Starting phenix.real_space_refine on Wed May 15 10:46:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xea_38284/05_2024/8xea_38284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xea_38284/05_2024/8xea_38284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xea_38284/05_2024/8xea_38284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xea_38284/05_2024/8xea_38284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xea_38284/05_2024/8xea_38284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xea_38284/05_2024/8xea_38284.pdb" } resolution = 3.42 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= 0.041 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 138 5.16 5 C 19265 2.51 5 N 5065 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 40": "OD1" <-> "OD2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D ASP 574": "OD1" <-> "OD2" Residue "D ASP 936": "OD1" <-> "OD2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 574": "OD1" <-> "OD2" Residue "E GLU 780": "OE1" <-> "OE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 40": "OD1" <-> "OD2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 198": "OD1" <-> "OD2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 574": "OD1" <-> "OD2" Residue "F GLU 780": "OE1" <-> "OE2" Residue "F ASP 985": "OD1" <-> "OD2" Residue "F PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 104": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 30213 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "I" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "J" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 15.01, per 1000 atoms: 0.50 Number of scatterers: 30213 At special positions: 0 Unit cell: (154.96, 164.32, 209.04, 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 138 16.00 O 5745 8.00 N 5065 7.00 C 19265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.05 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 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=2.03 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 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " 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: 11.54 Conformation dependent library (CDL) restraints added in 5.5 seconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7208 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 60 sheets defined 18.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.980A pdb=" N ASN A 32 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 406 through 410 removed outlier: 3.580A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 743 removed outlier: 4.227A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.640A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 783 removed outlier: 3.603A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 850 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 907 Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.960A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 964 removed outlier: 4.639A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS D 954 " --> pdb=" O ASP D 950 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 984 removed outlier: 3.619A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 993 removed outlier: 3.870A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1032 removed outlier: 3.658A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.628A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.740A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 783 removed outlier: 4.140A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 851 through 855 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.544A pdb=" N GLY E 889 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 907 Processing helix chain 'E' and resid 908 through 910 No H-bonds generated for 'chain 'E' and resid 908 through 910' Processing helix chain 'E' and resid 913 through 941 removed outlier: 3.657A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 964 removed outlier: 4.837A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS E 954 " --> pdb=" O ASP E 950 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 959 " --> pdb=" O ASN E 955 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN E 960 " --> pdb=" O ALA E 956 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 962 " --> pdb=" O ALA E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 984 removed outlier: 3.562A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 988 Processing helix chain 'E' and resid 989 through 1032 removed outlier: 4.396A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) 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 370 removed outlier: 3.653A pdb=" N ILE F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 389 removed outlier: 4.147A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 removed outlier: 3.597A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 removed outlier: 4.438A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN F 422 " --> pdb=" O ILE F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 422' Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 757 removed outlier: 3.714A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR F 756 " --> pdb=" O LEU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 783 removed outlier: 3.687A pdb=" N LEU F 763 " --> pdb=" O PHE F 759 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR F 778 " --> pdb=" O GLN F 774 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.523A 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 removed outlier: 3.530A pdb=" N ILE F 870 " --> pdb=" O THR F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.513A 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 913 through 941 removed outlier: 3.606A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 934 " --> pdb=" O ALA F 930 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR F 941 " --> pdb=" O SER F 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 removed outlier: 4.825A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS F 954 " --> pdb=" O ASP F 950 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 955 " --> pdb=" O VAL F 951 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 959 " --> pdb=" O ASN F 955 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN F 960 " --> pdb=" O ALA F 956 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 962 " --> pdb=" O ALA F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 984 removed outlier: 3.715A pdb=" N LEU F 981 " --> pdb=" O LEU F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.064A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU F 996 " --> pdb=" O GLN F 992 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.052A pdb=" N SER A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.722A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.454A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.271A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER D 94 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 55 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AA9, first strand: chain 'D' and resid 277 through 279 removed outlier: 7.439A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 286 " --> pdb=" O LYS D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 311 through 314 removed outlier: 3.618A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 597 " --> pdb=" O TYR D 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AB3, first strand: chain 'D' and resid 394 through 402 Processing sheet with id=AB4, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.255A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.320A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.971A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D1047 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.611A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 861 " --> pdb=" O LYS D 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 787 through 788 removed outlier: 3.504A pdb=" N ILE D 788 " --> pdb=" O ALA F 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 3.685A pdb=" N SER D1123 " --> pdb=" O ALA D1087 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.556A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 94 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 52 through 55 Processing sheet with id=AC6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.778A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 172 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 277 through 279 removed outlier: 7.096A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.544A pdb=" N TYR E 313 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 597 " --> pdb=" O TYR E 313 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'E' and resid 394 through 402 removed outlier: 3.582A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 513 " --> pdb=" O CYS E 432 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.239A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.731A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.890A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.771A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 28 through 31 removed outlier: 8.275A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 267 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER F 94 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG F 190 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AE3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.964A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 126 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 172 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 277 through 279 removed outlier: 7.059A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 313 through 314 removed outlier: 3.542A pdb=" N TYR F 313 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 597 " --> pdb=" O TYR F 313 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'F' and resid 394 through 403 removed outlier: 4.602A pdb=" N THR F 430 " --> pdb=" O PHE F 515 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'F' and resid 654 through 660 removed outlier: 6.273A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 664 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.148A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'F' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.878A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.538A pdb=" N SER G 106 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.700A pdb=" N SER I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 45 through 49 removed outlier: 6.362A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.712A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AG5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.853A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2568 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: 13.12 Time building geometry restraints manager: 12.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9726 1.35 - 1.47: 7959 1.47 - 1.60: 13071 1.60 - 1.72: 0 1.72 - 1.84: 177 Bond restraints: 30933 Sorted by residual: bond pdb=" C PRO F 986 " pdb=" N PRO F 987 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.17e+01 bond pdb=" C THR F 250 " pdb=" N PRO F 251 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.43e+01 bond pdb=" C THR E 250 " pdb=" N PRO E 251 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.08e+01 bond pdb=" C THR D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 1.334 1.390 -0.057 2.34e-02 1.83e+03 5.84e+00 bond pdb=" C LEU F 560 " pdb=" N PRO F 561 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.44e-02 4.82e+03 4.24e+00 ... (remaining 30928 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.64: 904 106.64 - 113.75: 16752 113.75 - 120.87: 13552 120.87 - 127.98: 10674 127.98 - 135.10: 199 Bond angle restraints: 42081 Sorted by residual: angle pdb=" CB LYS E 786 " pdb=" CG LYS E 786 " pdb=" CD LYS E 786 " ideal model delta sigma weight residual 111.30 124.09 -12.79 2.30e+00 1.89e-01 3.09e+01 angle pdb=" C TYR E 489 " pdb=" N SER E 490 " pdb=" CA SER E 490 " ideal model delta sigma weight residual 120.68 128.29 -7.61 1.52e+00 4.33e-01 2.51e+01 angle pdb=" C LEU F 249 " pdb=" N THR F 250 " pdb=" CA THR F 250 " ideal model delta sigma weight residual 121.80 133.92 -12.12 2.44e+00 1.68e-01 2.47e+01 angle pdb=" N PRO D 986 " pdb=" CA PRO D 986 " pdb=" C PRO D 986 " ideal model delta sigma weight residual 110.70 116.45 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" CA LYS E 786 " pdb=" CB LYS E 786 " pdb=" CG LYS E 786 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 ... (remaining 42076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15889 17.69 - 35.39: 1881 35.39 - 53.08: 480 53.08 - 70.78: 133 70.78 - 88.47: 37 Dihedral angle restraints: 18420 sinusoidal: 7188 harmonic: 11232 Sorted by residual: dihedral pdb=" CB CYS F 15 " pdb=" SG CYS F 15 " pdb=" SG CYS F 136 " pdb=" CB CYS F 136 " ideal model delta sinusoidal sigma weight residual -86.00 -174.47 88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " pdb=" SG CYS D 136 " pdb=" CB CYS D 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.04 84.96 1 1.00e+01 1.00e-02 8.76e+01 ... (remaining 18417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4075 0.074 - 0.147: 614 0.147 - 0.221: 19 0.221 - 0.295: 4 0.295 - 0.368: 3 Chirality restraints: 4715 Sorted by residual: chirality pdb=" CG LEU G 80 " pdb=" CB LEU G 80 " pdb=" CD1 LEU G 80 " pdb=" CD2 LEU G 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB ILE E 101 " pdb=" CA ILE E 101 " pdb=" CG1 ILE E 101 " pdb=" CG2 ILE E 101 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE D 101 " pdb=" CA ILE D 101 " pdb=" CG1 ILE D 101 " pdb=" CG2 ILE D 101 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4712 not shown) Planarity restraints: 5443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 985 " 0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO D 986 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 986 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 986 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.23e+00 pdb=" N PRO D 987 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " -0.025 2.00e-02 2.50e+03 1.92e-02 9.18e+00 pdb=" CG TRP D 152 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " -0.009 2.00e-02 2.50e+03 ... (remaining 5440 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2625 2.74 - 3.28: 28846 3.28 - 3.82: 51578 3.82 - 4.36: 57037 4.36 - 4.90: 98576 Nonbonded interactions: 238662 Sorted by model distance: nonbonded pdb=" OG SER F 27 " pdb=" O TRP F 64 " model vdw 2.204 2.440 nonbonded pdb=" OG SER D 27 " pdb=" O TRP D 64 " model vdw 2.219 2.440 nonbonded pdb=" O ASN F 417 " pdb=" OH TYR F 453 " model vdw 2.224 2.440 nonbonded pdb=" OG SER E 27 " pdb=" O TRP E 64 " model vdw 2.238 2.440 nonbonded pdb=" O LEU D 966 " pdb=" OG SER D 975 " model vdw 2.265 2.440 ... (remaining 238657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'D' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'E' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'F' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.520 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 78.150 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.180 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.003 0.088 30933 Z= 0.214 Angle : 0.815 12.798 42081 Z= 0.429 Chirality : 0.049 0.368 4715 Planarity : 0.006 0.077 5443 Dihedral : 16.745 87.382 11068 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 0.45 % Allowed : 25.63 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.84 (0.13), residues: 3817 helix: -0.02 (0.21), residues: 613 sheet: -0.49 (0.17), residues: 886 loop : -1.94 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 152 HIS 0.004 0.001 HIS D 505 PHE 0.024 0.001 PHE E 79 TYR 0.036 0.001 TYR D 351 ARG 0.005 0.000 ARG F 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.2754 (mmt) cc_final: 0.2262 (mmm) REVERT: A 82 MET cc_start: -0.0826 (ptt) cc_final: -0.1212 (mtm) REVERT: D 77 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5987 (ptpp) REVERT: D 177 MET cc_start: 0.4228 (ptt) cc_final: 0.4016 (ptm) REVERT: D 201 PHE cc_start: 0.8668 (t80) cc_final: 0.8174 (t80) REVERT: D 421 TYR cc_start: 0.5763 (m-80) cc_final: 0.5370 (m-10) REVERT: D 907 ASN cc_start: 0.8286 (t0) cc_final: 0.8028 (m110) REVERT: D 1031 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8274 (mt-10) REVERT: D 1088 HIS cc_start: 0.7309 (m90) cc_final: 0.7031 (m90) REVERT: D 1125 ASN cc_start: 0.6597 (p0) cc_final: 0.6299 (p0) REVERT: E 51 THR cc_start: 0.7656 (p) cc_final: 0.7404 (p) REVERT: E 420 ASP cc_start: 0.5116 (t0) cc_final: 0.4562 (t0) REVERT: E 716 THR cc_start: 0.7881 (p) cc_final: 0.7298 (p) REVERT: F 134 GLN cc_start: 0.9239 (mm110) cc_final: 0.8746 (pm20) REVERT: F 201 PHE cc_start: 0.8885 (t80) cc_final: 0.8397 (t80) REVERT: F 907 ASN cc_start: 0.8324 (t0) cc_final: 0.8049 (m110) REVERT: G 34 MET cc_start: 0.4082 (mmt) cc_final: 0.3829 (mmm) REVERT: I 103 THR cc_start: 0.3297 (p) cc_final: 0.3026 (p) outliers start: 15 outliers final: 2 residues processed: 266 average time/residue: 0.4328 time to fit residues: 185.9020 Evaluate side-chains 155 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 3.9990 chunk 288 optimal weight: 0.0030 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 154 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN D 370 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 GLN D1011 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN E 370 ASN ** E 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 GLN F 234 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN F 690 GLN F 804 GLN F 920 GLN F 955 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30933 Z= 0.258 Angle : 0.647 10.664 42081 Z= 0.336 Chirality : 0.044 0.185 4715 Planarity : 0.005 0.063 5443 Dihedral : 4.966 46.461 4179 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 4.11 % Allowed : 24.47 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.56 (0.13), residues: 3817 helix: 0.39 (0.21), residues: 655 sheet: -0.39 (0.18), residues: 851 loop : -1.80 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F1102 HIS 0.006 0.001 HIS D 954 PHE 0.021 0.002 PHE D1095 TYR 0.026 0.002 TYR D 904 ARG 0.007 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 146 time to evaluate : 3.551 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: E 201 PHE cc_start: 0.8984 (t80) cc_final: 0.8773 (t80) REVERT: E 1050 MET cc_start: 0.8557 (ptm) cc_final: 0.8325 (ptp) REVERT: F 822 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9449 (mt) REVERT: G 34 MET cc_start: 0.3036 (mmt) cc_final: 0.2715 (mmm) REVERT: G 82 MET cc_start: -0.1796 (mtm) cc_final: -0.2998 (mtm) outliers start: 138 outliers final: 53 residues processed: 272 average time/residue: 0.3846 time to fit residues: 178.1137 Evaluate side-chains 168 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 1067 TYR Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 906 PHE Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 0.0970 chunk 107 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 346 optimal weight: 30.0000 chunk 374 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 343 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 278 optimal weight: 0.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 ASN ** E 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS F 234 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 955 ASN F1011 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 30933 Z= 0.305 Angle : 0.645 11.908 42081 Z= 0.342 Chirality : 0.044 0.328 4715 Planarity : 0.005 0.055 5443 Dihedral : 4.984 52.573 4175 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.86 % Favored : 92.01 % Rotamer: Outliers : 4.74 % Allowed : 24.05 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.51 (0.13), residues: 3817 helix: 0.65 (0.21), residues: 649 sheet: -0.45 (0.18), residues: 815 loop : -1.77 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 36 HIS 0.008 0.001 HIS D 339 PHE 0.020 0.002 PHE E 79 TYR 0.022 0.002 TYR F 453 ARG 0.008 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 107 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.1627 (mmm) cc_final: 0.1419 (mmm) REVERT: D 153 MET cc_start: 0.7271 (mpp) cc_final: 0.7047 (mpp) REVERT: D 192 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7768 (m-10) REVERT: D 796 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: E 95 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8394 (t) REVERT: E 644 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8632 (tp40) REVERT: E 985 ASP cc_start: 0.9036 (t0) cc_final: 0.8685 (t0) REVERT: E 988 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: F 896 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9112 (mm) REVERT: F 995 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.9044 (ptp-110) REVERT: G 34 MET cc_start: 0.3118 (mmt) cc_final: 0.2904 (mmm) outliers start: 159 outliers final: 76 residues processed: 257 average time/residue: 0.3803 time to fit residues: 165.9043 Evaluate side-chains 171 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 88 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 896 ILE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 755 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1109 PHE Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 50.0000 chunk 260 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 165 optimal weight: 0.0070 chunk 232 optimal weight: 0.0570 chunk 347 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 329 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN D 856 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN F 992 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30933 Z= 0.178 Angle : 0.567 11.561 42081 Z= 0.289 Chirality : 0.043 0.213 4715 Planarity : 0.004 0.056 5443 Dihedral : 4.753 55.722 4175 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 3.37 % Allowed : 25.25 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.38 (0.14), residues: 3817 helix: 0.81 (0.21), residues: 656 sheet: -0.33 (0.18), residues: 813 loop : -1.73 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 36 HIS 0.005 0.001 HIS D1088 PHE 0.019 0.001 PHE E 79 TYR 0.022 0.001 TYR A 94 ARG 0.012 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 94 time to evaluate : 3.412 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: D 77 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6619 (mmmt) REVERT: D 177 MET cc_start: 0.3941 (ptm) cc_final: 0.3432 (ptm) REVERT: D 178 ASP cc_start: 0.8642 (p0) cc_final: 0.7815 (t70) REVERT: D 192 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7925 (m-10) REVERT: D 635 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8159 (m) REVERT: D 697 MET cc_start: 0.8916 (mmm) cc_final: 0.8639 (tmm) REVERT: D 774 GLN cc_start: 0.9005 (mt0) cc_final: 0.8799 (mt0) REVERT: D 796 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.6162 (m-80) REVERT: D 983 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8361 (mtm110) REVERT: D 1050 MET cc_start: 0.8342 (mtp) cc_final: 0.8059 (mtp) REVERT: D 1125 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8368 (p0) REVERT: E 95 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8265 (t) REVERT: E 644 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8673 (tp40) REVERT: E 900 MET cc_start: 0.8274 (mmt) cc_final: 0.8056 (mmp) REVERT: E 985 ASP cc_start: 0.9007 (t0) cc_final: 0.8604 (t0) REVERT: E 988 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8889 (pm20) REVERT: F 1029 MET cc_start: 0.9391 (tpp) cc_final: 0.8922 (tpp) REVERT: F 1041 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8243 (t0) outliers start: 113 outliers final: 61 residues processed: 203 average time/residue: 0.3994 time to fit residues: 137.7422 Evaluate side-chains 159 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 88 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 883 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 GLN Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1040 VAL Chi-restraints excluded: chain F residue 1041 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 3.9990 chunk 209 optimal weight: 0.0270 chunk 5 optimal weight: 0.2980 chunk 274 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 188 optimal weight: 10.0000 chunk 330 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN E 804 GLN E 935 GLN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30933 Z= 0.183 Angle : 0.553 12.573 42081 Z= 0.283 Chirality : 0.042 0.178 4715 Planarity : 0.004 0.055 5443 Dihedral : 4.623 54.455 4175 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 3.49 % Allowed : 24.56 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.31 (0.14), residues: 3817 helix: 0.89 (0.22), residues: 659 sheet: -0.26 (0.18), residues: 837 loop : -1.71 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 36 HIS 0.015 0.001 HIS E 505 PHE 0.032 0.001 PHE D 855 TYR 0.019 0.001 TYR F 453 ARG 0.007 0.000 ARG F 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 93 time to evaluate : 3.724 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: D 192 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: D 774 GLN cc_start: 0.9010 (mt0) cc_final: 0.8802 (mt0) REVERT: D 796 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: D 983 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8254 (mtm110) REVERT: D 1125 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8660 (p0) REVERT: E 985 ASP cc_start: 0.9018 (t0) cc_final: 0.8604 (t0) REVERT: E 988 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8930 (pm20) REVERT: F 303 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9361 (mm) REVERT: F 779 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8743 (mp10) REVERT: F 995 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.9138 (ptp-110) REVERT: F 1029 MET cc_start: 0.9426 (tpp) cc_final: 0.8931 (tpp) outliers start: 117 outliers final: 70 residues processed: 199 average time/residue: 0.3906 time to fit residues: 132.7846 Evaluate side-chains 163 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 85 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 755 GLN Chi-restraints excluded: chain F residue 779 GLN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 368 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 0.0570 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN E 658 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN I 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 30933 Z= 0.250 Angle : 0.604 13.490 42081 Z= 0.314 Chirality : 0.043 0.234 4715 Planarity : 0.005 0.074 5443 Dihedral : 4.761 56.674 4175 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.12 % Favored : 91.72 % Rotamer: Outliers : 4.11 % Allowed : 23.99 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.34 (0.14), residues: 3817 helix: 0.96 (0.22), residues: 645 sheet: -0.40 (0.18), residues: 839 loop : -1.69 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.004 0.001 HIS E 66 PHE 0.029 0.001 PHE I 29 TYR 0.033 0.001 TYR D 38 ARG 0.009 0.001 ARG F 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 100 time to evaluate : 3.330 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: D 177 MET cc_start: 0.4483 (ptm) cc_final: 0.3750 (ppp) REVERT: D 178 ASP cc_start: 0.8507 (p0) cc_final: 0.8077 (t0) REVERT: D 192 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: D 983 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8691 (mtm110) REVERT: D 1002 GLN cc_start: 0.9329 (mm-40) cc_final: 0.9124 (tm-30) REVERT: D 1125 ASN cc_start: 0.9361 (OUTLIER) cc_final: 0.9002 (p0) REVERT: E 559 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7461 (t80) REVERT: F 201 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8785 (t80) REVERT: F 697 MET cc_start: 0.8999 (mmm) cc_final: 0.8768 (mmm) REVERT: F 779 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8719 (mp10) REVERT: F 796 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6621 (m-80) REVERT: F 1002 GLN cc_start: 0.9407 (mm-40) cc_final: 0.9099 (mm-40) REVERT: F 1029 MET cc_start: 0.9471 (tpp) cc_final: 0.8921 (tpp) REVERT: F 1113 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8578 (mp-120) REVERT: H 34 MET cc_start: 0.1692 (mmm) cc_final: 0.0673 (mmm) outliers start: 138 outliers final: 87 residues processed: 228 average time/residue: 0.3761 time to fit residues: 146.6506 Evaluate side-chains 184 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 89 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 421 TYR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 755 GLN Chi-restraints excluded: chain F residue 779 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 796 TYR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 310 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 367 optimal weight: 4.9990 chunk 229 optimal weight: 0.0980 chunk 223 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30933 Z= 0.185 Angle : 0.561 10.822 42081 Z= 0.286 Chirality : 0.043 0.243 4715 Planarity : 0.004 0.061 5443 Dihedral : 4.665 55.621 4175 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.70 % Favored : 92.17 % Rotamer: Outliers : 3.25 % Allowed : 25.10 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.29 (0.14), residues: 3817 helix: 1.01 (0.22), residues: 646 sheet: -0.34 (0.18), residues: 845 loop : -1.69 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP I 35 HIS 0.012 0.001 HIS F 505 PHE 0.018 0.001 PHE E 79 TYR 0.019 0.001 TYR F 453 ARG 0.005 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 94 time to evaluate : 3.558 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: D 177 MET cc_start: 0.4584 (ptm) cc_final: 0.3978 (ptm) REVERT: D 178 ASP cc_start: 0.8508 (p0) cc_final: 0.7628 (t0) REVERT: D 179 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7017 (pt) REVERT: D 983 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8646 (mtm110) REVERT: D 1002 GLN cc_start: 0.9312 (mm-40) cc_final: 0.9109 (tm-30) REVERT: D 1125 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8981 (p0) REVERT: E 61 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8091 (t0) REVERT: E 559 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7515 (t80) REVERT: E 985 ASP cc_start: 0.9189 (t0) cc_final: 0.8836 (t0) REVERT: F 779 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8763 (mp10) REVERT: F 1002 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9068 (mm-40) REVERT: F 1018 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9436 (tt) REVERT: F 1113 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8533 (mp-120) REVERT: H 34 MET cc_start: 0.1044 (mmm) cc_final: 0.0653 (mmm) outliers start: 109 outliers final: 86 residues processed: 196 average time/residue: 0.3873 time to fit residues: 130.7432 Evaluate side-chains 177 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 83 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 755 GLN Chi-restraints excluded: chain F residue 779 GLN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1040 VAL Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 110 optimal weight: 0.0670 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 233 optimal weight: 0.0070 chunk 250 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 288 optimal weight: 9.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN E 69 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E1010 GLN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30933 Z= 0.143 Angle : 0.557 11.439 42081 Z= 0.280 Chirality : 0.043 0.208 4715 Planarity : 0.004 0.053 5443 Dihedral : 4.498 54.111 4175 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 2.68 % Allowed : 25.48 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.18 (0.14), residues: 3817 helix: 1.11 (0.22), residues: 635 sheet: -0.22 (0.18), residues: 843 loop : -1.63 (0.13), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 36 HIS 0.008 0.001 HIS F 505 PHE 0.018 0.001 PHE E 79 TYR 0.016 0.001 TYR F 453 ARG 0.005 0.000 ARG F 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 88 time to evaluate : 3.437 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: D 177 MET cc_start: 0.4325 (ptm) cc_final: 0.3932 (ptm) REVERT: D 178 ASP cc_start: 0.8429 (p0) cc_final: 0.7581 (t0) REVERT: D 179 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7032 (pp) REVERT: D 983 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8638 (mtm110) REVERT: D 995 ARG cc_start: 0.9468 (ptp-170) cc_final: 0.9159 (mtm110) REVERT: D 1125 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8970 (p0) REVERT: E 559 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7608 (t80) REVERT: F 779 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8787 (mp10) REVERT: F 1002 GLN cc_start: 0.9378 (mm-40) cc_final: 0.9044 (mm-40) REVERT: F 1018 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9383 (tt) outliers start: 90 outliers final: 68 residues processed: 172 average time/residue: 0.4026 time to fit residues: 117.6392 Evaluate side-chains 154 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 80 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 779 GLN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 320 optimal weight: 2.9990 chunk 342 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 309 optimal weight: 5.9990 chunk 323 optimal weight: 0.3980 chunk 341 optimal weight: 50.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 GLN ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 ASN ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30933 Z= 0.260 Angle : 0.614 13.983 42081 Z= 0.313 Chirality : 0.043 0.242 4715 Planarity : 0.004 0.053 5443 Dihedral : 4.687 55.426 4175 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.36 % Favored : 91.51 % Rotamer: Outliers : 3.13 % Allowed : 25.28 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.27 (0.14), residues: 3817 helix: 0.96 (0.21), residues: 650 sheet: -0.35 (0.18), residues: 849 loop : -1.65 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 36 HIS 0.007 0.001 HIS F 505 PHE 0.019 0.001 PHE E 970 TYR 0.018 0.001 TYR F 453 ARG 0.006 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 83 time to evaluate : 3.386 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: D 902 MET cc_start: 0.9322 (tpp) cc_final: 0.9019 (tpt) REVERT: D 983 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8753 (mtm110) REVERT: E 61 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8298 (t0) REVERT: E 559 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7894 (t80) REVERT: E 635 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8905 (m) REVERT: E 740 MET cc_start: 0.9050 (ttp) cc_final: 0.8801 (ttp) REVERT: F 779 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8799 (mp10) REVERT: F 1002 GLN cc_start: 0.9386 (mm-40) cc_final: 0.9068 (mm-40) REVERT: F 1113 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8562 (mp-120) outliers start: 105 outliers final: 81 residues processed: 182 average time/residue: 0.3786 time to fit residues: 120.3737 Evaluate side-chains 166 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 79 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1113 GLN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 734 THR Chi-restraints excluded: chain F residue 745 ASP Chi-restraints excluded: chain F residue 779 GLN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 chunk 251 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 349 optimal weight: 30.0000 chunk 302 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.8416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30933 Z= 0.281 Angle : 0.639 12.588 42081 Z= 0.327 Chirality : 0.044 0.273 4715 Planarity : 0.004 0.047 5443 Dihedral : 4.930 56.743 4175 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.59 % Favored : 91.25 % Rotamer: Outliers : 2.80 % Allowed : 25.75 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -1.42 (0.14), residues: 3817 helix: 1.03 (0.22), residues: 632 sheet: -0.60 (0.18), residues: 864 loop : -1.72 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 36 HIS 0.010 0.001 HIS F1048 PHE 0.021 0.002 PHE F 43 TYR 0.022 0.002 TYR D 660 ARG 0.007 0.001 ARG D 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 79 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 177 MET cc_start: 0.6201 (ptm) cc_final: 0.5719 (ppp) REVERT: D 178 ASP cc_start: 0.8605 (p0) cc_final: 0.8160 (t0) REVERT: E 61 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8473 (t0) REVERT: E 559 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7874 (t80) REVERT: E 697 MET cc_start: 0.8892 (mmm) cc_final: 0.8562 (tpt) REVERT: F 242 LEU cc_start: 0.8364 (tp) cc_final: 0.8107 (tp) REVERT: F 587 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8445 (mp) REVERT: F 1002 GLN cc_start: 0.9402 (mm-40) cc_final: 0.9156 (mm-40) REVERT: F 1113 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8548 (mp-120) outliers start: 94 outliers final: 77 residues processed: 168 average time/residue: 0.3735 time to fit residues: 109.3870 Evaluate side-chains 156 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 75 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 635 VAL Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1084 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 709 ASN Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 988 GLU Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1084 ASP Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1106 GLN Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 chunk 44 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN E 69 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.081420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061156 restraints weight = 245059.770| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 6.10 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.8430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.283 30933 Z= 0.359 Angle : 0.755 59.198 42081 Z= 0.408 Chirality : 0.045 0.763 4715 Planarity : 0.004 0.046 5443 Dihedral : 4.934 56.740 4175 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.57 % Favored : 91.28 % Rotamer: Outliers : 2.92 % Allowed : 25.60 % Favored : 71.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % 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: -1.42 (0.14), residues: 3817 helix: 1.02 (0.22), residues: 632 sheet: -0.60 (0.18), residues: 864 loop : -1.72 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 36 HIS 0.008 0.001 HIS F1048 PHE 0.038 0.002 PHE F1052 TYR 0.020 0.001 TYR F 453 ARG 0.018 0.001 ARG D 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5706.00 seconds wall clock time: 106 minutes 43.83 seconds (6403.83 seconds total)