Starting phenix.real_space_refine on Thu Mar 21 11:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrm_37781/03_2024/8wrm_37781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrm_37781/03_2024/8wrm_37781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrm_37781/03_2024/8wrm_37781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrm_37781/03_2024/8wrm_37781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrm_37781/03_2024/8wrm_37781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrm_37781/03_2024/8wrm_37781.pdb" } resolution = 4.34 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= 0.043 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 146 5.16 5 C 19139 2.51 5 N 4992 2.21 5 O 5654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1031": "OE1" <-> "OE2" Residue "F PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 868": "OE1" <-> "OE2" Residue "G TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" 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: 29931 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8360 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "G" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8359 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "C" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8367 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 6 Chain: "D" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 14.52, per 1000 atoms: 0.49 Number of scatterers: 29931 At special positions: 0 Unit cell: (150.8, 157.04, 237.12, 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 146 16.00 O 5654 8.00 N 4992 7.00 C 19139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.04 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.04 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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: 10.62 Conformation dependent library (CDL) restraints added in 5.5 seconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7126 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 45 sheets defined 29.2% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'F' and resid 96 through 99 removed outlier: 4.157A pdb=" N ASN F 99 " --> pdb=" O GLU F 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 96 through 99' Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 364 through 369 removed outlier: 4.433A pdb=" N ILE F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 4.069A pdb=" N LEU F 387 " --> pdb=" O PRO F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 411 removed outlier: 3.678A pdb=" N ALA F 411 " --> pdb=" O SER F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 757 removed outlier: 3.637A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 783 removed outlier: 4.047A pdb=" N THR F 778 " --> pdb=" O GLN F 774 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL F 781 " --> pdb=" O ASN F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.782A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 855 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.596A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.478A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.639A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR F 941 " --> pdb=" O SER F 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 942 through 944 No H-bonds generated for 'chain 'F' and resid 942 through 944' Processing helix chain 'F' and resid 945 through 964 removed outlier: 3.679A pdb=" N ASP F 950 " --> pdb=" O GLY F 946 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 954 " --> pdb=" O ASP F 950 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN F 955 " --> pdb=" O VAL F 951 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA F 958 " --> pdb=" O HIS F 954 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 982 removed outlier: 4.134A pdb=" N ILE F 980 " --> pdb=" O VAL F 976 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 981 " --> pdb=" O LEU F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 993 removed outlier: 3.941A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 994 through 1033 removed outlier: 3.902A pdb=" N THR F 998 " --> pdb=" O ASP F 994 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'F' and resid 1116 through 1118 No H-bonds generated for 'chain 'F' and resid 1116 through 1118' Processing helix chain 'G' and resid 96 through 99 removed outlier: 3.714A pdb=" N ASN G 99 " --> pdb=" O GLU G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 96 through 99' Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 366 through 370 removed outlier: 3.530A pdb=" N TYR G 369 " --> pdb=" O SER G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 removed outlier: 3.929A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 removed outlier: 3.712A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 755 removed outlier: 3.587A pdb=" N SER G 750 " --> pdb=" O SER G 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 755 " --> pdb=" O ASN G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 759 through 776 Processing helix chain 'G' and resid 776 through 783 removed outlier: 4.559A pdb=" N GLU G 780 " --> pdb=" O LYS G 776 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL G 781 " --> pdb=" O ASN G 777 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 825 Processing helix chain 'G' and resid 851 through 855 Processing helix chain 'G' and resid 866 through 884 removed outlier: 3.592A pdb=" N ILE G 870 " --> pdb=" O THR G 866 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 890 removed outlier: 3.613A pdb=" N GLY G 889 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 removed outlier: 3.588A pdb=" N TYR G 904 " --> pdb=" O MET G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 941 removed outlier: 6.779A pdb=" N LYS G 921 " --> pdb=" O TYR G 917 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU G 922 " --> pdb=" O GLU G 918 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR G 941 " --> pdb=" O SER G 937 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 964 removed outlier: 3.596A pdb=" N GLN G 949 " --> pdb=" O LEU G 945 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP G 950 " --> pdb=" O GLY G 946 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 977 through 982 Processing helix chain 'G' and resid 989 through 1033 removed outlier: 4.141A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G1003 " --> pdb=" O GLY G 999 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G1033 " --> pdb=" O MET G1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 1116 through 1118 No H-bonds generated for 'chain 'G' and resid 1116 through 1118' Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.869A pdb=" N ASN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.588A pdb=" N GLU C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.668A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 4.004A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.297A pdb=" N ILE C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.958A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 4.386A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.789A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.809A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.765A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 777 removed outlier: 4.026A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.698A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 940 removed outlier: 4.413A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.551A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.573A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.332A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.501A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.715A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.556A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 247 removed outlier: 3.944A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.796A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.840A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.893A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.638A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 414 removed outlier: 3.608A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 445 through 466 removed outlier: 4.220A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix removed outlier: 3.525A pdb=" N GLY D 466 " --> pdb=" O MET D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.610A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.157A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.554A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.723A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 571 removed outlier: 4.555A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'F' and resid 28 through 30 removed outlier: 7.912A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 227 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.798A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 277 through 278 removed outlier: 4.084A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 325 through 328 removed outlier: 6.467A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 356 through 357 removed outlier: 6.544A pdb=" N ALA F 435 " --> pdb=" O PHE F 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 595 through 598 Processing sheet with id=AA8, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.194A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 701 through 702 removed outlier: 6.667A pdb=" N ALA F 701 " --> pdb=" O ILE G 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN F 717 " --> pdb=" O ALA F1070 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 733 through 735 removed outlier: 4.207A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 787 through 788 removed outlier: 3.584A pdb=" N ILE F 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 3.538A pdb=" N SER F1123 " --> pdb=" O ALA F1087 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.625A pdb=" N SER G 31 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER G 60 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR G 63 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL G 267 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 48 through 49 removed outlier: 3.758A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 52 through 55 Processing sheet with id=AB9, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.972A pdb=" N LEU G 84 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG G 237 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE G 106 " --> pdb=" O ARG G 237 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN G 239 " --> pdb=" O TRP G 104 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP G 104 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU G 241 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 311 through 314 removed outlier: 4.108A pdb=" N THR G 599 " --> pdb=" O GLY G 311 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR G 313 " --> pdb=" O VAL G 597 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 324 through 328 removed outlier: 6.447A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE G 326 " --> pdb=" O ASN G 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.670A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 374 through 378 removed outlier: 7.236A pdb=" N PHE G 374 " --> pdb=" O ASN G 437 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN G 437 " --> pdb=" O PHE G 374 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'G' and resid 654 through 660 removed outlier: 3.523A pdb=" N GLU G 654 " --> pdb=" O ILE G 692 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR G 696 " --> pdb=" O VAL G 656 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN G 658 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 664 " --> pdb=" O ALA G 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 711 through 715 Processing sheet with id=AC8, first strand: chain 'G' and resid 718 through 728 removed outlier: 6.386A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.273A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'G' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.809A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 49 removed outlier: 4.083A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.215A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.631A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.314A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.509A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.969A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.405A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.334A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 1035 hydrogen bonds defined for protein. 2883 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: 10.75 Time building geometry restraints manager: 11.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9592 1.34 - 1.47: 7554 1.47 - 1.59: 13327 1.59 - 1.71: 0 1.71 - 1.84: 197 Bond restraints: 30670 Sorted by residual: bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.517 1.499 0.018 6.70e-03 2.23e+04 7.47e+00 bond pdb=" C GLU D 145 " pdb=" N PRO D 146 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.39e+00 bond pdb=" C THR G 250 " pdb=" N PRO G 251 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.90e+00 bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.46e+00 bond pdb=" C GLY F 485 " pdb=" N PRO F 486 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.30e-02 5.92e+03 4.34e+00 ... (remaining 30665 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.73: 552 104.73 - 112.15: 14391 112.15 - 119.56: 10779 119.56 - 126.98: 15630 126.98 - 134.39: 368 Bond angle restraints: 41720 Sorted by residual: angle pdb=" C PHE F 559 " pdb=" CA PHE F 559 " pdb=" CB PHE F 559 " ideal model delta sigma weight residual 115.79 108.12 7.67 1.19e+00 7.06e-01 4.15e+01 angle pdb=" N ILE C 909 " pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 112.29 106.41 5.88 9.40e-01 1.13e+00 3.92e+01 angle pdb=" N GLU C 773 " pdb=" CA GLU C 773 " pdb=" CB GLU C 773 " ideal model delta sigma weight residual 110.40 119.32 -8.92 1.63e+00 3.76e-01 2.99e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.21 -6.51 1.22e+00 6.72e-01 2.85e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 123.84 -5.91 1.20e+00 6.94e-01 2.42e+01 ... (remaining 41715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16417 17.99 - 35.99: 1538 35.99 - 53.98: 218 53.98 - 71.98: 58 71.98 - 89.97: 41 Dihedral angle restraints: 18272 sinusoidal: 7201 harmonic: 11071 Sorted by residual: dihedral pdb=" CB CYS F 738 " pdb=" SG CYS F 738 " pdb=" SG CYS F 760 " pdb=" CB CYS F 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.37 88.63 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS G 15 " pdb=" SG CYS G 15 " pdb=" SG CYS G 136 " pdb=" CB CYS G 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.46 85.46 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS G 738 " pdb=" SG CYS G 738 " pdb=" SG CYS G 760 " pdb=" CB CYS G 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.93 84.07 1 1.00e+01 1.00e-02 8.61e+01 ... (remaining 18269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4070 0.083 - 0.166: 533 0.166 - 0.249: 35 0.249 - 0.332: 2 0.332 - 0.415: 2 Chirality restraints: 4642 Sorted by residual: chirality pdb=" CB ILE G 410 " pdb=" CA ILE G 410 " pdb=" CG1 ILE G 410 " pdb=" CG2 ILE G 410 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CB ILE C 714 " pdb=" CA ILE C 714 " pdb=" CG1 ILE C 714 " pdb=" CG2 ILE C 714 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB VAL D 293 " pdb=" CA VAL D 293 " pdb=" CG1 VAL D 293 " pdb=" CG2 VAL D 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 4639 not shown) Planarity restraints: 5401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 436 " -0.017 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP C 436 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 436 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP C 436 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 436 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 436 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 436 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 436 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 436 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 560 " 0.065 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO F 561 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 561 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 561 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 769 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C GLY C 769 " 0.059 2.00e-02 2.50e+03 pdb=" O GLY C 769 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE C 770 " -0.020 2.00e-02 2.50e+03 ... (remaining 5398 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2140 2.74 - 3.28: 29909 3.28 - 3.82: 49789 3.82 - 4.36: 57172 4.36 - 4.90: 95588 Nonbonded interactions: 234598 Sorted by model distance: nonbonded pdb=" OG SER F 27 " pdb=" O TRP F 64 " model vdw 2.196 2.440 nonbonded pdb=" OG SER C 27 " pdb=" O TRP C 64 " model vdw 2.204 2.440 nonbonded pdb=" OG SER G 27 " pdb=" O TRP G 64 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR G 396 " pdb=" OE1 GLU G 516 " model vdw 2.244 2.440 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.248 2.440 ... (remaining 234593 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 'C' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'F' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'G' and (resid 14 through 826 or resid 850 through 1140)) } 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: 2.340 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: 11.510 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 72.570 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30670 Z= 0.239 Angle : 0.894 14.267 41720 Z= 0.477 Chirality : 0.054 0.415 4642 Planarity : 0.007 0.105 5401 Dihedral : 14.465 89.974 11026 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.40 % Favored : 91.52 % Rotamer: Outliers : 0.03 % Allowed : 0.54 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.12), residues: 3749 helix: -0.93 (0.15), residues: 967 sheet: -0.20 (0.22), residues: 551 loop : -2.52 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 436 HIS 0.007 0.001 HIS G 245 PHE 0.040 0.002 PHE F1052 TYR 0.038 0.002 TYR D 199 ARG 0.011 0.001 ARG G1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 740 MET cc_start: 0.8592 (tmm) cc_final: 0.8317 (tmm) REVERT: F 759 PHE cc_start: 0.8114 (m-80) cc_final: 0.7888 (m-80) REVERT: F 773 GLU cc_start: 0.8824 (tt0) cc_final: 0.8602 (tm-30) REVERT: F 979 ASP cc_start: 0.8894 (p0) cc_final: 0.8684 (p0) REVERT: F 1017 GLU cc_start: 0.9227 (tt0) cc_final: 0.8898 (tt0) REVERT: G 740 MET cc_start: 0.8550 (mtp) cc_final: 0.8165 (mtp) REVERT: G 773 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8840 (tm-30) REVERT: G 1019 ARG cc_start: 0.9142 (ttp-110) cc_final: 0.8808 (ttp80) REVERT: C 855 PHE cc_start: 0.6922 (m-80) cc_final: 0.6511 (m-80) REVERT: C 936 ASP cc_start: 0.9139 (t0) cc_final: 0.8891 (t0) REVERT: D 62 MET cc_start: 0.6213 (mmp) cc_final: 0.5958 (mmm) REVERT: D 82 MET cc_start: 0.4953 (ppp) cc_final: 0.4603 (ppp) REVERT: D 152 MET cc_start: 0.2421 (mtt) cc_final: 0.1949 (mtt) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.3878 time to fit residues: 177.1495 Evaluate side-chains 188 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 152 optimal weight: 20.0000 chunk 295 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 342 optimal weight: 0.7980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN F 965 GLN F1048 HIS ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 920 GLN G 954 HIS G 955 ASN G 965 GLN G1010 GLN ** G1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 69 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1106 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 30670 Z= 0.261 Angle : 0.625 7.988 41720 Z= 0.330 Chirality : 0.044 0.198 4642 Planarity : 0.005 0.063 5401 Dihedral : 5.093 26.430 4071 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.10 % Favored : 90.82 % Rotamer: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3749 helix: 0.08 (0.16), residues: 1010 sheet: -0.39 (0.22), residues: 587 loop : -2.36 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 459 HIS 0.013 0.001 HIS G 954 PHE 0.026 0.002 PHE F 592 TYR 0.039 0.002 TYR G 904 ARG 0.017 0.001 ARG F 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 255 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 759 PHE cc_start: 0.8110 (m-80) cc_final: 0.7788 (m-80) REVERT: F 773 GLU cc_start: 0.8904 (tt0) cc_final: 0.8668 (tp30) REVERT: F 779 GLN cc_start: 0.8947 (mp10) cc_final: 0.8637 (mp10) REVERT: C 731 MET cc_start: 0.8882 (ppp) cc_final: 0.8510 (ppp) REVERT: C 855 PHE cc_start: 0.7148 (m-80) cc_final: 0.6878 (m-80) REVERT: C 936 ASP cc_start: 0.8954 (t0) cc_final: 0.8667 (p0) REVERT: D 62 MET cc_start: 0.6268 (mmp) cc_final: 0.6054 (mmp) REVERT: D 82 MET cc_start: 0.5013 (ppp) cc_final: 0.4780 (ppp) REVERT: D 152 MET cc_start: 0.2466 (mtt) cc_final: 0.2117 (mtt) REVERT: D 190 MET cc_start: 0.1344 (ptt) cc_final: 0.0983 (ptm) REVERT: D 455 MET cc_start: -0.1945 (ttt) cc_final: -0.2535 (ttt) outliers start: 2 outliers final: 1 residues processed: 257 average time/residue: 0.3955 time to fit residues: 168.1197 Evaluate side-chains 167 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 370 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 641 ASN F 895 GLN F 955 ASN G 52 GLN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 955 ASN G 965 GLN C 52 GLN C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30670 Z= 0.235 Angle : 0.614 8.190 41720 Z= 0.322 Chirality : 0.044 0.172 4642 Planarity : 0.005 0.061 5401 Dihedral : 5.104 33.827 4071 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 3749 helix: 0.32 (0.17), residues: 1000 sheet: -0.36 (0.22), residues: 577 loop : -2.32 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 459 HIS 0.010 0.001 HIS D 373 PHE 0.023 0.002 PHE F1052 TYR 0.032 0.001 TYR D 183 ARG 0.009 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ILE cc_start: 0.8710 (mp) cc_final: 0.8435 (mp) REVERT: F 731 MET cc_start: 0.8874 (ppp) cc_final: 0.8439 (ppp) REVERT: F 740 MET cc_start: 0.8645 (tmm) cc_final: 0.8341 (tmm) REVERT: F 759 PHE cc_start: 0.8030 (m-80) cc_final: 0.7705 (m-80) REVERT: F 773 GLU cc_start: 0.8814 (tt0) cc_final: 0.8588 (tp30) REVERT: G 697 MET cc_start: 0.8868 (tpp) cc_final: 0.8349 (mmm) REVERT: G 740 MET cc_start: 0.8279 (mtp) cc_final: 0.7981 (mtt) REVERT: G 1050 MET cc_start: 0.8603 (tmm) cc_final: 0.7533 (tmm) REVERT: G 1052 PHE cc_start: 0.8961 (m-10) cc_final: 0.8483 (m-10) REVERT: C 239 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6689 (mp10) REVERT: C 360 ASN cc_start: 0.8868 (t0) cc_final: 0.8665 (t0) REVERT: C 731 MET cc_start: 0.8917 (ppp) cc_final: 0.8575 (ppp) REVERT: C 855 PHE cc_start: 0.7348 (m-80) cc_final: 0.7024 (m-80) REVERT: C 882 ILE cc_start: 0.9515 (tt) cc_final: 0.9294 (mt) REVERT: C 936 ASP cc_start: 0.8825 (t0) cc_final: 0.8485 (t0) REVERT: D 82 MET cc_start: 0.5177 (ppp) cc_final: 0.4951 (ppp) REVERT: D 152 MET cc_start: 0.2532 (mtt) cc_final: 0.2164 (mtt) REVERT: D 190 MET cc_start: 0.1171 (ptt) cc_final: 0.0886 (ptm) REVERT: D 270 MET cc_start: 0.4878 (tpt) cc_final: 0.4396 (tpp) outliers start: 3 outliers final: 0 residues processed: 244 average time/residue: 0.3813 time to fit residues: 156.3929 Evaluate side-chains 161 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 230 optimal weight: 0.4980 chunk 344 optimal weight: 20.0000 chunk 364 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 GLN ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 955 ASN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30670 Z= 0.193 Angle : 0.580 7.571 41720 Z= 0.300 Chirality : 0.043 0.241 4642 Planarity : 0.004 0.058 5401 Dihedral : 4.939 30.976 4071 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.75 % Favored : 91.17 % Rotamer: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3749 helix: 0.53 (0.17), residues: 1016 sheet: -0.36 (0.22), residues: 592 loop : -2.24 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.004 0.001 HIS C1048 PHE 0.017 0.001 PHE G1103 TYR 0.019 0.001 TYR D 183 ARG 0.008 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 697 MET cc_start: 0.8956 (tpp) cc_final: 0.8706 (tpp) REVERT: F 731 MET cc_start: 0.9026 (ppp) cc_final: 0.8570 (ppp) REVERT: F 740 MET cc_start: 0.8726 (tmm) cc_final: 0.8411 (tmm) REVERT: F 759 PHE cc_start: 0.8124 (m-80) cc_final: 0.7894 (m-80) REVERT: F 779 GLN cc_start: 0.9079 (mp10) cc_final: 0.8773 (mp10) REVERT: G 740 MET cc_start: 0.8305 (mtp) cc_final: 0.7883 (mtt) REVERT: G 904 TYR cc_start: 0.8062 (m-10) cc_final: 0.7710 (m-80) REVERT: G 1050 MET cc_start: 0.8615 (tmm) cc_final: 0.8414 (tmm) REVERT: C 239 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6686 (mp10) REVERT: C 351 TYR cc_start: 0.8123 (t80) cc_final: 0.7745 (t80) REVERT: C 360 ASN cc_start: 0.8797 (t0) cc_final: 0.8566 (t0) REVERT: C 731 MET cc_start: 0.8926 (ppp) cc_final: 0.8574 (ppp) REVERT: C 858 LEU cc_start: 0.9498 (mt) cc_final: 0.9270 (mt) REVERT: C 936 ASP cc_start: 0.8829 (t0) cc_final: 0.8479 (t0) REVERT: C 979 ASP cc_start: 0.8833 (p0) cc_final: 0.7702 (p0) REVERT: C 983 ARG cc_start: 0.8813 (tpp80) cc_final: 0.8590 (ptp-110) REVERT: D 82 MET cc_start: 0.5091 (ppp) cc_final: 0.4855 (ppp) REVERT: D 152 MET cc_start: 0.2507 (mtt) cc_final: 0.2263 (mtt) REVERT: D 190 MET cc_start: 0.1970 (ptt) cc_final: 0.1578 (ptt) REVERT: D 499 ASP cc_start: 0.1537 (m-30) cc_final: 0.1271 (m-30) outliers start: 2 outliers final: 1 residues processed: 228 average time/residue: 0.3643 time to fit residues: 140.1894 Evaluate side-chains 151 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 271 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 69 HIS ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** F1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 920 GLN G 955 ASN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 330 ASN D 340 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 30670 Z= 0.372 Angle : 0.724 9.417 41720 Z= 0.383 Chirality : 0.046 0.189 4642 Planarity : 0.005 0.067 5401 Dihedral : 5.473 32.926 4071 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.70 % Favored : 89.22 % Rotamer: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3749 helix: 0.19 (0.16), residues: 1016 sheet: -0.50 (0.23), residues: 513 loop : -2.31 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 459 HIS 0.010 0.002 HIS G 245 PHE 0.023 0.002 PHE G 592 TYR 0.025 0.002 TYR C 248 ARG 0.017 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 3.486 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: F 697 MET cc_start: 0.9112 (tpp) cc_final: 0.8822 (tpp) REVERT: F 731 MET cc_start: 0.8956 (ppp) cc_final: 0.8566 (ppp) REVERT: F 740 MET cc_start: 0.8983 (tmm) cc_final: 0.8613 (tmm) REVERT: F 759 PHE cc_start: 0.8208 (m-80) cc_final: 0.7942 (m-80) REVERT: F 779 GLN cc_start: 0.9088 (mp10) cc_final: 0.8776 (mp10) REVERT: G 697 MET cc_start: 0.8668 (tpp) cc_final: 0.8323 (mmm) REVERT: G 740 MET cc_start: 0.8480 (mtp) cc_final: 0.8136 (mtt) REVERT: G 1050 MET cc_start: 0.8725 (tmm) cc_final: 0.8473 (tmm) REVERT: C 351 TYR cc_start: 0.8120 (t80) cc_final: 0.7841 (t80) REVERT: C 360 ASN cc_start: 0.8818 (t0) cc_final: 0.8465 (m-40) REVERT: C 731 MET cc_start: 0.8812 (ppp) cc_final: 0.8339 (ppp) REVERT: C 858 LEU cc_start: 0.9309 (mt) cc_final: 0.9090 (mt) REVERT: C 936 ASP cc_start: 0.8917 (t0) cc_final: 0.8605 (t0) REVERT: D 152 MET cc_start: 0.2695 (mtt) cc_final: 0.2318 (mtt) REVERT: D 190 MET cc_start: 0.2641 (ptt) cc_final: 0.2091 (ptt) REVERT: D 297 MET cc_start: 0.2281 (mtm) cc_final: 0.0769 (tpp) REVERT: D 474 MET cc_start: -0.2474 (mmt) cc_final: -0.2738 (mmt) REVERT: D 499 ASP cc_start: 0.2402 (m-30) cc_final: 0.2173 (m-30) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.3840 time to fit residues: 130.3437 Evaluate side-chains 132 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 364 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 168 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN F 955 ASN F1048 HIS G 52 GLN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 955 ASN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 935 GLN C 955 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 330 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30670 Z= 0.201 Angle : 0.614 8.826 41720 Z= 0.317 Chirality : 0.045 0.206 4642 Planarity : 0.004 0.059 5401 Dihedral : 5.176 31.047 4071 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.04 % Favored : 90.88 % Rotamer: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 3749 helix: 0.49 (0.17), residues: 1014 sheet: -0.34 (0.22), residues: 558 loop : -2.34 (0.12), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 152 HIS 0.008 0.001 HIS F1048 PHE 0.031 0.002 PHE F 201 TYR 0.025 0.001 TYR C 248 ARG 0.010 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 697 MET cc_start: 0.9073 (tpp) cc_final: 0.8775 (tpp) REVERT: F 731 MET cc_start: 0.8970 (ppp) cc_final: 0.8540 (ppp) REVERT: F 740 MET cc_start: 0.8840 (tmm) cc_final: 0.8524 (tmm) REVERT: F 759 PHE cc_start: 0.8151 (m-80) cc_final: 0.7771 (m-80) REVERT: F 779 GLN cc_start: 0.9117 (mp10) cc_final: 0.8759 (mp10) REVERT: G 740 MET cc_start: 0.8428 (mtp) cc_final: 0.8071 (mtt) REVERT: G 1050 MET cc_start: 0.8619 (tmm) cc_final: 0.8364 (tmm) REVERT: G 1067 TYR cc_start: 0.8286 (t80) cc_final: 0.8073 (t80) REVERT: C 351 TYR cc_start: 0.8131 (t80) cc_final: 0.7847 (t80) REVERT: C 360 ASN cc_start: 0.8913 (t0) cc_final: 0.8639 (m-40) REVERT: C 731 MET cc_start: 0.8857 (ppp) cc_final: 0.8428 (ppp) REVERT: C 855 PHE cc_start: 0.7896 (m-10) cc_final: 0.7672 (m-80) REVERT: C 858 LEU cc_start: 0.9210 (mt) cc_final: 0.8991 (mt) REVERT: D 82 MET cc_start: 0.5311 (ppp) cc_final: 0.4923 (ppp) REVERT: D 152 MET cc_start: 0.2817 (mtt) cc_final: 0.2576 (mtt) REVERT: D 190 MET cc_start: 0.2311 (ptt) cc_final: 0.1880 (ptt) REVERT: D 297 MET cc_start: 0.2200 (mtm) cc_final: 0.0868 (tpp) REVERT: D 455 MET cc_start: -0.2018 (ttt) cc_final: -0.2247 (ttt) REVERT: D 474 MET cc_start: -0.2305 (mmt) cc_final: -0.2619 (mmt) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.3710 time to fit residues: 132.8416 Evaluate side-chains 143 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 207 optimal weight: 0.0170 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 363 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN F 965 GLN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 935 GLN G 955 ASN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30670 Z= 0.207 Angle : 0.603 8.046 41720 Z= 0.313 Chirality : 0.045 0.202 4642 Planarity : 0.004 0.058 5401 Dihedral : 5.076 29.052 4071 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.50 % Rotamer: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3749 helix: 0.58 (0.17), residues: 1013 sheet: -0.30 (0.23), residues: 544 loop : -2.29 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 152 HIS 0.004 0.001 HIS F 245 PHE 0.020 0.001 PHE D 512 TYR 0.028 0.001 TYR C 248 ARG 0.009 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 191 GLU cc_start: 0.9097 (tt0) cc_final: 0.8795 (tt0) REVERT: F 697 MET cc_start: 0.8989 (tpp) cc_final: 0.8756 (tpp) REVERT: F 731 MET cc_start: 0.8951 (ppp) cc_final: 0.8538 (ppp) REVERT: F 740 MET cc_start: 0.8916 (tmm) cc_final: 0.8562 (tmm) REVERT: F 759 PHE cc_start: 0.8168 (m-80) cc_final: 0.7751 (m-80) REVERT: F 779 GLN cc_start: 0.9152 (mp10) cc_final: 0.8793 (mp10) REVERT: G 740 MET cc_start: 0.8392 (mtp) cc_final: 0.8005 (mtt) REVERT: G 1050 MET cc_start: 0.8629 (tmm) cc_final: 0.8348 (tmm) REVERT: C 360 ASN cc_start: 0.8816 (t0) cc_final: 0.8552 (m-40) REVERT: C 731 MET cc_start: 0.8860 (ppp) cc_final: 0.8410 (ppp) REVERT: C 858 LEU cc_start: 0.9216 (mt) cc_final: 0.9000 (mt) REVERT: D 82 MET cc_start: 0.5301 (ppp) cc_final: 0.5019 (ppp) REVERT: D 152 MET cc_start: 0.2945 (mtt) cc_final: 0.2727 (mtt) REVERT: D 190 MET cc_start: 0.2335 (ptt) cc_final: 0.1604 (ptp) REVERT: D 297 MET cc_start: 0.2139 (mtm) cc_final: 0.0892 (tpp) REVERT: D 447 VAL cc_start: 0.6911 (t) cc_final: 0.6447 (t) REVERT: D 474 MET cc_start: -0.2537 (mmt) cc_final: -0.2857 (mmt) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.3869 time to fit residues: 128.6997 Evaluate side-chains 143 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 285 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 955 ASN G1010 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 955 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 330 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30670 Z= 0.184 Angle : 0.598 8.533 41720 Z= 0.308 Chirality : 0.044 0.188 4642 Planarity : 0.004 0.057 5401 Dihedral : 4.946 28.943 4071 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.07 % Favored : 90.85 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3749 helix: 0.67 (0.17), residues: 1010 sheet: -0.28 (0.22), residues: 554 loop : -2.26 (0.12), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 152 HIS 0.004 0.001 HIS F 245 PHE 0.018 0.001 PHE G1109 TYR 0.030 0.001 TYR C 248 ARG 0.007 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 191 GLU cc_start: 0.9086 (tt0) cc_final: 0.8781 (tt0) REVERT: F 731 MET cc_start: 0.8952 (ppp) cc_final: 0.8579 (ppp) REVERT: F 740 MET cc_start: 0.9013 (tmm) cc_final: 0.8634 (tmm) REVERT: F 754 LEU cc_start: 0.9526 (pp) cc_final: 0.9323 (tt) REVERT: F 773 GLU cc_start: 0.8954 (tp30) cc_final: 0.8716 (tp30) REVERT: G 731 MET cc_start: 0.9037 (pmm) cc_final: 0.8532 (pmm) REVERT: G 740 MET cc_start: 0.8331 (mtp) cc_final: 0.7931 (mtt) REVERT: G 1050 MET cc_start: 0.8634 (tmm) cc_final: 0.8368 (tmm) REVERT: C 731 MET cc_start: 0.8861 (ppp) cc_final: 0.8419 (ppp) REVERT: C 858 LEU cc_start: 0.9183 (mt) cc_final: 0.8954 (mt) REVERT: D 82 MET cc_start: 0.5361 (ppp) cc_final: 0.5085 (ppp) REVERT: D 190 MET cc_start: 0.2265 (ptt) cc_final: 0.1873 (ptp) REVERT: D 297 MET cc_start: 0.2270 (mtm) cc_final: 0.0986 (ttm) REVERT: D 474 MET cc_start: -0.2141 (mmt) cc_final: -0.2483 (mmt) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.3878 time to fit residues: 133.6303 Evaluate side-chains 140 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 317 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 955 ASN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS C 282 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30670 Z= 0.249 Angle : 0.643 9.436 41720 Z= 0.334 Chirality : 0.045 0.187 4642 Planarity : 0.004 0.054 5401 Dihedral : 5.128 30.120 4071 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.98 % Favored : 89.94 % Rotamer: Outliers : 0.09 % Allowed : 1.08 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3749 helix: 0.64 (0.17), residues: 999 sheet: -0.47 (0.23), residues: 515 loop : -2.17 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 459 HIS 0.004 0.001 HIS G 505 PHE 0.019 0.002 PHE G1052 TYR 0.022 0.001 TYR F 873 ARG 0.005 0.001 ARG G 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 697 MET cc_start: 0.8809 (tpp) cc_final: 0.8458 (tpp) REVERT: F 731 MET cc_start: 0.9006 (ppp) cc_final: 0.8632 (ppp) REVERT: F 740 MET cc_start: 0.9081 (tmm) cc_final: 0.8700 (tmm) REVERT: F 754 LEU cc_start: 0.9545 (pp) cc_final: 0.9310 (tt) REVERT: F 759 PHE cc_start: 0.8215 (m-80) cc_final: 0.7814 (m-80) REVERT: F 773 GLU cc_start: 0.9046 (tp30) cc_final: 0.8804 (tp30) REVERT: G 731 MET cc_start: 0.8981 (pmm) cc_final: 0.8516 (pmm) REVERT: G 740 MET cc_start: 0.8313 (mtp) cc_final: 0.7917 (mtt) REVERT: G 1023 ASN cc_start: 0.9349 (t0) cc_final: 0.9142 (t0) REVERT: G 1050 MET cc_start: 0.8801 (tmm) cc_final: 0.8515 (tmm) REVERT: C 731 MET cc_start: 0.8798 (ppp) cc_final: 0.8339 (ppp) REVERT: C 858 LEU cc_start: 0.9201 (mt) cc_final: 0.8973 (mt) REVERT: C 936 ASP cc_start: 0.8784 (m-30) cc_final: 0.8503 (t0) REVERT: D 82 MET cc_start: 0.5520 (ppp) cc_final: 0.5246 (ppp) REVERT: D 152 MET cc_start: 0.2753 (mtt) cc_final: 0.2538 (mtt) REVERT: D 190 MET cc_start: 0.2556 (ptt) cc_final: 0.2036 (ptt) REVERT: D 297 MET cc_start: 0.2359 (mtm) cc_final: 0.1275 (tpp) REVERT: D 474 MET cc_start: -0.1474 (mmt) cc_final: -0.1838 (mmt) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.3887 time to fit residues: 125.1378 Evaluate side-chains 132 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 375 optimal weight: 10.0000 chunk 345 optimal weight: 0.0050 chunk 299 optimal weight: 8.9990 chunk 31 optimal weight: 0.0970 chunk 231 optimal weight: 0.0060 chunk 183 optimal weight: 5.9990 overall best weight: 1.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN G 895 GLN G 920 GLN G 955 ASN G1010 GLN C 69 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30670 Z= 0.179 Angle : 0.608 9.381 41720 Z= 0.311 Chirality : 0.044 0.180 4642 Planarity : 0.004 0.055 5401 Dihedral : 4.984 27.100 4071 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.39 % Favored : 90.53 % Rotamer: Outliers : 0.12 % Allowed : 0.63 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3749 helix: 0.75 (0.17), residues: 995 sheet: -0.21 (0.23), residues: 531 loop : -2.17 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 459 HIS 0.009 0.001 HIS C1083 PHE 0.022 0.001 PHE F 374 TYR 0.016 0.001 TYR D 183 ARG 0.005 0.000 ARG C 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 3.382 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: F 697 MET cc_start: 0.8869 (tpp) cc_final: 0.8496 (tpp) REVERT: F 731 MET cc_start: 0.8656 (ppp) cc_final: 0.8293 (ppp) REVERT: F 740 MET cc_start: 0.9020 (tmm) cc_final: 0.8661 (tmm) REVERT: F 754 LEU cc_start: 0.9537 (pp) cc_final: 0.9293 (tt) REVERT: F 759 PHE cc_start: 0.8097 (m-80) cc_final: 0.7661 (m-80) REVERT: F 773 GLU cc_start: 0.9000 (tp30) cc_final: 0.8751 (tp30) REVERT: F 1052 PHE cc_start: 0.8644 (m-10) cc_final: 0.8410 (m-10) REVERT: G 265 TYR cc_start: 0.8862 (p90) cc_final: 0.8560 (p90) REVERT: G 697 MET cc_start: 0.8696 (mmp) cc_final: 0.8311 (mmp) REVERT: G 740 MET cc_start: 0.8292 (mtp) cc_final: 0.7905 (mtt) REVERT: G 988 GLU cc_start: 0.9086 (mp0) cc_final: 0.8835 (mp0) REVERT: G 1023 ASN cc_start: 0.9424 (t0) cc_final: 0.9115 (t0) REVERT: G 1050 MET cc_start: 0.8675 (tmm) cc_final: 0.8364 (tmm) REVERT: C 55 PHE cc_start: 0.8872 (m-10) cc_final: 0.8585 (m-80) REVERT: C 481 ASN cc_start: 0.7582 (m-40) cc_final: 0.7356 (t0) REVERT: C 731 MET cc_start: 0.8862 (ppp) cc_final: 0.8398 (ppp) REVERT: C 858 LEU cc_start: 0.9160 (mt) cc_final: 0.8939 (mt) REVERT: C 985 ASP cc_start: 0.9452 (m-30) cc_final: 0.9249 (m-30) REVERT: C 1111 GLU cc_start: 0.8041 (pp20) cc_final: 0.7703 (pp20) REVERT: C 1113 GLN cc_start: 0.8953 (mt0) cc_final: 0.8301 (mt0) REVERT: D 82 MET cc_start: 0.5490 (ppp) cc_final: 0.5217 (ppp) REVERT: D 152 MET cc_start: 0.2337 (mtt) cc_final: 0.2101 (mtt) REVERT: D 190 MET cc_start: 0.2531 (ptt) cc_final: 0.1791 (ptp) REVERT: D 297 MET cc_start: 0.2409 (mtm) cc_final: 0.1488 (ttm) REVERT: D 474 MET cc_start: -0.1388 (mmt) cc_final: -0.1792 (mmt) outliers start: 4 outliers final: 0 residues processed: 202 average time/residue: 0.3955 time to fit residues: 133.5410 Evaluate side-chains 141 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 8.9990 chunk 318 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.0370 overall best weight: 1.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** F1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 955 ASN G1010 GLN C 69 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.099156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.078829 restraints weight = 220665.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.077959 restraints weight = 135179.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.078745 restraints weight = 92495.194| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30670 Z= 0.181 Angle : 0.604 9.229 41720 Z= 0.309 Chirality : 0.044 0.206 4642 Planarity : 0.004 0.054 5401 Dihedral : 4.934 28.419 4071 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.44 % Favored : 90.48 % Rotamer: Outliers : 0.12 % Allowed : 0.33 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3749 helix: 0.80 (0.17), residues: 995 sheet: -0.21 (0.23), residues: 529 loop : -2.15 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.006 0.001 HIS C 69 PHE 0.018 0.001 PHE C 140 TYR 0.017 0.001 TYR D 183 ARG 0.004 0.000 ARG C1000 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4854.67 seconds wall clock time: 90 minutes 38.60 seconds (5438.60 seconds total)