 Z= 0.812 Angle : 0.732 45.960 39397 Z= 0.363 Chirality : 0.047 0.895 4423 Planarity : 0.005 0.083 5115 Dihedral : 5.477 27.995 3842 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.23 % Favored : 92.57 % Rotamer: Outliers : 4.13 % Allowed : 19.90 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3540 helix: 0.70 (0.17), residues: 958 sheet: -0.48 (0.21), residues: 555 loop : -2.37 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 461 HIS 0.008 0.001 HIS D 374 PHE 0.024 0.001 PHE A 855 TYR 0.028 0.002 TYR D 279 ARG 0.012 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 186 time to evaluate : 3.461 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 104 TRP cc_start: 0.6577 (OUTLIER) cc_final: 0.6000 (m-10) REVERT: A 131 CYS cc_start: -0.2978 (OUTLIER) cc_final: -0.3274 (p) REVERT: A 508 TYR cc_start: 0.5352 (OUTLIER) cc_final: 0.4967 (m-10) REVERT: A 697 MET cc_start: 0.7846 (pmm) cc_final: 0.7223 (ptt) REVERT: A 779 GLN cc_start: 0.8583 (mm110) cc_final: 0.8338 (tm-30) REVERT: A 853 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: B 33 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6456 (p) REVERT: B 988 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8215 (tp30) REVERT: C 14 GLN cc_start: 0.5566 (mp10) cc_final: 0.4656 (tp40) REVERT: C 126 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8061 (m) REVERT: C 190 ARG cc_start: 0.6705 (mtt180) cc_final: 0.6441 (mmt180) REVERT: C 780 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 869 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7594 (pmm) REVERT: C 1029 MET cc_start: 0.8719 (tpp) cc_final: 0.8318 (tmm) REVERT: D 158 TYR cc_start: 0.0413 (OUTLIER) cc_final: -0.0128 (t80) REVERT: D 305 ARG cc_start: 0.4433 (OUTLIER) cc_final: 0.2690 (tpt170) REVERT: D 335 GLU cc_start: 0.3034 (mt-10) cc_final: 0.1691 (pp20) REVERT: D 381 TYR cc_start: 0.2867 (OUTLIER) cc_final: 0.1942 (t80) REVERT: D 449 THR cc_start: 0.4498 (t) cc_final: 0.4204 (m) REVERT: D 608 THR cc_start: 0.7425 (m) cc_final: 0.6984 (p) outliers start: 130 outliers final: 89 residues processed: 290 average time/residue: 0.3723 time to fit residues: 182.4251 Evaluate side-chains 267 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 168 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 381 TYR Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 0.0170 chunk 195 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 256 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 overall best weight: 2.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 437 ASN D 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.984 28947 Z= 0.828 Angle : 0.749 46.170 39397 Z= 0.373 Chirality : 0.047 0.878 4423 Planarity : 0.005 0.066 5115 Dihedral : 5.404 27.722 3842 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.96 % Favored : 90.84 % Rotamer: Outliers : 5.18 % Allowed : 20.03 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3540 helix: 0.77 (0.17), residues: 957 sheet: -0.42 (0.21), residues: 545 loop : -2.37 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 461 HIS 0.025 0.002 HIS D 374 PHE 0.019 0.001 PHE D 464 TYR 0.027 0.002 TYR A 495 ARG 0.013 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 183 time to evaluate : 3.628 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 104 TRP cc_start: 0.6630 (OUTLIER) cc_final: 0.5979 (m-10) REVERT: A 131 CYS cc_start: -0.3426 (OUTLIER) cc_final: -0.3697 (p) REVERT: A 200 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7603 (t80) REVERT: A 697 MET cc_start: 0.7820 (pmm) cc_final: 0.7459 (ptt) REVERT: A 755 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: A 779 GLN cc_start: 0.8613 (mm110) cc_final: 0.8353 (tm-30) REVERT: A 853 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: B 115 GLN cc_start: 0.5544 (OUTLIER) cc_final: 0.4792 (mm-40) REVERT: B 759 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8081 (t80) REVERT: B 988 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8168 (tp30) REVERT: C 14 GLN cc_start: 0.5610 (mp10) cc_final: 0.4781 (tp40) REVERT: C 126 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8217 (m) REVERT: C 780 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8507 (tm-30) REVERT: C 1029 MET cc_start: 0.8697 (tpp) cc_final: 0.8299 (tmm) REVERT: D 50 TYR cc_start: 0.3346 (t80) cc_final: 0.3021 (t80) REVERT: D 158 TYR cc_start: 0.0229 (OUTLIER) cc_final: -0.0273 (t80) REVERT: D 305 ARG cc_start: 0.4367 (OUTLIER) cc_final: 0.2789 (tpt170) REVERT: D 335 GLU cc_start: 0.2871 (mt-10) cc_final: 0.1564 (pp20) REVERT: D 381 TYR cc_start: 0.2926 (OUTLIER) cc_final: 0.2070 (t80) REVERT: D 449 THR cc_start: 0.4349 (OUTLIER) cc_final: 0.4030 (m) REVERT: D 459 TRP cc_start: -0.0867 (t60) cc_final: -0.1617 (t60) REVERT: D 462 MET cc_start: 0.3897 (mmt) cc_final: 0.2799 (mmp) REVERT: D 512 PHE cc_start: 0.2236 (OUTLIER) cc_final: 0.1939 (m-80) REVERT: D 608 THR cc_start: 0.7444 (m) cc_final: 0.7155 (p) outliers start: 163 outliers final: 115 residues processed: 322 average time/residue: 0.3699 time to fit residues: 196.2444 Evaluate side-chains 292 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 164 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 381 TYR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.984 28947 Z= 0.806 Angle : 0.706 46.112 39397 Z= 0.347 Chirality : 0.046 0.876 4423 Planarity : 0.005 0.075 5115 Dihedral : 5.149 27.696 3842 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.21 % Favored : 92.71 % Rotamer: Outliers : 4.29 % Allowed : 21.04 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3540 helix: 1.00 (0.17), residues: 959 sheet: -0.33 (0.21), residues: 549 loop : -2.30 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 165 HIS 0.009 0.001 HIS D 241 PHE 0.033 0.001 PHE B 453 TYR 0.026 0.001 TYR D 279 ARG 0.012 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 179 time to evaluate : 3.132 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 104 TRP cc_start: 0.6566 (OUTLIER) cc_final: 0.5995 (m-10) REVERT: A 131 CYS cc_start: -0.3770 (OUTLIER) cc_final: -0.4030 (p) REVERT: A 200 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 697 MET cc_start: 0.7794 (pmm) cc_final: 0.7443 (ptt) REVERT: A 740 MET cc_start: 0.9394 (tpt) cc_final: 0.9115 (mmm) REVERT: A 755 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: A 779 GLN cc_start: 0.8642 (mm110) cc_final: 0.8359 (tm-30) REVERT: A 853 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: A 1029 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7980 (tpp) REVERT: B 115 GLN cc_start: 0.5418 (OUTLIER) cc_final: 0.4716 (mm-40) REVERT: B 417 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8745 (tppt) REVERT: B 759 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 988 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8184 (tp30) REVERT: C 14 GLN cc_start: 0.5356 (mp10) cc_final: 0.4545 (tp40) REVERT: C 126 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 190 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6654 (mmt180) REVERT: C 780 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8477 (tm-30) REVERT: C 869 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7640 (pmm) REVERT: C 1029 MET cc_start: 0.8671 (tpp) cc_final: 0.8285 (tmm) REVERT: D 51 ASN cc_start: 0.4970 (m-40) cc_final: 0.4488 (m110) REVERT: D 83 TYR cc_start: 0.2706 (OUTLIER) cc_final: 0.1986 (t80) REVERT: D 190 MET cc_start: 0.4966 (ptp) cc_final: 0.4746 (ptm) REVERT: D 305 ARG cc_start: 0.4110 (OUTLIER) cc_final: 0.2673 (tpt170) REVERT: D 335 GLU cc_start: 0.2467 (mt-10) cc_final: 0.1576 (pp20) REVERT: D 381 TYR cc_start: 0.3237 (OUTLIER) cc_final: 0.2648 (t80) REVERT: D 459 TRP cc_start: -0.0814 (t60) cc_final: -0.2057 (t60) REVERT: D 462 MET cc_start: 0.3618 (mmt) cc_final: 0.2571 (mmp) REVERT: D 512 PHE cc_start: 0.2250 (OUTLIER) cc_final: 0.1989 (m-80) REVERT: D 608 THR cc_start: 0.7085 (m) cc_final: 0.6755 (p) outliers start: 135 outliers final: 94 residues processed: 294 average time/residue: 0.3643 time to fit residues: 176.1546 Evaluate side-chains 277 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 169 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 381 TYR Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 196 optimal weight: 0.0270 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.985 28947 Z= 0.824 Angle : 0.731 46.454 39397 Z= 0.360 Chirality : 0.047 0.869 4423 Planarity : 0.005 0.060 5115 Dihedral : 5.164 27.009 3842 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.07 % Favored : 90.84 % Rotamer: Outliers : 5.12 % Allowed : 20.44 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3540 helix: 1.02 (0.17), residues: 957 sheet: -0.33 (0.22), residues: 537 loop : -2.32 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 478 HIS 0.012 0.001 HIS D 265 PHE 0.024 0.001 PHE B 453 TYR 0.029 0.002 TYR A 495 ARG 0.013 0.001 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 173 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.3694 (m-80) cc_final: 0.3359 (m-80) REVERT: A 104 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.5934 (m100) REVERT: A 131 CYS cc_start: -0.3848 (OUTLIER) cc_final: -0.4084 (p) REVERT: A 200 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7600 (t80) REVERT: A 421 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.5497 (m-80) REVERT: A 740 MET cc_start: 0.9397 (tpt) cc_final: 0.9161 (mmm) REVERT: A 755 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: A 779 GLN cc_start: 0.8595 (mm110) cc_final: 0.8324 (tm-30) REVERT: A 853 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: A 1029 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8021 (tpp) REVERT: B 115 GLN cc_start: 0.5597 (OUTLIER) cc_final: 0.4883 (mm-40) REVERT: B 386 LYS cc_start: 0.9221 (tptt) cc_final: 0.8647 (tptp) REVERT: B 417 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8775 (tppt) REVERT: B 759 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8194 (t80) REVERT: B 988 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8169 (tp30) REVERT: C 14 GLN cc_start: 0.5221 (mp10) cc_final: 0.4365 (tp40) REVERT: C 126 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8310 (m) REVERT: C 780 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 1029 MET cc_start: 0.8672 (tpp) cc_final: 0.8294 (tmm) REVERT: D 51 ASN cc_start: 0.5031 (m-40) cc_final: 0.4466 (m110) REVERT: D 83 TYR cc_start: 0.2846 (OUTLIER) cc_final: 0.2043 (t80) REVERT: D 305 ARG cc_start: 0.4166 (OUTLIER) cc_final: 0.2716 (tpt170) REVERT: D 335 GLU cc_start: 0.2670 (mt-10) cc_final: 0.1710 (pp20) REVERT: D 449 THR cc_start: 0.4522 (OUTLIER) cc_final: 0.4272 (m) REVERT: D 455 MET cc_start: 0.0050 (OUTLIER) cc_final: -0.0268 (mmt) REVERT: D 462 MET cc_start: 0.4376 (mmt) cc_final: 0.3383 (mmp) REVERT: D 478 TRP cc_start: 0.1567 (m100) cc_final: 0.0831 (t60) REVERT: D 512 PHE cc_start: 0.2363 (OUTLIER) cc_final: 0.2071 (m-80) REVERT: D 608 THR cc_start: 0.7001 (m) cc_final: 0.6704 (p) outliers start: 161 outliers final: 121 residues processed: 310 average time/residue: 0.3642 time to fit residues: 187.0841 Evaluate side-chains 304 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 168 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 103 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 218 optimal weight: 7.9990 chunk 234 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 270 optimal weight: 0.0270 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 641 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.982 28947 Z= 0.798 Angle : 0.689 46.304 39397 Z= 0.333 Chirality : 0.046 0.865 4423 Planarity : 0.005 0.071 5115 Dihedral : 4.849 27.998 3842 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.39 % Favored : 93.50 % Rotamer: Outliers : 3.34 % Allowed : 21.96 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3540 helix: 1.37 (0.17), residues: 947 sheet: -0.12 (0.22), residues: 537 loop : -2.19 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 478 HIS 0.007 0.001 HIS D 241 PHE 0.017 0.001 PHE D 464 TYR 0.025 0.001 TYR D 279 ARG 0.012 0.000 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 187 time to evaluate : 3.388 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 32 PHE cc_start: 0.3585 (m-80) cc_final: 0.3262 (m-80) REVERT: A 104 TRP cc_start: 0.6487 (OUTLIER) cc_final: 0.6085 (m100) REVERT: A 131 CYS cc_start: -0.3710 (OUTLIER) cc_final: -0.3952 (p) REVERT: A 200 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 697 MET cc_start: 0.7782 (pmm) cc_final: 0.7439 (ptt) REVERT: A 740 MET cc_start: 0.9363 (tpt) cc_final: 0.9081 (mmm) REVERT: A 755 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 779 GLN cc_start: 0.8582 (mm110) cc_final: 0.8358 (tm-30) REVERT: A 853 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: B 115 GLN cc_start: 0.5578 (OUTLIER) cc_final: 0.4936 (mm-40) REVERT: B 226 LEU cc_start: 0.7300 (tp) cc_final: 0.6890 (tp) REVERT: B 386 LYS cc_start: 0.9208 (tptt) cc_final: 0.8757 (tptp) REVERT: B 417 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8832 (tppt) REVERT: B 759 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 14 GLN cc_start: 0.4599 (mp10) cc_final: 0.4077 (tp40) REVERT: C 126 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8277 (m) REVERT: C 190 ARG cc_start: 0.6800 (mtt180) cc_final: 0.6353 (mtt-85) REVERT: C 869 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7556 (pmm) REVERT: C 1029 MET cc_start: 0.8527 (tpp) cc_final: 0.7998 (tmm) REVERT: D 83 TYR cc_start: 0.2852 (OUTLIER) cc_final: 0.1942 (t80) REVERT: D 265 HIS cc_start: -0.0250 (OUTLIER) cc_final: -0.0929 (p90) REVERT: D 305 ARG cc_start: 0.3747 (OUTLIER) cc_final: 0.2866 (tpt170) REVERT: D 335 GLU cc_start: 0.3163 (mt-10) cc_final: 0.2358 (pp20) REVERT: D 459 TRP cc_start: -0.1387 (t60) cc_final: -0.3286 (t60) REVERT: D 462 MET cc_start: 0.3616 (mmt) cc_final: 0.2750 (mmp) REVERT: D 608 THR cc_start: 0.6895 (m) cc_final: 0.6579 (p) outliers start: 105 outliers final: 70 residues processed: 276 average time/residue: 0.4024 time to fit residues: 187.6993 Evaluate side-chains 252 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 170 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 192 optimal weight: 0.2980 chunk 139 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 289 optimal weight: 0.0870 chunk 303 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.971 28947 Z= 0.800 Angle : 0.687 46.352 39397 Z= 0.332 Chirality : 0.046 0.900 4423 Planarity : 0.005 0.060 5115 Dihedral : 4.732 29.099 3842 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.85 % Rotamer: Outliers : 3.18 % Allowed : 22.28 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3540 helix: 1.44 (0.17), residues: 949 sheet: -0.19 (0.22), residues: 527 loop : -2.10 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP D 478 HIS 0.008 0.001 HIS D 241 PHE 0.032 0.001 PHE C 855 TYR 0.042 0.001 TYR D 381 ARG 0.012 0.000 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 177 time to evaluate : 3.311 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 32 PHE cc_start: 0.3593 (m-80) cc_final: 0.3257 (m-80) REVERT: A 104 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.5950 (m100) REVERT: A 131 CYS cc_start: -0.3867 (OUTLIER) cc_final: -0.4249 (p) REVERT: A 200 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7666 (t80) REVERT: A 697 MET cc_start: 0.7775 (pmm) cc_final: 0.7463 (ptt) REVERT: A 740 MET cc_start: 0.9360 (tpt) cc_final: 0.9111 (mmm) REVERT: A 755 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: A 779 GLN cc_start: 0.8612 (mm110) cc_final: 0.8325 (tm-30) REVERT: A 853 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: B 115 GLN cc_start: 0.5584 (OUTLIER) cc_final: 0.4956 (mm-40) REVERT: B 226 LEU cc_start: 0.7276 (tp) cc_final: 0.6877 (tp) REVERT: B 386 LYS cc_start: 0.9194 (tptt) cc_final: 0.8555 (tptp) REVERT: B 417 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8834 (tppt) REVERT: B 759 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7914 (t80) REVERT: C 14 GLN cc_start: 0.4731 (mp10) cc_final: 0.4141 (tp40) REVERT: C 126 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8271 (m) REVERT: C 1029 MET cc_start: 0.8503 (tpp) cc_final: 0.7987 (tmm) REVERT: D 83 TYR cc_start: 0.2848 (OUTLIER) cc_final: 0.1932 (t80) REVERT: D 96 GLN cc_start: 0.2799 (OUTLIER) cc_final: 0.1282 (mt0) REVERT: D 190 MET cc_start: 0.4588 (ptp) cc_final: 0.4383 (ptt) REVERT: D 305 ARG cc_start: 0.3758 (OUTLIER) cc_final: 0.2859 (tpt170) REVERT: D 335 GLU cc_start: 0.3176 (mt-10) cc_final: 0.2222 (pp20) REVERT: D 459 TRP cc_start: -0.1415 (t60) cc_final: -0.3285 (t60) REVERT: D 462 MET cc_start: 0.3725 (mmt) cc_final: 0.2836 (mmp) REVERT: D 474 MET cc_start: 0.0336 (mpp) cc_final: -0.2667 (ttp) REVERT: D 478 TRP cc_start: 0.1403 (m100) cc_final: 0.1163 (t60) REVERT: D 608 THR cc_start: 0.7368 (m) cc_final: 0.7130 (p) outliers start: 100 outliers final: 76 residues processed: 263 average time/residue: 0.3664 time to fit residues: 159.8934 Evaluate side-chains 256 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 169 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 355 optimal weight: 0.9990 chunk 327 optimal weight: 5.9990 chunk 283 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 218 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.977 28947 Z= 0.818 Angle : 0.719 45.862 39397 Z= 0.351 Chirality : 0.046 0.848 4423 Planarity : 0.005 0.072 5115 Dihedral : 4.850 28.911 3842 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.05 % Favored : 91.86 % Rotamer: Outliers : 3.43 % Allowed : 22.22 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3540 helix: 1.27 (0.17), residues: 961 sheet: -0.12 (0.22), residues: 531 loop : -2.16 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 478 HIS 0.008 0.001 HIS D 265 PHE 0.032 0.001 PHE C 855 TYR 0.030 0.002 TYR B 369 ARG 0.015 0.001 ARG D 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 173 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.3652 (m-80) cc_final: 0.3359 (m-80) REVERT: A 104 TRP cc_start: 0.6507 (OUTLIER) cc_final: 0.6036 (m100) REVERT: A 200 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 697 MET cc_start: 0.7792 (pmm) cc_final: 0.7497 (ptt) REVERT: A 755 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: A 779 GLN cc_start: 0.8653 (mm110) cc_final: 0.8348 (tm-30) REVERT: A 853 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: A 869 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7573 (mtm) REVERT: B 115 GLN cc_start: 0.5516 (OUTLIER) cc_final: 0.4839 (mm-40) REVERT: B 226 LEU cc_start: 0.7471 (tp) cc_final: 0.7096 (tp) REVERT: B 386 LYS cc_start: 0.9193 (tptt) cc_final: 0.8562 (tptp) REVERT: B 417 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8830 (tppt) REVERT: B 759 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8145 (t80) REVERT: C 14 GLN cc_start: 0.4887 (mp10) cc_final: 0.4246 (tp40) REVERT: C 126 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8271 (m) REVERT: C 1029 MET cc_start: 0.8569 (tpp) cc_final: 0.8221 (tmm) REVERT: D 51 ASN cc_start: 0.4947 (m-40) cc_final: 0.4409 (m-40) REVERT: D 83 TYR cc_start: 0.2904 (OUTLIER) cc_final: 0.1991 (t80) REVERT: D 96 GLN cc_start: 0.2668 (OUTLIER) cc_final: 0.1163 (mt0) REVERT: D 270 MET cc_start: 0.2265 (OUTLIER) cc_final: 0.1161 (mpp) REVERT: D 305 ARG cc_start: 0.3841 (OUTLIER) cc_final: 0.2703 (tpt170) REVERT: D 335 GLU cc_start: 0.3215 (mt-10) cc_final: 0.2384 (pp20) REVERT: D 459 TRP cc_start: -0.1407 (t60) cc_final: -0.3577 (t60) REVERT: D 462 MET cc_start: 0.3788 (mmt) cc_final: 0.2856 (mmp) REVERT: D 474 MET cc_start: 0.0448 (mpp) cc_final: -0.2499 (ttp) outliers start: 108 outliers final: 88 residues processed: 265 average time/residue: 0.3829 time to fit residues: 168.3729 Evaluate side-chains 269 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 169 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 390 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.128628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091305 restraints weight = 118335.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093556 restraints weight = 64556.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092815 restraints weight = 38373.889| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.985 28947 Z= 0.805 Angle : 0.702 46.707 39397 Z= 0.339 Chirality : 0.046 0.849 4423 Planarity : 0.005 0.075 5115 Dihedral : 4.787 29.364 3842 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.52 % Favored : 92.40 % Rotamer: Outliers : 3.34 % Allowed : 22.41 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3540 helix: 1.37 (0.17), residues: 953 sheet: -0.15 (0.22), residues: 521 loop : -2.13 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 461 HIS 0.006 0.001 HIS D 265 PHE 0.032 0.001 PHE C 855 TYR 0.038 0.001 TYR D 381 ARG 0.013 0.000 ARG D 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5712.32 seconds wall clock time: 105 minutes 4.93 seconds (6304.93 seconds total)