Starting phenix.real_space_refine on Tue Mar 19 05:57:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t21_40977/03_2024/8t21_40977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t21_40977/03_2024/8t21_40977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t21_40977/03_2024/8t21_40977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t21_40977/03_2024/8t21_40977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t21_40977/03_2024/8t21_40977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t21_40977/03_2024/8t21_40977.pdb" } resolution = 3.6 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= 0.055 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 105 5.16 5 C 14970 2.51 5 N 3891 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23430 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "B" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Chain: "C" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 53, 'TRANS': 947} Chain breaks: 7 Time building chain proxies: 11.39, per 1000 atoms: 0.49 Number of scatterers: 23430 At special positions: 0 Unit cell: (134.31, 144.3, 177.6, 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 105 16.00 O 4464 8.00 N 3891 7.00 C 14970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 10.11 Conformation dependent library (CDL) restraints added in 4.4 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 34 sheets defined 24.0% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.951A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.942A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.717A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.721A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.796A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.740A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.816A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 5.688A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.938A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.654A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.841A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.302A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.675A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.651A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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: 3.582A pdb=" N ILE B 980 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1000 removed outlier: 5.533A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1033 removed outlier: 3.524A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.898A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.065A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.792A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.604A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.572A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.530A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.578A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.561A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.851A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.226A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.958A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.988A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.579A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 192 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.620A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.614A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 538 removed outlier: 3.751A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 660 removed outlier: 8.012A pdb=" N VAL A 656 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA A 694 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 658 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR A 696 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.922A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.237A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.672A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.859A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.907A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AB8, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 659 removed outlier: 5.964A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.902A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.372A 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=AC3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.902A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.759A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.802A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.811A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.409A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.090A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.816A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 433 through 434 Processing sheet with id=AD2, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AD3, first strand: chain 'C' and resid 655 through 660 removed outlier: 8.495A pdb=" N VAL C 656 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA C 694 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN C 658 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 696 " --> pdb=" O ASN C 658 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 660 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.789A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.545A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C1065 " --> pdb=" O MET C1050 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.531A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1815 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: 8.73 Time building geometry restraints manager: 10.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7540 1.35 - 1.50: 6672 1.50 - 1.65: 9623 1.65 - 1.80: 64 1.80 - 1.95: 65 Bond restraints: 23964 Sorted by residual: bond pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 1.523 1.598 -0.075 1.27e-02 6.20e+03 3.44e+01 bond pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.10e+01 bond pdb=" N PHE A 59 " pdb=" CA PHE A 59 " ideal model delta sigma weight residual 1.457 1.526 -0.068 1.29e-02 6.01e+03 2.80e+01 bond pdb=" CG PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 1.503 1.347 0.156 3.40e-02 8.65e+02 2.10e+01 bond pdb=" N ASN A 544 " pdb=" CA ASN A 544 " ideal model delta sigma weight residual 1.456 1.516 -0.059 1.31e-02 5.83e+03 2.03e+01 ... (remaining 23959 not shown) Histogram of bond angle deviations from ideal: 90.88 - 102.07: 55 102.07 - 113.27: 13250 113.27 - 124.46: 18919 124.46 - 135.65: 393 135.65 - 146.84: 2 Bond angle restraints: 32619 Sorted by residual: angle pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 112.00 92.71 19.29 1.40e+00 5.10e-01 1.90e+02 angle pdb=" C VAL A 88 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta sigma weight residual 121.54 146.84 -25.30 1.91e+00 2.74e-01 1.76e+02 angle pdb=" C PHE A 58 " pdb=" N PHE A 59 " pdb=" CA PHE A 59 " ideal model delta sigma weight residual 121.54 142.17 -20.63 1.91e+00 2.74e-01 1.17e+02 angle pdb=" O LEU A 56 " pdb=" C LEU A 56 " pdb=" N PRO A 57 " ideal model delta sigma weight residual 121.32 109.82 11.50 1.15e+00 7.56e-01 1.00e+02 angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 110.28 124.60 -14.32 1.48e+00 4.57e-01 9.36e+01 ... (remaining 32614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12247 17.94 - 35.88: 1613 35.88 - 53.82: 349 53.82 - 71.76: 64 71.76 - 89.70: 40 Dihedral angle restraints: 14313 sinusoidal: 5586 harmonic: 8727 Sorted by residual: dihedral pdb=" CA PHE B 55 " pdb=" C PHE B 55 " pdb=" N LEU B 56 " pdb=" CA LEU B 56 " ideal model delta harmonic sigma weight residual 180.00 122.91 57.09 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA PHE A 92 " pdb=" C PHE A 92 " pdb=" N ALA A 93 " pdb=" CA ALA A 93 " ideal model delta harmonic sigma weight residual 180.00 123.09 56.91 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA VAL A 88 " pdb=" C VAL A 88 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual -180.00 -127.43 -52.57 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 14310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3660 0.138 - 0.277: 57 0.277 - 0.415: 5 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 3723 Sorted by residual: chirality pdb=" CG LEU A 518 " pdb=" CB LEU A 518 " pdb=" CD1 LEU A 518 " pdb=" CD2 LEU A 518 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN A 85 " pdb=" N ASN A 85 " pdb=" C ASN A 85 " pdb=" CB ASN A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CG LEU B 56 " pdb=" CB LEU B 56 " pdb=" CD1 LEU B 56 " pdb=" CD2 LEU B 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3720 not shown) Planarity restraints: 4236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 56 " -0.036 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" C LEU A 56 " 0.112 2.00e-02 2.50e+03 pdb=" O LEU A 56 " -0.037 2.00e-02 2.50e+03 pdb=" N PRO A 57 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 38 " -0.110 5.00e-02 4.00e+02 1.48e-01 3.49e+01 pdb=" N PRO A 39 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 91 " -0.028 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C TYR A 91 " 0.097 2.00e-02 2.50e+03 pdb=" O TYR A 91 " -0.037 2.00e-02 2.50e+03 pdb=" N PHE A 92 " -0.032 2.00e-02 2.50e+03 ... (remaining 4233 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 290 2.53 - 3.13: 18845 3.13 - 3.72: 36650 3.72 - 4.31: 47093 4.31 - 4.90: 75436 Nonbonded interactions: 178314 Sorted by model distance: nonbonded pdb=" N SER A 60 " pdb=" O VAL A 88 " model vdw 1.943 2.520 nonbonded pdb=" N TYR B 423 " pdb=" O ARG B 466 " model vdw 2.040 2.520 nonbonded pdb=" O LEU A 56 " pdb=" N GLY A 87 " model vdw 2.045 2.520 nonbonded pdb=" N HIS B 519 " pdb=" O PHE B 562 " model vdw 2.056 2.520 nonbonded pdb=" OG1 THR B 385 " pdb=" O LEU C 977 " model vdw 2.071 2.440 ... (remaining 178309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.800 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: 0.010 Extract box with map and model: 28.450 Check model and map are aligned: 0.360 Set scattering table: 0.240 Process input model: 62.210 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.160 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 23964 Z= 0.337 Angle : 1.029 25.304 32619 Z= 0.587 Chirality : 0.053 0.691 3723 Planarity : 0.007 0.148 4236 Dihedral : 16.988 89.697 8574 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.64 % Favored : 88.02 % Rotamer: Outliers : 0.34 % Allowed : 24.06 % Favored : 75.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 1.03 % 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: -2.22 (0.15), residues: 2955 helix: 1.94 (0.22), residues: 557 sheet: -0.72 (0.28), residues: 359 loop : -2.86 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 64 HIS 0.005 0.001 HIS C 519 PHE 0.071 0.002 PHE B 55 TYR 0.039 0.002 TYR B 37 ARG 0.011 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 266 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7506 (t-90) cc_final: 0.7232 (t-170) REVERT: A 615 VAL cc_start: 0.9085 (t) cc_final: 0.8840 (m) REVERT: A 968 SER cc_start: 0.8404 (m) cc_final: 0.8155 (p) REVERT: A 1138 TYR cc_start: 0.7609 (t80) cc_final: 0.7228 (t80) REVERT: B 113 LYS cc_start: 0.5418 (tptp) cc_final: 0.5216 (mmtm) REVERT: B 133 PHE cc_start: 0.5331 (t80) cc_final: 0.4947 (m-80) REVERT: B 206 LYS cc_start: 0.7959 (tptt) cc_final: 0.7353 (mtpt) REVERT: B 731 MET cc_start: 0.8894 (pmm) cc_final: 0.8001 (pmm) REVERT: B 960 ASN cc_start: 0.7876 (m-40) cc_final: 0.7600 (t0) REVERT: B 979 ASP cc_start: 0.4949 (t0) cc_final: 0.4255 (t0) REVERT: B 1029 MET cc_start: 0.7212 (tmm) cc_final: 0.6759 (ttm) REVERT: C 191 GLU cc_start: 0.8247 (mp0) cc_final: 0.7917 (mp0) REVERT: C 900 MET cc_start: 0.7770 (mmp) cc_final: 0.7368 (mtt) REVERT: C 973 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6001 (tt) REVERT: C 995 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7563 (ptm-80) REVERT: C 1002 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7971 (tm-30) REVERT: C 1050 MET cc_start: 0.7078 (mmp) cc_final: 0.6499 (mmp) outliers start: 9 outliers final: 1 residues processed: 272 average time/residue: 0.3796 time to fit residues: 159.6339 Evaluate side-chains 149 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 272 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 519 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 969 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 23964 Z= 0.289 Angle : 0.885 22.783 32619 Z= 0.473 Chirality : 0.051 0.346 3723 Planarity : 0.006 0.092 4236 Dihedral : 7.426 59.856 3205 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.00 % Favored : 88.70 % Rotamer: Outliers : 4.07 % Allowed : 22.88 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.92 % 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: -2.19 (0.15), residues: 2955 helix: 1.97 (0.22), residues: 561 sheet: -0.66 (0.26), residues: 382 loop : -2.88 (0.12), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 104 HIS 0.004 0.001 HIS A 66 PHE 0.054 0.002 PHE A 392 TYR 0.032 0.002 TYR B 204 ARG 0.006 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 162 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.2373 (t80) cc_final: 0.1195 (m-80) REVERT: A 553 THR cc_start: 0.5756 (OUTLIER) cc_final: 0.5554 (p) REVERT: A 615 VAL cc_start: 0.9285 (t) cc_final: 0.9033 (m) REVERT: A 740 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8011 (tmm) REVERT: A 968 SER cc_start: 0.8473 (m) cc_final: 0.8179 (p) REVERT: A 1111 GLU cc_start: 0.6630 (pp20) cc_final: 0.6217 (pp20) REVERT: A 1138 TYR cc_start: 0.7670 (t80) cc_final: 0.7252 (t80) REVERT: B 206 LYS cc_start: 0.7999 (tptt) cc_final: 0.7489 (tttt) REVERT: B 960 ASN cc_start: 0.7983 (m-40) cc_final: 0.7697 (t0) REVERT: B 1029 MET cc_start: 0.7474 (tmm) cc_final: 0.6979 (ttm) REVERT: C 360 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6192 (t0) REVERT: C 402 ILE cc_start: -0.1119 (OUTLIER) cc_final: -0.1770 (tt) REVERT: C 449 TYR cc_start: 0.7905 (t80) cc_final: 0.7657 (t80) REVERT: C 489 TYR cc_start: 0.6769 (p90) cc_final: 0.6485 (m-80) REVERT: C 513 LEU cc_start: 0.1263 (OUTLIER) cc_final: 0.0892 (pt) REVERT: C 991 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 995 ARG cc_start: 0.7619 (ptm160) cc_final: 0.7348 (ptm-80) REVERT: C 1050 MET cc_start: 0.7353 (mmp) cc_final: 0.6948 (mmp) outliers start: 107 outliers final: 49 residues processed: 259 average time/residue: 0.2974 time to fit residues: 128.7051 Evaluate side-chains 179 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 294 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 188 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 23964 Z= 0.294 Angle : 0.831 21.820 32619 Z= 0.448 Chirality : 0.050 0.366 3723 Planarity : 0.006 0.093 4236 Dihedral : 6.993 50.082 3203 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.00 % Favored : 88.70 % Rotamer: Outliers : 4.71 % Allowed : 23.15 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.74 % 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: -2.15 (0.15), residues: 2955 helix: 1.99 (0.22), residues: 562 sheet: -0.76 (0.26), residues: 375 loop : -2.82 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.006 0.001 HIS A 207 PHE 0.045 0.002 PHE B 55 TYR 0.022 0.001 TYR A 265 ARG 0.005 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 136 time to evaluate : 3.033 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 110 LEU cc_start: 0.3646 (OUTLIER) cc_final: 0.3435 (mt) REVERT: A 615 VAL cc_start: 0.9374 (t) cc_final: 0.9135 (m) REVERT: A 740 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7876 (tmm) REVERT: A 968 SER cc_start: 0.8540 (m) cc_final: 0.8224 (p) REVERT: A 1106 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: A 1111 GLU cc_start: 0.6973 (pp20) cc_final: 0.6264 (pp20) REVERT: A 1138 TYR cc_start: 0.7732 (t80) cc_final: 0.7321 (t80) REVERT: B 206 LYS cc_start: 0.7948 (tptt) cc_final: 0.7481 (mttt) REVERT: B 207 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7430 (t-90) REVERT: B 697 MET cc_start: 0.8399 (mmt) cc_final: 0.8108 (mmm) REVERT: B 731 MET cc_start: 0.8777 (pmm) cc_final: 0.8468 (ptt) REVERT: B 960 ASN cc_start: 0.7915 (m-40) cc_final: 0.7566 (t0) REVERT: B 1029 MET cc_start: 0.7288 (tmm) cc_final: 0.6851 (ttm) REVERT: C 166 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7792 (t) REVERT: C 489 TYR cc_start: 0.6572 (p90) cc_final: 0.6342 (m-80) REVERT: C 968 SER cc_start: 0.6671 (t) cc_final: 0.6416 (t) REVERT: C 1050 MET cc_start: 0.7419 (mmp) cc_final: 0.7095 (mmp) outliers start: 124 outliers final: 66 residues processed: 248 average time/residue: 0.2979 time to fit residues: 123.5617 Evaluate side-chains 190 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 119 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 259 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 23964 Z= 0.291 Angle : 0.822 20.644 32619 Z= 0.437 Chirality : 0.050 0.384 3723 Planarity : 0.006 0.087 4236 Dihedral : 6.801 48.696 3201 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.17 % Favored : 88.60 % Rotamer: Outliers : 5.74 % Allowed : 21.93 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.71 % 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: -2.15 (0.15), residues: 2955 helix: 1.88 (0.22), residues: 580 sheet: -0.70 (0.26), residues: 374 loop : -2.83 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 64 HIS 0.004 0.001 HIS A1088 PHE 0.049 0.002 PHE A 59 TYR 0.018 0.001 TYR C 200 ARG 0.009 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 130 time to evaluate : 2.921 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 58 PHE cc_start: 0.3263 (m-80) cc_final: 0.2650 (m-10) REVERT: A 110 LEU cc_start: 0.3628 (OUTLIER) cc_final: 0.3404 (mt) REVERT: A 553 THR cc_start: 0.5786 (OUTLIER) cc_final: 0.5585 (p) REVERT: A 615 VAL cc_start: 0.9425 (t) cc_final: 0.9203 (m) REVERT: A 740 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7813 (tmm) REVERT: A 968 SER cc_start: 0.8614 (m) cc_final: 0.8271 (p) REVERT: A 1106 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: A 1111 GLU cc_start: 0.7218 (pp20) cc_final: 0.6471 (pp20) REVERT: A 1138 TYR cc_start: 0.7799 (t80) cc_final: 0.7399 (t80) REVERT: B 206 LYS cc_start: 0.7935 (tptt) cc_final: 0.7575 (mttt) REVERT: B 900 MET cc_start: 0.8461 (mmm) cc_final: 0.8211 (mtp) REVERT: B 935 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7504 (tp40) REVERT: B 960 ASN cc_start: 0.7928 (m-40) cc_final: 0.7577 (t0) REVERT: C 360 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6714 (t0) REVERT: C 402 ILE cc_start: -0.1021 (OUTLIER) cc_final: -0.1565 (tt) REVERT: C 488 CYS cc_start: 0.3130 (OUTLIER) cc_final: 0.1674 (m) REVERT: C 489 TYR cc_start: 0.6509 (p90) cc_final: 0.6306 (m-80) REVERT: C 791 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8516 (t) REVERT: C 1050 MET cc_start: 0.7580 (mmp) cc_final: 0.7246 (mmp) REVERT: C 1125 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.7983 (p0) outliers start: 151 outliers final: 85 residues processed: 270 average time/residue: 0.2964 time to fit residues: 136.5121 Evaluate side-chains 209 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 114 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 23964 Z= 0.289 Angle : 0.811 20.277 32619 Z= 0.434 Chirality : 0.049 0.427 3723 Planarity : 0.006 0.084 4236 Dihedral : 6.725 52.396 3201 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.10 % Favored : 88.66 % Rotamer: Outliers : 5.40 % Allowed : 21.82 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.71 % 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: -2.12 (0.15), residues: 2955 helix: 1.92 (0.22), residues: 574 sheet: -0.70 (0.25), residues: 375 loop : -2.81 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.003 0.001 HIS A1088 PHE 0.035 0.001 PHE B 55 TYR 0.015 0.001 TYR A 265 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 127 time to evaluate : 2.861 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 110 LEU cc_start: 0.3602 (OUTLIER) cc_final: 0.3387 (mt) REVERT: A 535 LYS cc_start: 0.4438 (OUTLIER) cc_final: 0.3988 (tttm) REVERT: A 553 THR cc_start: 0.5659 (OUTLIER) cc_final: 0.5310 (p) REVERT: A 615 VAL cc_start: 0.9428 (t) cc_final: 0.9210 (m) REVERT: A 740 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7882 (tmm) REVERT: A 902 MET cc_start: 0.8125 (tpp) cc_final: 0.7892 (mmt) REVERT: A 968 SER cc_start: 0.8648 (m) cc_final: 0.8301 (p) REVERT: A 1106 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: A 1111 GLU cc_start: 0.7284 (pp20) cc_final: 0.6534 (pp20) REVERT: A 1138 TYR cc_start: 0.7850 (t80) cc_final: 0.7465 (t80) REVERT: B 206 LYS cc_start: 0.7987 (tptt) cc_final: 0.7533 (tttt) REVERT: B 207 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7551 (t-90) REVERT: B 235 ILE cc_start: 0.2718 (OUTLIER) cc_final: 0.2265 (tt) REVERT: B 238 PHE cc_start: 0.2700 (OUTLIER) cc_final: 0.2160 (p90) REVERT: B 697 MET cc_start: 0.8542 (mmt) cc_final: 0.8288 (mmm) REVERT: B 900 MET cc_start: 0.8475 (mmm) cc_final: 0.8238 (mtp) REVERT: B 935 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7486 (tp40) REVERT: B 960 ASN cc_start: 0.7950 (m-40) cc_final: 0.7605 (t0) REVERT: C 104 TRP cc_start: 0.6549 (p90) cc_final: 0.6150 (p90) REVERT: C 360 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6729 (t0) REVERT: C 402 ILE cc_start: -0.0655 (OUTLIER) cc_final: -0.1305 (tt) REVERT: C 488 CYS cc_start: 0.3081 (OUTLIER) cc_final: 0.1822 (m) REVERT: C 489 TYR cc_start: 0.6509 (p90) cc_final: 0.6288 (m-80) REVERT: C 791 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8625 (t) REVERT: C 1050 MET cc_start: 0.7631 (mmp) cc_final: 0.7329 (mmp) REVERT: C 1125 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8011 (p0) outliers start: 142 outliers final: 90 residues processed: 257 average time/residue: 0.2995 time to fit residues: 130.1364 Evaluate side-chains 220 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 116 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 655 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 23964 Z= 0.468 Angle : 0.931 20.143 32619 Z= 0.499 Chirality : 0.053 0.451 3723 Planarity : 0.007 0.091 4236 Dihedral : 7.244 58.067 3201 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.03 % Favored : 86.70 % Rotamer: Outliers : 6.31 % Allowed : 21.51 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.74 % 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: -2.59 (0.15), residues: 2955 helix: 1.30 (0.22), residues: 588 sheet: -1.14 (0.25), residues: 399 loop : -3.06 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 64 HIS 0.008 0.002 HIS C1058 PHE 0.044 0.003 PHE B 55 TYR 0.028 0.002 TYR A 279 ARG 0.007 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 112 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7333 (p90) cc_final: 0.7034 (p90) REVERT: A 275 PHE cc_start: 0.8762 (m-80) cc_final: 0.8356 (m-80) REVERT: A 740 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7650 (tmm) REVERT: A 968 SER cc_start: 0.8964 (m) cc_final: 0.8725 (p) REVERT: A 1106 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: A 1111 GLU cc_start: 0.7854 (pp20) cc_final: 0.7038 (pp20) REVERT: A 1138 TYR cc_start: 0.7835 (t80) cc_final: 0.7438 (t80) REVERT: B 206 LYS cc_start: 0.7785 (tptt) cc_final: 0.7360 (tttt) REVERT: B 207 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7202 (t-90) REVERT: B 238 PHE cc_start: 0.2374 (OUTLIER) cc_final: 0.1789 (p90) REVERT: B 900 MET cc_start: 0.8564 (mmm) cc_final: 0.8319 (mtp) REVERT: B 935 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7609 (tp40) REVERT: B 960 ASN cc_start: 0.8013 (m-40) cc_final: 0.7601 (t0) REVERT: C 229 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8250 (pp) REVERT: C 360 ASN cc_start: 0.6868 (OUTLIER) cc_final: 0.6577 (t0) REVERT: C 402 ILE cc_start: -0.0580 (OUTLIER) cc_final: -0.1118 (tt) REVERT: C 791 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8553 (t) REVERT: C 1031 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7515 (tm-30) outliers start: 166 outliers final: 108 residues processed: 268 average time/residue: 0.2925 time to fit residues: 130.8752 Evaluate side-chains 218 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 101 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 935 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 23964 Z= 0.267 Angle : 0.812 18.027 32619 Z= 0.430 Chirality : 0.050 0.454 3723 Planarity : 0.006 0.088 4236 Dihedral : 6.777 56.810 3201 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.66 % Favored : 89.00 % Rotamer: Outliers : 4.45 % Allowed : 23.38 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.50 % 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: -2.28 (0.15), residues: 2955 helix: 1.75 (0.22), residues: 571 sheet: -0.75 (0.26), residues: 366 loop : -2.90 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.006 0.001 HIS B 66 PHE 0.027 0.001 PHE A 59 TYR 0.015 0.001 TYR B 380 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 134 time to evaluate : 2.847 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 195 LYS cc_start: 0.5339 (mmmt) cc_final: 0.4277 (ttpt) REVERT: A 740 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7834 (tmm) REVERT: A 902 MET cc_start: 0.8013 (tpp) cc_final: 0.7777 (mmt) REVERT: A 968 SER cc_start: 0.8837 (m) cc_final: 0.8575 (p) REVERT: A 1106 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: A 1111 GLU cc_start: 0.7810 (pp20) cc_final: 0.7062 (pp20) REVERT: A 1138 TYR cc_start: 0.7928 (t80) cc_final: 0.7515 (t80) REVERT: B 55 PHE cc_start: 0.5028 (m-80) cc_final: 0.4712 (m-80) REVERT: B 106 PHE cc_start: 0.3532 (OUTLIER) cc_final: 0.2587 (m-80) REVERT: B 206 LYS cc_start: 0.7926 (tptt) cc_final: 0.7481 (tttt) REVERT: B 207 HIS cc_start: 0.7839 (OUTLIER) cc_final: 0.7450 (t-90) REVERT: B 235 ILE cc_start: 0.2211 (OUTLIER) cc_final: 0.1526 (tt) REVERT: B 238 PHE cc_start: 0.2535 (OUTLIER) cc_final: 0.2038 (p90) REVERT: B 271 GLN cc_start: 0.4345 (OUTLIER) cc_final: 0.3507 (mm-40) REVERT: B 275 PHE cc_start: 0.6640 (m-10) cc_final: 0.6362 (m-10) REVERT: B 697 MET cc_start: 0.8552 (mmt) cc_final: 0.8319 (mmm) REVERT: B 960 ASN cc_start: 0.7984 (m-40) cc_final: 0.7649 (t0) REVERT: B 1132 ILE cc_start: 0.9416 (pt) cc_final: 0.9103 (mt) REVERT: C 360 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6551 (t0) REVERT: C 402 ILE cc_start: -0.0558 (OUTLIER) cc_final: -0.1123 (tt) REVERT: C 489 TYR cc_start: 0.6609 (p90) cc_final: 0.6305 (m-80) REVERT: C 791 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8670 (t) REVERT: C 1029 MET cc_start: 0.7911 (ttp) cc_final: 0.7205 (tmm) REVERT: C 1031 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6797 (tm-30) REVERT: C 1125 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8147 (p0) outliers start: 117 outliers final: 75 residues processed: 239 average time/residue: 0.3071 time to fit residues: 121.5114 Evaluate side-chains 201 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 115 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.6980 chunk 115 optimal weight: 0.0470 chunk 172 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 23964 Z= 0.256 Angle : 0.797 17.461 32619 Z= 0.419 Chirality : 0.049 0.427 3723 Planarity : 0.006 0.086 4236 Dihedral : 6.605 58.444 3201 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.07 % Favored : 88.60 % Rotamer: Outliers : 4.07 % Allowed : 23.98 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.53 % 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: -2.17 (0.15), residues: 2955 helix: 1.80 (0.22), residues: 577 sheet: -0.56 (0.26), residues: 358 loop : -2.84 (0.12), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.003 0.001 HIS A 519 PHE 0.025 0.001 PHE B 55 TYR 0.037 0.001 TYR A 37 ARG 0.003 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 121 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.5407 (mmmt) cc_final: 0.4233 (ttpt) REVERT: A 740 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7648 (tmm) REVERT: A 902 MET cc_start: 0.8001 (tpp) cc_final: 0.7772 (mmt) REVERT: A 968 SER cc_start: 0.8766 (m) cc_final: 0.8447 (p) REVERT: A 1106 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: A 1111 GLU cc_start: 0.7797 (pp20) cc_final: 0.7076 (pp20) REVERT: A 1138 TYR cc_start: 0.7928 (t80) cc_final: 0.7509 (t80) REVERT: B 106 PHE cc_start: 0.2044 (OUTLIER) cc_final: 0.1761 (m-80) REVERT: B 169 GLU cc_start: 0.2760 (OUTLIER) cc_final: 0.2346 (mm-30) REVERT: B 207 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7573 (t-90) REVERT: B 235 ILE cc_start: 0.2214 (OUTLIER) cc_final: 0.1605 (tt) REVERT: B 238 PHE cc_start: 0.2644 (OUTLIER) cc_final: 0.2116 (p90) REVERT: B 271 GLN cc_start: 0.4438 (OUTLIER) cc_final: 0.3619 (mm-40) REVERT: B 697 MET cc_start: 0.8581 (mmt) cc_final: 0.8334 (mmm) REVERT: B 960 ASN cc_start: 0.7952 (m-40) cc_final: 0.7637 (t0) REVERT: B 1132 ILE cc_start: 0.9395 (pt) cc_final: 0.9070 (mt) REVERT: C 360 ASN cc_start: 0.6953 (OUTLIER) cc_final: 0.6653 (t0) REVERT: C 402 ILE cc_start: -0.0579 (OUTLIER) cc_final: -0.0877 (pt) REVERT: C 403 ARG cc_start: -0.1351 (OUTLIER) cc_final: -0.1647 (ptt90) REVERT: C 489 TYR cc_start: 0.6648 (p90) cc_final: 0.6311 (m-80) REVERT: C 791 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8673 (t) REVERT: C 1029 MET cc_start: 0.7782 (ttp) cc_final: 0.7332 (tmm) REVERT: C 1031 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6675 (tm-30) REVERT: C 1125 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8106 (p0) outliers start: 107 outliers final: 72 residues processed: 216 average time/residue: 0.3210 time to fit residues: 113.0994 Evaluate side-chains 201 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 116 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 992 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 23964 Z= 0.300 Angle : 0.809 17.232 32619 Z= 0.428 Chirality : 0.049 0.420 3723 Planarity : 0.006 0.088 4236 Dihedral : 6.637 62.280 3201 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.47 % Favored : 88.22 % Rotamer: Outliers : 3.95 % Allowed : 24.33 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.53 % 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: -2.19 (0.15), residues: 2955 helix: 1.92 (0.22), residues: 569 sheet: -0.86 (0.24), residues: 397 loop : -2.85 (0.12), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS C1058 PHE 0.035 0.002 PHE A 92 TYR 0.030 0.001 TYR A 37 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 117 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.5754 (mmmt) cc_final: 0.4987 (ttpt) REVERT: A 902 MET cc_start: 0.8019 (tpp) cc_final: 0.7782 (mmt) REVERT: A 968 SER cc_start: 0.8816 (m) cc_final: 0.8579 (p) REVERT: A 1106 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: A 1111 GLU cc_start: 0.7950 (pp20) cc_final: 0.7208 (pp20) REVERT: A 1138 TYR cc_start: 0.7945 (t80) cc_final: 0.7518 (t80) REVERT: B 55 PHE cc_start: 0.6168 (m-80) cc_final: 0.5675 (m-80) REVERT: B 106 PHE cc_start: 0.2101 (OUTLIER) cc_final: 0.1847 (m-80) REVERT: B 169 GLU cc_start: 0.2742 (OUTLIER) cc_final: 0.2325 (mm-30) REVERT: B 207 HIS cc_start: 0.7800 (OUTLIER) cc_final: 0.7544 (t-90) REVERT: B 235 ILE cc_start: 0.1724 (OUTLIER) cc_final: 0.1032 (tt) REVERT: B 238 PHE cc_start: 0.2838 (OUTLIER) cc_final: 0.2218 (p90) REVERT: B 271 GLN cc_start: 0.4521 (OUTLIER) cc_final: 0.4194 (mm-40) REVERT: B 275 PHE cc_start: 0.6592 (m-10) cc_final: 0.6237 (m-10) REVERT: B 697 MET cc_start: 0.8614 (mmt) cc_final: 0.8346 (mmm) REVERT: B 960 ASN cc_start: 0.8014 (m-40) cc_final: 0.7670 (t0) REVERT: B 1132 ILE cc_start: 0.9449 (pt) cc_final: 0.9119 (mt) REVERT: C 360 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6783 (t0) REVERT: C 402 ILE cc_start: -0.0408 (OUTLIER) cc_final: -0.0915 (pt) REVERT: C 403 ARG cc_start: -0.0985 (OUTLIER) cc_final: -0.1223 (ptt90) REVERT: C 489 TYR cc_start: 0.6737 (p90) cc_final: 0.6379 (m-80) REVERT: C 791 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8666 (t) REVERT: C 1029 MET cc_start: 0.7927 (ttp) cc_final: 0.7202 (tmm) REVERT: C 1031 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6885 (tm-30) REVERT: C 1125 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8171 (p0) outliers start: 104 outliers final: 81 residues processed: 211 average time/residue: 0.3119 time to fit residues: 108.0928 Evaluate side-chains 209 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 116 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 237 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 23964 Z= 0.305 Angle : 0.805 16.435 32619 Z= 0.425 Chirality : 0.049 0.401 3723 Planarity : 0.006 0.097 4236 Dihedral : 6.644 60.188 3201 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.13 % Favored : 88.60 % Rotamer: Outliers : 3.84 % Allowed : 24.55 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.50 % 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: -2.17 (0.15), residues: 2955 helix: 1.89 (0.22), residues: 575 sheet: -0.71 (0.25), residues: 382 loop : -2.85 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.004 0.001 HIS A1088 PHE 0.028 0.001 PHE A 329 TYR 0.027 0.001 TYR A 37 ARG 0.005 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 117 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.4396 (OUTLIER) cc_final: 0.3911 (p90) REVERT: A 195 LYS cc_start: 0.5736 (mmmt) cc_final: 0.5008 (pttt) REVERT: A 902 MET cc_start: 0.8012 (tpp) cc_final: 0.7777 (mmt) REVERT: A 968 SER cc_start: 0.8796 (m) cc_final: 0.8567 (p) REVERT: A 1106 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: A 1111 GLU cc_start: 0.8033 (pp20) cc_final: 0.7273 (pp20) REVERT: A 1138 TYR cc_start: 0.7945 (t80) cc_final: 0.7520 (t80) REVERT: B 169 GLU cc_start: 0.2501 (OUTLIER) cc_final: 0.2115 (mm-30) REVERT: B 235 ILE cc_start: 0.1691 (OUTLIER) cc_final: 0.1097 (tt) REVERT: B 238 PHE cc_start: 0.2643 (OUTLIER) cc_final: 0.2096 (p90) REVERT: B 271 GLN cc_start: 0.4614 (OUTLIER) cc_final: 0.4097 (mm-40) REVERT: B 697 MET cc_start: 0.8615 (mmt) cc_final: 0.8334 (mmm) REVERT: B 960 ASN cc_start: 0.7989 (m-40) cc_final: 0.7637 (t0) REVERT: B 1132 ILE cc_start: 0.9430 (pt) cc_final: 0.9090 (mt) REVERT: C 360 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6722 (t0) REVERT: C 402 ILE cc_start: 0.0019 (OUTLIER) cc_final: -0.0655 (tt) REVERT: C 403 ARG cc_start: -0.0972 (OUTLIER) cc_final: -0.1474 (ptt90) REVERT: C 489 TYR cc_start: 0.6626 (p90) cc_final: 0.6304 (m-80) REVERT: C 791 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (t) REVERT: C 1029 MET cc_start: 0.7923 (ttp) cc_final: 0.7198 (tmm) REVERT: C 1031 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 1125 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8098 (p0) outliers start: 101 outliers final: 83 residues processed: 210 average time/residue: 0.3218 time to fit residues: 110.1009 Evaluate side-chains 207 residues out of total 2631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 113 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 423 TYR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 244 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.157866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109302 restraints weight = 63484.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112453 restraints weight = 31032.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114598 restraints weight = 19934.165| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 23964 Z= 0.260 Angle : 0.778 16.305 32619 Z= 0.411 Chirality : 0.048 0.384 3723 Planarity : 0.006 0.092 4236 Dihedral : 6.488 59.041 3201 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.42 % Favored : 89.34 % Rotamer: Outliers : 3.69 % Allowed : 24.78 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.43 % 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: -2.06 (0.15), residues: 2955 helix: 1.99 (0.22), residues: 575 sheet: -0.63 (0.25), residues: 383 loop : -2.79 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.037 0.001 HIS B 207 PHE 0.027 0.001 PHE A 329 TYR 0.027 0.001 TYR A 37 ARG 0.003 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.46 seconds wall clock time: 79 minutes 55.48 seconds (4795.48 seconds total)