Starting phenix.real_space_refine on Fri Mar 15 14:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjl_14750/03_2024/7zjl_14750.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjl_14750/03_2024/7zjl_14750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjl_14750/03_2024/7zjl_14750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjl_14750/03_2024/7zjl_14750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjl_14750/03_2024/7zjl_14750.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjl_14750/03_2024/7zjl_14750.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.090 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: 5 Type Number sf(0) Gaussians S 153 5.16 5 C 22279 2.51 5 N 5887 2.21 5 O 6821 1.98 5 H 34272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69412 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 16630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 16630 Classifications: {'peptide': 1078} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 3 Chain: "B" Number of atoms: 16631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 16631 Classifications: {'peptide': 1077} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 3 Chain: "C" Number of atoms: 16569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 16569 Classifications: {'peptide': 1073} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1021} Chain breaks: 3 Chain: "i" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3218 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain: "j" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3309 Classifications: {'peptide': 223} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "g" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3219 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain: "h" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3309 Classifications: {'peptide': 223} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "k" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3218 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain: "l" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3309 Classifications: {'peptide': 223} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Time building chain proxies: 23.89, per 1000 atoms: 0.34 Number of scatterers: 69412 At special positions: 0 Unit cell: (215.528, 165.362, 235.037, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 153 16.00 O 6821 8.00 N 5887 7.00 C 22279 6.00 H 34272 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 138 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.01 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 138 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 138 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 90 " distance=2.02 Simple disulfide: pdb=" SG CYS i 138 " - pdb=" SG CYS i 198 " distance=2.04 Simple disulfide: pdb=" SG CYS i 218 " - pdb=" SG CYS j 223 " distance=2.03 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 96 " distance=2.04 Simple disulfide: pdb=" SG CYS j 147 " - pdb=" SG CYS j 203 " distance=2.04 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 90 " distance=2.02 Simple disulfide: pdb=" SG CYS g 138 " - pdb=" SG CYS g 198 " distance=2.04 Simple disulfide: pdb=" SG CYS g 218 " - pdb=" SG CYS h 223 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS h 147 " - pdb=" SG CYS h 203 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 90 " distance=2.02 Simple disulfide: pdb=" SG CYS k 138 " - pdb=" SG CYS k 198 " distance=2.05 Simple disulfide: pdb=" SG CYS k 218 " - pdb=" SG CYS l 223 " distance=2.04 Simple disulfide: pdb=" SG CYS l 22 " - pdb=" SG CYS l 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 147 " - pdb=" SG CYS l 203 " 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: 40.54 Conformation dependent library (CDL) restraints added in 5.4 seconds 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 86 sheets defined 20.8% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.544A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.771A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.653A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.604A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.742A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.805A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.913A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.524A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.017A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.599A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.975A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.095A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.295A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.806A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.837A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.655A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.571A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.911A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.118A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.611A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.562A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.540A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.969A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.063A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.562A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.673A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.367A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'i' and resid 81 through 85 Processing helix chain 'i' and resid 125 through 131 Processing helix chain 'i' and resid 187 through 192 Processing helix chain 'i' and resid 216 through 218 No H-bonds generated for 'chain 'i' and resid 216 through 218' Processing helix chain 'j' and resid 28 through 32 Processing helix chain 'j' and resid 87 through 91 Processing helix chain 'j' and resid 134 through 136 No H-bonds generated for 'chain 'j' and resid 134 through 136' Processing helix chain 'j' and resid 163 through 165 No H-bonds generated for 'chain 'j' and resid 163 through 165' Processing helix chain 'j' and resid 194 through 196 No H-bonds generated for 'chain 'j' and resid 194 through 196' Processing helix chain 'j' and resid 208 through 211 Processing helix chain 'g' and resid 81 through 85 Processing helix chain 'g' and resid 125 through 130 Processing helix chain 'g' and resid 187 through 193 removed outlier: 3.736A pdb=" N HIS g 193 " --> pdb=" O ASP g 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'h' and resid 134 through 136 No H-bonds generated for 'chain 'h' and resid 134 through 136' Processing helix chain 'h' and resid 163 through 165 No H-bonds generated for 'chain 'h' and resid 163 through 165' Processing helix chain 'h' and resid 194 through 196 No H-bonds generated for 'chain 'h' and resid 194 through 196' Processing helix chain 'h' and resid 208 through 211 Processing helix chain 'k' and resid 81 through 85 Processing helix chain 'k' and resid 125 through 130 Processing helix chain 'k' and resid 187 through 193 removed outlier: 3.871A pdb=" N HIS k 193 " --> pdb=" O ASP k 189 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 32 Processing helix chain 'l' and resid 87 through 91 Processing helix chain 'l' and resid 134 through 136 No H-bonds generated for 'chain 'l' and resid 134 through 136' Processing helix chain 'l' and resid 163 through 165 No H-bonds generated for 'chain 'l' and resid 163 through 165' Processing helix chain 'l' and resid 194 through 196 No H-bonds generated for 'chain 'l' and resid 194 through 196' Processing helix chain 'l' and resid 208 through 211 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.856A pdb=" N ALA A 29 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASN A 63 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR A 269 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 38 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.856A pdb=" N ALA A 29 " --> pdb=" O TRP A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 45 removed outlier: 5.020A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 57 removed outlier: 3.592A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 87 removed outlier: 6.381A pdb=" N LEU A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 87 removed outlier: 6.307A pdb=" N ALA A 243 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 103 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ARG A 104 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 168 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLU A 134 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS A 166 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN A 136 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASN A 164 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.936A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.510A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE A 565 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.799A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.636A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.674A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.504A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.419A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.654A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.746A pdb=" N ALA B 29 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.746A pdb=" N ALA B 29 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASN B 63 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B 269 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.740A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AC6, first strand: chain 'B' and resid 85 through 87 removed outlier: 6.385A pdb=" N ALA B 243 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 103 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG B 104 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 168 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 136 through 137 removed outlier: 3.626A pdb=" N SER B 162 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.979A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.631A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.633A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.378A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE B 565 " --> pdb=" O PHE C 45 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.603A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.511A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.580A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.995A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.738A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.673A pdb=" N ALA C 29 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.673A pdb=" N ALA C 29 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASN C 63 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR C 269 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.628A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 85 through 87 Processing sheet with id=AE6, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.530A pdb=" N GLY C 105 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA C 243 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 103 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG C 104 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 168 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.695A pdb=" N SER C 162 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.502A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.852A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.613A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.598A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.647A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.521A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.450A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 9 through 12 removed outlier: 6.722A pdb=" N VAL i 10 " --> pdb=" O THR i 108 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP i 37 " --> pdb=" O MET i 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'i' and resid 9 through 12 removed outlier: 6.722A pdb=" N VAL i 10 " --> pdb=" O THR i 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR i 98 " --> pdb=" O THR i 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'i' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'i' and resid 118 through 122 removed outlier: 5.148A pdb=" N TYR i 177 " --> pdb=" O ASN i 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 157 through 158 Processing sheet with id=AG5, first strand: chain 'j' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'j' and resid 11 through 12 removed outlier: 6.612A pdb=" N MET j 34 " --> pdb=" O VAL j 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL j 50 " --> pdb=" O MET j 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP j 36 " --> pdb=" O VAL j 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'j' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'j' and resid 127 through 131 removed outlier: 6.171A pdb=" N TYR j 183 " --> pdb=" O ASP j 151 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 138 through 139 removed outlier: 6.171A pdb=" N TYR j 183 " --> pdb=" O ASP j 151 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 158 through 161 removed outlier: 4.362A pdb=" N TYR j 201 " --> pdb=" O VAL j 218 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 9 through 12 removed outlier: 6.493A pdb=" N TRP g 37 " --> pdb=" O MET g 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 9 through 12 Processing sheet with id=AH4, first strand: chain 'g' and resid 18 through 23 Processing sheet with id=AH5, first strand: chain 'g' and resid 118 through 122 removed outlier: 5.622A pdb=" N TYR g 177 " --> pdb=" O ASN g 142 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'g' and resid 157 through 158 Processing sheet with id=AH7, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AH8, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLY h 10 " --> pdb=" O THR h 117 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET h 34 " --> pdb=" O VAL h 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLY h 10 " --> pdb=" O THR h 117 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'h' and resid 127 through 131 removed outlier: 6.017A pdb=" N TYR h 183 " --> pdb=" O ASP h 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'h' and resid 138 through 139 removed outlier: 6.017A pdb=" N TYR h 183 " --> pdb=" O ASP h 151 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'h' and resid 158 through 161 removed outlier: 4.433A pdb=" N TYR h 201 " --> pdb=" O VAL h 218 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'k' and resid 9 through 12 removed outlier: 6.596A pdb=" N VAL k 10 " --> pdb=" O THR k 108 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP k 37 " --> pdb=" O MET k 49 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'k' and resid 9 through 12 removed outlier: 6.596A pdb=" N VAL k 10 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'k' and resid 17 through 23 Processing sheet with id=AI7, first strand: chain 'k' and resid 118 through 122 removed outlier: 5.494A pdb=" N TYR k 177 " --> pdb=" O ASN k 142 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'k' and resid 157 through 158 Processing sheet with id=AI9, first strand: chain 'l' and resid 3 through 7 Processing sheet with id=AJ1, first strand: chain 'l' and resid 11 through 12 removed outlier: 6.643A pdb=" N MET l 34 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL l 50 " --> pdb=" O MET l 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP l 36 " --> pdb=" O VAL l 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'l' and resid 11 through 12 Processing sheet with id=AJ3, first strand: chain 'l' and resid 127 through 131 removed outlier: 6.034A pdb=" N TYR l 183 " --> pdb=" O ASP l 151 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'l' and resid 138 through 139 removed outlier: 6.034A pdb=" N TYR l 183 " --> pdb=" O ASP l 151 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'l' and resid 158 through 161 removed outlier: 4.349A pdb=" N TYR l 201 " --> pdb=" O VAL l 218 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4179 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: 30.22 Time building geometry restraints manager: 42.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 34272 1.11 - 1.29: 5779 1.29 - 1.46: 12510 1.46 - 1.64: 17463 1.64 - 1.82: 192 Bond restraints: 70216 Sorted by residual: bond pdb=" N TRP j 36 " pdb=" H TRP j 36 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N HIS A 245 " pdb=" H HIS A 245 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE B 201 " pdb=" HE2 PHE B 201 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN i 81 " pdb="HE22 GLN i 81 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN B 314 " pdb="HE21 GLN B 314 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 70211 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.67: 1453 105.67 - 113.03: 77741 113.03 - 120.39: 31569 120.39 - 127.75: 15479 127.75 - 135.11: 220 Bond angle restraints: 126462 Sorted by residual: angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 120.89 -7.09 1.00e+00 1.00e+00 5.02e+01 angle pdb=" CA PHE h 68 " pdb=" CB PHE h 68 " pdb=" CG PHE h 68 " ideal model delta sigma weight residual 113.80 119.94 -6.14 1.00e+00 1.00e+00 3.77e+01 angle pdb=" CA ASP B 796 " pdb=" CB ASP B 796 " pdb=" CG ASP B 796 " ideal model delta sigma weight residual 112.60 118.54 -5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" OE1 GLN g 6 " pdb=" CD GLN g 6 " pdb=" NE2 GLN g 6 " ideal model delta sigma weight residual 122.60 117.06 5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 126457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 31207 17.80 - 35.60: 1768 35.60 - 53.40: 568 53.40 - 71.20: 189 71.20 - 89.01: 42 Dihedral angle restraints: 33774 sinusoidal: 18067 harmonic: 15707 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -173.89 87.89 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS i 218 " pdb=" SG CYS i 218 " pdb=" SG CYS j 223 " pdb=" CB CYS j 223 " ideal model delta sinusoidal sigma weight residual 93.00 169.75 -76.75 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.10 71.10 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 33771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4385 0.112 - 0.224: 1043 0.224 - 0.335: 87 0.335 - 0.447: 11 0.447 - 0.559: 3 Chirality restraints: 5529 Sorted by residual: chirality pdb=" CA TYR i 51 " pdb=" N TYR i 51 " pdb=" C TYR i 51 " pdb=" CB TYR i 51 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA ASP C 745 " pdb=" N ASP C 745 " pdb=" C ASP C 745 " pdb=" CB ASP C 745 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CA ASP B 745 " pdb=" N ASP B 745 " pdb=" C ASP B 745 " pdb=" CB ASP B 745 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 5526 not shown) Planarity restraints: 10645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP g 99 " -0.333 2.00e-02 2.50e+03 1.46e-01 8.55e+02 pdb=" CG TRP g 99 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP g 99 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP g 99 " 0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP g 99 " 0.122 2.00e-02 2.50e+03 pdb=" CE2 TRP g 99 " 0.052 2.00e-02 2.50e+03 pdb=" CE3 TRP g 99 " 0.142 2.00e-02 2.50e+03 pdb=" CZ2 TRP g 99 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP g 99 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP g 99 " -0.090 2.00e-02 2.50e+03 pdb=" HD1 TRP g 99 " -0.078 2.00e-02 2.50e+03 pdb=" HE1 TRP g 99 " 0.206 2.00e-02 2.50e+03 pdb=" HE3 TRP g 99 " 0.248 2.00e-02 2.50e+03 pdb=" HZ2 TRP g 99 " -0.078 2.00e-02 2.50e+03 pdb=" HZ3 TRP g 99 " 0.030 2.00e-02 2.50e+03 pdb=" HH2 TRP g 99 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP k 99 " 0.281 2.00e-02 2.50e+03 1.26e-01 6.32e+02 pdb=" CG TRP k 99 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP k 99 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP k 99 " -0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP k 99 " -0.098 2.00e-02 2.50e+03 pdb=" CE2 TRP k 99 " -0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP k 99 " -0.119 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 99 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 99 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP k 99 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 TRP k 99 " 0.055 2.00e-02 2.50e+03 pdb=" HE1 TRP k 99 " -0.196 2.00e-02 2.50e+03 pdb=" HE3 TRP k 99 " -0.210 2.00e-02 2.50e+03 pdb=" HZ2 TRP k 99 " 0.074 2.00e-02 2.50e+03 pdb=" HZ3 TRP k 99 " -0.043 2.00e-02 2.50e+03 pdb=" HH2 TRP k 99 " 0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 99 " -0.242 2.00e-02 2.50e+03 1.04e-01 4.35e+02 pdb=" CG TRP i 99 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP i 99 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP i 99 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP i 99 " 0.102 2.00e-02 2.50e+03 pdb=" CE2 TRP i 99 " 0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP i 99 " 0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 99 " -0.047 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 99 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP i 99 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TRP i 99 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP i 99 " 0.155 2.00e-02 2.50e+03 pdb=" HE3 TRP i 99 " 0.183 2.00e-02 2.50e+03 pdb=" HZ2 TRP i 99 " -0.066 2.00e-02 2.50e+03 pdb=" HZ3 TRP i 99 " 0.050 2.00e-02 2.50e+03 pdb=" HH2 TRP i 99 " -0.136 2.00e-02 2.50e+03 ... (remaining 10642 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3457 2.15 - 2.76: 114157 2.76 - 3.38: 196777 3.38 - 3.99: 269128 3.99 - 4.60: 390652 Nonbonded interactions: 974171 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" HG SER C 366 " model vdw 1.538 1.850 nonbonded pdb=" OD1 ASP B 364 " pdb=" HG SER B 366 " model vdw 1.555 1.850 nonbonded pdb=" OD1 ASP i 174 " pdb=" HG1 THR i 176 " model vdw 1.582 1.850 nonbonded pdb=" OE2 GLU A 918 " pdb=" HG SER C1123 " model vdw 1.586 1.850 nonbonded pdb=" HG1 THR C 415 " pdb=" OD1 ASP C 420 " model vdw 1.591 1.850 ... (remaining 974166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 620 or resid 640 through 1047 or (resid 1048 an \ d (name N or name CA or name C or name O or name CB or name CG or name ND1 or na \ me CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or n \ ame HD1 or name HD2 or name HE1)) or resid 1049 through 1146)) selection = (chain 'B' and (resid 17 through 620 or resid 640 through 826 or resid 855 throu \ gh 1146)) selection = (chain 'C' and (resid 17 through 826 or resid 855 through 1146)) } ncs_group { reference = (chain 'g' and (resid 1 through 201 or (resid 202 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 203 through 218)) selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'h' selection = chain 'j' selection = chain 'l' } 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: 2.780 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.760 Extract box with map and model: 13.200 Check model and map are aligned: 0.780 Set scattering table: 0.460 Process input model: 173.400 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.350 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: 0.020 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.012 0.050 35944 Z= 0.806 Angle : 1.765 8.851 48911 Z= 1.186 Chirality : 0.093 0.559 5529 Planarity : 0.014 0.210 6330 Dihedral : 12.922 89.006 12830 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 0.48 % Allowed : 2.66 % Favored : 96.85 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.24 (0.11), residues: 4515 helix: -0.43 (0.17), residues: 729 sheet: 0.86 (0.14), residues: 1162 loop : -0.52 (0.11), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.196 0.022 TRP g 99 HIS 0.012 0.003 HIS A1048 PHE 0.131 0.014 PHE C 718 TYR 0.199 0.023 TYR B 495 ARG 0.014 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 718 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.5301 (m-80) cc_final: 0.4609 (m-80) REVERT: A 206 LYS cc_start: 0.7828 (tttt) cc_final: 0.7020 (mmtt) REVERT: A 224 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6737 (mp0) REVERT: A 287 ASP cc_start: 0.7611 (t0) cc_final: 0.7397 (t0) REVERT: A 505 TYR cc_start: 0.7729 (m-80) cc_final: 0.7493 (m-80) REVERT: A 646 ARG cc_start: 0.8372 (mtt90) cc_final: 0.7823 (mtp180) REVERT: A 661 GLU cc_start: 0.8250 (tt0) cc_final: 0.7956 (pm20) REVERT: A 773 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7233 (tt0) REVERT: A 957 GLN cc_start: 0.8377 (tt0) cc_final: 0.7999 (tp-100) REVERT: A 1038 LYS cc_start: 0.7878 (mttt) cc_final: 0.7529 (mppt) REVERT: B 177 MET cc_start: -0.0916 (ttm) cc_final: -0.1439 (tpp) REVERT: B 472 ILE cc_start: 0.8060 (mm) cc_final: 0.7475 (pp) REVERT: B 613 GLN cc_start: 0.8228 (mt0) cc_final: 0.7964 (mt0) REVERT: B 646 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7452 (mpp-170) REVERT: B 804 GLN cc_start: 0.8158 (mt0) cc_final: 0.7820 (mm110) REVERT: B 855 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5576 (t80) REVERT: B 868 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7097 (mp0) REVERT: B 936 ASP cc_start: 0.7800 (m-30) cc_final: 0.7592 (m-30) REVERT: B 957 GLN cc_start: 0.8356 (tt0) cc_final: 0.7964 (tt0) REVERT: B 1045 LYS cc_start: 0.8348 (mttt) cc_final: 0.7806 (ttmp) REVERT: B 1073 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8033 (mmtp) REVERT: C 284 THR cc_start: 0.8243 (m) cc_final: 0.8014 (p) REVERT: C 304 LYS cc_start: 0.7257 (mttt) cc_final: 0.7025 (ttmt) REVERT: C 403 ARG cc_start: 0.7338 (ttm170) cc_final: 0.7122 (ttp80) REVERT: C 421 TYR cc_start: 0.8672 (m-10) cc_final: 0.8418 (m-10) REVERT: C 427 ASP cc_start: 0.7872 (m-30) cc_final: 0.7385 (p0) REVERT: C 498 GLN cc_start: 0.7473 (mt0) cc_final: 0.7243 (mt0) REVERT: C 646 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7466 (tmt-80) REVERT: C 651 ILE cc_start: 0.9059 (mt) cc_final: 0.8856 (mp) REVERT: C 740 MET cc_start: 0.8555 (ttt) cc_final: 0.8288 (ttm) REVERT: C 780 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8263 (mp0) REVERT: C 796 ASP cc_start: 0.6549 (t0) cc_final: 0.6044 (p0) REVERT: C 1019 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8121 (ttp-110) REVERT: C 1091 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7284 (mtt-85) REVERT: C 1113 GLN cc_start: 0.8400 (mt0) cc_final: 0.8130 (mm110) REVERT: i 56 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7878 (mtm-85) REVERT: i 108 THR cc_start: 0.8695 (m) cc_final: 0.8486 (p) REVERT: g 47 LYS cc_start: 0.7188 (tttt) cc_final: 0.6440 (mtmm) outliers start: 19 outliers final: 2 residues processed: 733 average time/residue: 2.4268 time to fit residues: 2168.5123 Evaluate side-chains 429 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 426 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain k residue 93 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 230 optimal weight: 30.0000 chunk 182 optimal weight: 0.7980 chunk 352 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 408 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 751 ASN A 764 ASN A 907 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A 957 GLN A1002 GLN A1005 GLN A1074 ASN A1113 GLN B 117 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 935 GLN C 117 GLN C 450 ASN C 779 GLN C 907 ASN j 77 ASN j 112 GLN h 31 ASN k 142 ASN k 170 GLN l 31 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35944 Z= 0.234 Angle : 0.660 6.540 48911 Z= 0.362 Chirality : 0.045 0.196 5529 Planarity : 0.005 0.073 6330 Dihedral : 6.680 72.154 4902 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 1.78 % Allowed : 8.04 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.04 (0.12), residues: 4515 helix: 0.81 (0.19), residues: 715 sheet: 0.69 (0.13), residues: 1371 loop : -0.58 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 66 HIS 0.009 0.001 HIS B 519 PHE 0.031 0.002 PHE B 562 TYR 0.025 0.002 TYR i 51 ARG 0.007 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 482 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7842 (m) REVERT: A 92 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7512 (p) REVERT: A 206 LYS cc_start: 0.7835 (tttt) cc_final: 0.7046 (mmtt) REVERT: A 223 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6636 (mp) REVERT: A 224 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6634 (mp0) REVERT: A 319 ARG cc_start: 0.7605 (ptm160) cc_final: 0.7365 (ttp-110) REVERT: A 403 ARG cc_start: 0.6588 (mtp180) cc_final: 0.6010 (mtt-85) REVERT: A 406 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 505 TYR cc_start: 0.7857 (m-80) cc_final: 0.7657 (m-80) REVERT: A 646 ARG cc_start: 0.8330 (mtt90) cc_final: 0.7723 (mtm180) REVERT: A 661 GLU cc_start: 0.8150 (tt0) cc_final: 0.7843 (pm20) REVERT: A 764 ASN cc_start: 0.8697 (m-40) cc_final: 0.8338 (m-40) REVERT: A 773 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7197 (tt0) REVERT: A 796 ASP cc_start: 0.6732 (p0) cc_final: 0.6407 (t0) REVERT: A 814 LYS cc_start: 0.7522 (mttt) cc_final: 0.6973 (mtmt) REVERT: A 868 GLU cc_start: 0.8187 (tt0) cc_final: 0.7856 (tt0) REVERT: A 957 GLN cc_start: 0.8292 (tt0) cc_final: 0.8048 (tp-100) REVERT: A 1038 LYS cc_start: 0.7857 (mttt) cc_final: 0.7443 (mmtp) REVERT: A 1100 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.7078 (p) REVERT: B 177 MET cc_start: -0.0966 (ttm) cc_final: -0.1389 (tpp) REVERT: B 503 VAL cc_start: 0.8516 (t) cc_final: 0.8305 (m) REVERT: B 613 GLN cc_start: 0.8244 (mt0) cc_final: 0.7907 (mt0) REVERT: B 646 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7480 (mpp-170) REVERT: B 804 GLN cc_start: 0.8355 (mt0) cc_final: 0.8057 (mm110) REVERT: B 855 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.5571 (t80) REVERT: B 868 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7272 (pt0) REVERT: B 936 ASP cc_start: 0.7614 (m-30) cc_final: 0.7398 (m-30) REVERT: B 957 GLN cc_start: 0.8387 (tt0) cc_final: 0.7950 (tt0) REVERT: B 995 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7939 (mtp180) REVERT: B 1045 LYS cc_start: 0.8443 (mttt) cc_final: 0.7984 (tttp) REVERT: B 1073 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7982 (mmtp) REVERT: B 1092 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: C 206 LYS cc_start: 0.7523 (tttt) cc_final: 0.7237 (tttp) REVERT: C 403 ARG cc_start: 0.7350 (ttm170) cc_final: 0.7130 (ttp80) REVERT: C 421 TYR cc_start: 0.8609 (m-10) cc_final: 0.8385 (m-10) REVERT: C 427 ASP cc_start: 0.7858 (m-30) cc_final: 0.7396 (p0) REVERT: C 498 GLN cc_start: 0.7485 (mt0) cc_final: 0.7279 (mt0) REVERT: C 646 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7426 (tmt170) REVERT: C 794 ILE cc_start: 0.7134 (mt) cc_final: 0.6854 (mp) REVERT: C 796 ASP cc_start: 0.6682 (t0) cc_final: 0.6072 (p0) REVERT: C 804 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7505 (mm-40) REVERT: C 931 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8288 (mp) REVERT: C 1002 GLN cc_start: 0.8263 (tt0) cc_final: 0.7931 (tp-100) REVERT: C 1019 ARG cc_start: 0.8384 (ttt180) cc_final: 0.8020 (ttp-110) REVERT: C 1113 GLN cc_start: 0.8469 (mt0) cc_final: 0.8127 (mm110) REVERT: i 87 ASP cc_start: 0.7114 (m-30) cc_final: 0.6284 (t0) REVERT: i 218 CYS cc_start: 0.4132 (m) cc_final: 0.3647 (t) REVERT: g 47 LYS cc_start: 0.7241 (tttt) cc_final: 0.6501 (mtmm) REVERT: g 49 MET cc_start: 0.7618 (mmp) cc_final: 0.7046 (mmp) REVERT: g 83 GLU cc_start: 0.7755 (mp0) cc_final: 0.7496 (pp20) outliers start: 70 outliers final: 23 residues processed: 523 average time/residue: 2.3383 time to fit residues: 1502.9694 Evaluate side-chains 421 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 391 time to evaluate : 4.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain g residue 62 ASN Chi-restraints excluded: chain g residue 112 ARG Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 278 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 409 optimal weight: 3.9990 chunk 442 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 405 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 919 ASN A 926 GLN A1005 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN C 89 ASN C 450 ASN C 779 GLN C1002 GLN C1005 GLN i 170 GLN h 77 ASN k 91 ASN k 142 ASN ** k 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 35944 Z= 0.446 Angle : 0.686 9.824 48911 Z= 0.374 Chirality : 0.048 0.249 5529 Planarity : 0.005 0.080 6330 Dihedral : 6.301 69.481 4901 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.41 % Rotamer: Outliers : 2.05 % Allowed : 9.97 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % 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: -0.32 (0.12), residues: 4515 helix: 0.48 (0.19), residues: 721 sheet: 0.32 (0.13), residues: 1466 loop : -0.74 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 436 HIS 0.009 0.001 HIS B 519 PHE 0.039 0.002 PHE B 898 TYR 0.028 0.002 TYR A 146 ARG 0.008 0.001 ARG h 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 411 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7859 (m) REVERT: A 92 VAL cc_start: 0.7784 (t) cc_final: 0.7395 (p) REVERT: A 155 MET cc_start: 0.0773 (OUTLIER) cc_final: 0.0142 (pmm) REVERT: A 206 LYS cc_start: 0.7782 (tttt) cc_final: 0.6975 (tptt) REVERT: A 224 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6657 (mp0) REVERT: A 319 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7451 (ttm110) REVERT: A 505 TYR cc_start: 0.8009 (m-80) cc_final: 0.7798 (m-80) REVERT: A 646 ARG cc_start: 0.8383 (mtt90) cc_final: 0.7728 (mtm180) REVERT: A 661 GLU cc_start: 0.8151 (tt0) cc_final: 0.7827 (pm20) REVERT: A 697 MET cc_start: 0.8847 (ptm) cc_final: 0.8506 (ptm) REVERT: A 764 ASN cc_start: 0.8735 (m-40) cc_final: 0.8219 (m110) REVERT: A 773 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7408 (tt0) REVERT: A 796 ASP cc_start: 0.6671 (p0) cc_final: 0.6388 (t0) REVERT: A 814 LYS cc_start: 0.7676 (mttt) cc_final: 0.7131 (mtmt) REVERT: A 868 GLU cc_start: 0.8313 (tt0) cc_final: 0.7930 (tt0) REVERT: A 957 GLN cc_start: 0.8349 (tt0) cc_final: 0.8042 (tp-100) REVERT: A 993 ILE cc_start: 0.8691 (mm) cc_final: 0.8487 (mt) REVERT: A 1038 LYS cc_start: 0.7895 (mttt) cc_final: 0.7571 (mppt) REVERT: A 1045 LYS cc_start: 0.8417 (mttt) cc_final: 0.8145 (ttpt) REVERT: A 1100 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 177 MET cc_start: -0.0769 (ttm) cc_final: -0.1376 (tpp) REVERT: B 472 ILE cc_start: 0.6867 (pp) cc_final: 0.6568 (mp) REVERT: B 503 VAL cc_start: 0.8649 (t) cc_final: 0.8413 (m) REVERT: B 613 GLN cc_start: 0.8205 (mt0) cc_final: 0.7988 (mt0) REVERT: B 646 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7403 (mtp180) REVERT: B 755 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: B 804 GLN cc_start: 0.8316 (mt0) cc_final: 0.7974 (mm110) REVERT: B 855 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5609 (t80) REVERT: B 868 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7311 (pt0) REVERT: B 936 ASP cc_start: 0.7675 (m-30) cc_final: 0.7451 (m-30) REVERT: B 995 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7924 (mtp180) REVERT: B 1005 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8470 (mt0) REVERT: B 1045 LYS cc_start: 0.8560 (mttt) cc_final: 0.8092 (ttpp) REVERT: B 1073 LYS cc_start: 0.8425 (mtpt) cc_final: 0.7931 (mmtp) REVERT: C 43 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7807 (mtpp) REVERT: C 177 MET cc_start: 0.1521 (mtp) cc_final: 0.0864 (mtp) REVERT: C 206 LYS cc_start: 0.7620 (tttt) cc_final: 0.7273 (tttp) REVERT: C 403 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7260 (ttp-170) REVERT: C 427 ASP cc_start: 0.7917 (m-30) cc_final: 0.7346 (p0) REVERT: C 498 GLN cc_start: 0.7612 (mt0) cc_final: 0.7409 (mt0) REVERT: C 646 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7569 (tmt170) REVERT: C 740 MET cc_start: 0.8288 (ttp) cc_final: 0.7868 (ttm) REVERT: C 780 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: C 794 ILE cc_start: 0.6998 (mt) cc_final: 0.6760 (mp) REVERT: C 796 ASP cc_start: 0.6678 (t0) cc_final: 0.6081 (p0) REVERT: C 931 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 1002 GLN cc_start: 0.8291 (tt0) cc_final: 0.7951 (tp-100) REVERT: C 1019 ARG cc_start: 0.8382 (ttt180) cc_final: 0.8005 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8701 (mttt) cc_final: 0.8115 (tmmt) REVERT: C 1113 GLN cc_start: 0.8518 (mt0) cc_final: 0.8053 (mm110) REVERT: j 3 GLN cc_start: 0.7902 (tt0) cc_final: 0.7539 (tp40) REVERT: g 33 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8083 (m110) REVERT: g 47 LYS cc_start: 0.7259 (tttt) cc_final: 0.6522 (mtmm) REVERT: g 49 MET cc_start: 0.7511 (mmp) cc_final: 0.7096 (mmp) REVERT: g 203 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.5860 (tm130) REVERT: l 87 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6289 (mtm180) REVERT: l 215 ASP cc_start: 0.6010 (t0) cc_final: 0.5591 (m-30) outliers start: 81 outliers final: 38 residues processed: 461 average time/residue: 2.2317 time to fit residues: 1277.4537 Evaluate side-chains 420 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 369 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain i residue 214 ASN Chi-restraints excluded: chain j residue 106 LEU Chi-restraints excluded: chain g residue 33 ASN Chi-restraints excluded: chain g residue 62 ASN Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 203 GLN Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 145 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 200 VAL Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 0.9980 chunk 307 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 410 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 chunk 214 optimal weight: 40.0000 chunk 389 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 196 ASN A1002 GLN A1005 GLN B 123 ASN B 474 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 935 GLN B1002 GLN B1005 GLN C 89 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 779 GLN C1002 GLN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 206 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35944 Z= 0.237 Angle : 0.577 12.009 48911 Z= 0.309 Chirality : 0.044 0.178 5529 Planarity : 0.004 0.058 6330 Dihedral : 5.863 67.447 4901 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.00 % Allowed : 10.96 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % 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: -0.15 (0.12), residues: 4515 helix: 0.88 (0.19), residues: 717 sheet: 0.28 (0.13), residues: 1467 loop : -0.61 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 161 HIS 0.005 0.001 HIS B 519 PHE 0.026 0.001 PHE k 120 TYR 0.021 0.001 TYR i 51 ARG 0.008 0.000 ARG i 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 378 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7854 (m) REVERT: A 92 VAL cc_start: 0.7790 (t) cc_final: 0.7392 (p) REVERT: A 155 MET cc_start: 0.0817 (pmm) cc_final: 0.0225 (pmm) REVERT: A 206 LYS cc_start: 0.7693 (tttt) cc_final: 0.6942 (tptt) REVERT: A 224 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6639 (mp0) REVERT: A 319 ARG cc_start: 0.7711 (ptm160) cc_final: 0.7418 (ttm110) REVERT: A 646 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7709 (mtm180) REVERT: A 661 GLU cc_start: 0.8132 (tt0) cc_final: 0.7763 (pm20) REVERT: A 697 MET cc_start: 0.8797 (ptm) cc_final: 0.8471 (ptm) REVERT: A 764 ASN cc_start: 0.8749 (m-40) cc_final: 0.8238 (m110) REVERT: A 773 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7408 (tt0) REVERT: A 796 ASP cc_start: 0.6809 (p0) cc_final: 0.6452 (t0) REVERT: A 814 LYS cc_start: 0.7603 (mttt) cc_final: 0.7113 (mtmt) REVERT: A 868 GLU cc_start: 0.8236 (tt0) cc_final: 0.7926 (tt0) REVERT: A 957 GLN cc_start: 0.8268 (tt0) cc_final: 0.7998 (tp-100) REVERT: A 1038 LYS cc_start: 0.7914 (mttt) cc_final: 0.7591 (mppt) REVERT: A 1045 LYS cc_start: 0.8399 (mttt) cc_final: 0.8144 (ttpt) REVERT: A 1100 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7239 (p) REVERT: B 177 MET cc_start: -0.0592 (ttm) cc_final: -0.1360 (tpp) REVERT: B 613 GLN cc_start: 0.8214 (mt0) cc_final: 0.7873 (mt0) REVERT: B 646 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7404 (mtp180) REVERT: B 755 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: B 773 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: B 804 GLN cc_start: 0.8288 (mt0) cc_final: 0.7954 (mm110) REVERT: B 855 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5511 (t80) REVERT: B 868 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7243 (pt0) REVERT: B 936 ASP cc_start: 0.7640 (m-30) cc_final: 0.7438 (m-30) REVERT: B 995 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7856 (mtp180) REVERT: B 1038 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8004 (mmtp) REVERT: B 1045 LYS cc_start: 0.8550 (mttt) cc_final: 0.8105 (ttpt) REVERT: B 1073 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7928 (mmtp) REVERT: C 43 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7768 (mtpp) REVERT: C 177 MET cc_start: 0.1691 (mtp) cc_final: 0.1084 (mtp) REVERT: C 206 LYS cc_start: 0.7612 (tttt) cc_final: 0.7262 (tttp) REVERT: C 427 ASP cc_start: 0.7833 (m-30) cc_final: 0.7258 (p0) REVERT: C 498 GLN cc_start: 0.7563 (mt0) cc_final: 0.7334 (mt0) REVERT: C 646 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7556 (tmt170) REVERT: C 735 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7905 (p) REVERT: C 740 MET cc_start: 0.8229 (ttp) cc_final: 0.7898 (ttm) REVERT: C 780 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: C 794 ILE cc_start: 0.7038 (mt) cc_final: 0.6829 (mp) REVERT: C 796 ASP cc_start: 0.6687 (t0) cc_final: 0.6080 (p0) REVERT: C 931 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 986 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6925 (mmpt) REVERT: C 1002 GLN cc_start: 0.8275 (tt0) cc_final: 0.7960 (tp-100) REVERT: C 1019 ARG cc_start: 0.8353 (ttt180) cc_final: 0.8016 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8702 (mttt) cc_final: 0.8138 (tmmt) REVERT: C 1113 GLN cc_start: 0.8532 (mt0) cc_final: 0.8016 (mm110) REVERT: j 3 GLN cc_start: 0.8021 (tt0) cc_final: 0.7480 (tp-100) REVERT: j 16 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7432 (mmp80) REVERT: g 33 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8063 (m110) REVERT: g 47 LYS cc_start: 0.7179 (tttt) cc_final: 0.6434 (mtmm) REVERT: l 87 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6307 (mtm180) REVERT: l 183 TYR cc_start: 0.7419 (m-80) cc_final: 0.7149 (m-80) REVERT: l 215 ASP cc_start: 0.5964 (t0) cc_final: 0.5507 (m-30) outliers start: 79 outliers final: 42 residues processed: 432 average time/residue: 2.2858 time to fit residues: 1227.2729 Evaluate side-chains 413 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 358 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 986 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 214 ASN Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 106 LEU Chi-restraints excluded: chain g residue 33 ASN Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 145 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 54 ASP Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 323 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 390 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 580 GLN A 641 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN B1005 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 779 GLN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35944 Z= 0.296 Angle : 0.581 11.251 48911 Z= 0.311 Chirality : 0.044 0.182 5529 Planarity : 0.004 0.054 6330 Dihedral : 5.685 63.863 4901 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 11.64 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.12), residues: 4515 helix: 1.02 (0.19), residues: 705 sheet: 0.22 (0.13), residues: 1463 loop : -0.59 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 161 HIS 0.005 0.001 HIS B 655 PHE 0.029 0.002 PHE k 120 TYR 0.021 0.002 TYR C1067 ARG 0.006 0.000 ARG i 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 381 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7866 (m) REVERT: A 92 VAL cc_start: 0.7774 (t) cc_final: 0.7368 (p) REVERT: A 224 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6710 (mp0) REVERT: A 319 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7403 (ttm110) REVERT: A 349 SER cc_start: 0.7737 (OUTLIER) cc_final: 0.7321 (p) REVERT: A 646 ARG cc_start: 0.8364 (mtt90) cc_final: 0.7711 (mtm180) REVERT: A 661 GLU cc_start: 0.8129 (tt0) cc_final: 0.7774 (pm20) REVERT: A 697 MET cc_start: 0.8801 (ptm) cc_final: 0.8464 (ptm) REVERT: A 764 ASN cc_start: 0.8608 (m-40) cc_final: 0.8326 (m-40) REVERT: A 773 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7473 (tt0) REVERT: A 796 ASP cc_start: 0.6739 (p0) cc_final: 0.6403 (t0) REVERT: A 814 LYS cc_start: 0.7581 (mttt) cc_final: 0.7094 (mtmt) REVERT: A 868 GLU cc_start: 0.8243 (tt0) cc_final: 0.7943 (tt0) REVERT: A 957 GLN cc_start: 0.8296 (tt0) cc_final: 0.8013 (tp-100) REVERT: A 1038 LYS cc_start: 0.7923 (mttt) cc_final: 0.7524 (mmtp) REVERT: A 1045 LYS cc_start: 0.8402 (mttt) cc_final: 0.8161 (ttpt) REVERT: A 1100 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7286 (p) REVERT: B 177 MET cc_start: -0.0643 (ttm) cc_final: -0.1386 (tpp) REVERT: B 472 ILE cc_start: 0.6932 (pp) cc_final: 0.6659 (mp) REVERT: B 613 GLN cc_start: 0.8247 (mt0) cc_final: 0.7882 (mt0) REVERT: B 646 ARG cc_start: 0.7986 (mtt180) cc_final: 0.7505 (mpp-170) REVERT: B 755 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: B 773 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 804 GLN cc_start: 0.8296 (mt0) cc_final: 0.7980 (mm110) REVERT: B 855 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5577 (t80) REVERT: B 868 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7220 (pt0) REVERT: B 936 ASP cc_start: 0.7642 (m-30) cc_final: 0.7432 (m-30) REVERT: B 995 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7865 (mtp180) REVERT: B 1038 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7998 (mmtp) REVERT: B 1045 LYS cc_start: 0.8602 (mttt) cc_final: 0.8130 (ttpt) REVERT: B 1073 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7879 (mmtp) REVERT: C 43 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7782 (mtpp) REVERT: C 177 MET cc_start: 0.1722 (mtp) cc_final: 0.1124 (mtp) REVERT: C 206 LYS cc_start: 0.7560 (tttt) cc_final: 0.7245 (tttp) REVERT: C 646 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7553 (tmt170) REVERT: C 735 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7905 (p) REVERT: C 740 MET cc_start: 0.8230 (ttt) cc_final: 0.7896 (ttm) REVERT: C 780 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: C 794 ILE cc_start: 0.7034 (mt) cc_final: 0.6813 (mp) REVERT: C 796 ASP cc_start: 0.6691 (t0) cc_final: 0.6087 (p0) REVERT: C 931 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (mp) REVERT: C 1002 GLN cc_start: 0.8256 (tt0) cc_final: 0.7928 (tp-100) REVERT: C 1019 ARG cc_start: 0.8362 (ttt180) cc_final: 0.8015 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8715 (mttt) cc_final: 0.8164 (tmmt) REVERT: C 1113 GLN cc_start: 0.8571 (mt0) cc_final: 0.8029 (mm110) REVERT: j 3 GLN cc_start: 0.8053 (tt0) cc_final: 0.7539 (tp-100) REVERT: g 47 LYS cc_start: 0.7221 (tttt) cc_final: 0.6446 (mtmm) REVERT: g 55 LYS cc_start: 0.7372 (mtpp) cc_final: 0.7037 (mtpp) REVERT: l 87 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6288 (mtm180) REVERT: l 215 ASP cc_start: 0.5964 (t0) cc_final: 0.5492 (m-30) outliers start: 80 outliers final: 49 residues processed: 436 average time/residue: 2.2826 time to fit residues: 1239.1901 Evaluate side-chains 423 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 361 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain i residue 214 ASN Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 106 LEU Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 145 LEU Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 200 VAL Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 1.9990 chunk 391 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 435 optimal weight: 2.9990 chunk 361 optimal weight: 30.0000 chunk 201 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 228 optimal weight: 30.0000 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN B1005 GLN C 123 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1005 GLN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35944 Z= 0.190 Angle : 0.540 10.571 48911 Z= 0.288 Chirality : 0.043 0.205 5529 Planarity : 0.004 0.052 6330 Dihedral : 5.453 60.156 4901 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.83 % Allowed : 12.02 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.02 (0.12), residues: 4515 helix: 1.28 (0.20), residues: 705 sheet: 0.29 (0.13), residues: 1470 loop : -0.52 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 161 HIS 0.003 0.001 HIS B 655 PHE 0.025 0.001 PHE k 120 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG i 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 374 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (m) REVERT: A 92 VAL cc_start: 0.7789 (t) cc_final: 0.7372 (p) REVERT: A 224 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6706 (mp0) REVERT: A 319 ARG cc_start: 0.7767 (ptm160) cc_final: 0.7394 (ttm110) REVERT: A 349 SER cc_start: 0.7686 (OUTLIER) cc_final: 0.7269 (p) REVERT: A 646 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7696 (mtm180) REVERT: A 661 GLU cc_start: 0.8115 (tt0) cc_final: 0.7751 (pm20) REVERT: A 697 MET cc_start: 0.8794 (ptm) cc_final: 0.8560 (ptm) REVERT: A 762 GLN cc_start: 0.8365 (mt0) cc_final: 0.8149 (mt0) REVERT: A 773 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7460 (tt0) REVERT: A 796 ASP cc_start: 0.6701 (p0) cc_final: 0.6370 (t0) REVERT: A 814 LYS cc_start: 0.7571 (mttt) cc_final: 0.7093 (mtmt) REVERT: A 868 GLU cc_start: 0.8175 (tt0) cc_final: 0.7888 (tt0) REVERT: A 957 GLN cc_start: 0.8211 (tt0) cc_final: 0.7934 (tp-100) REVERT: A 1038 LYS cc_start: 0.7912 (mttt) cc_final: 0.7534 (mmtp) REVERT: A 1045 LYS cc_start: 0.8382 (mttt) cc_final: 0.8162 (ttpt) REVERT: A 1100 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7220 (p) REVERT: B 48 SER cc_start: 0.7451 (m) cc_final: 0.7143 (p) REVERT: B 177 MET cc_start: -0.0682 (ttm) cc_final: -0.1423 (tpp) REVERT: B 542 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6800 (p0) REVERT: B 613 GLN cc_start: 0.8231 (mt0) cc_final: 0.7923 (mt0) REVERT: B 646 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7500 (mpp-170) REVERT: B 804 GLN cc_start: 0.8253 (mt0) cc_final: 0.7972 (mm110) REVERT: B 855 PHE cc_start: 0.5935 (OUTLIER) cc_final: 0.5534 (t80) REVERT: B 868 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7190 (pt0) REVERT: B 936 ASP cc_start: 0.7662 (m-30) cc_final: 0.7457 (m-30) REVERT: B 1038 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8107 (mppt) REVERT: B 1045 LYS cc_start: 0.8607 (mttt) cc_final: 0.8174 (ttpt) REVERT: B 1073 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7892 (mmtp) REVERT: C 43 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7784 (mtpp) REVERT: C 206 LYS cc_start: 0.7498 (tttt) cc_final: 0.7224 (tttp) REVERT: C 427 ASP cc_start: 0.7943 (m-30) cc_final: 0.7215 (p0) REVERT: C 646 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7556 (tmt170) REVERT: C 735 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7912 (p) REVERT: C 740 MET cc_start: 0.8193 (ttt) cc_final: 0.7908 (ttm) REVERT: C 794 ILE cc_start: 0.7123 (mt) cc_final: 0.6888 (mp) REVERT: C 796 ASP cc_start: 0.6681 (t0) cc_final: 0.6092 (p0) REVERT: C 931 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 1002 GLN cc_start: 0.8284 (tt0) cc_final: 0.7972 (tp-100) REVERT: C 1019 ARG cc_start: 0.8380 (ttt180) cc_final: 0.8015 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8687 (mttt) cc_final: 0.8146 (tmmt) REVERT: C 1113 GLN cc_start: 0.8539 (mt0) cc_final: 0.8042 (mm110) REVERT: j 3 GLN cc_start: 0.8074 (tt0) cc_final: 0.7519 (tp-100) REVERT: g 47 LYS cc_start: 0.7210 (tttt) cc_final: 0.6416 (mtmm) REVERT: g 55 LYS cc_start: 0.7362 (mtpp) cc_final: 0.7049 (mtpp) REVERT: g 83 GLU cc_start: 0.7723 (mp0) cc_final: 0.7451 (pp20) REVERT: l 87 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6433 (mtm180) REVERT: l 215 ASP cc_start: 0.6093 (t0) cc_final: 0.5498 (m-30) outliers start: 72 outliers final: 38 residues processed: 423 average time/residue: 2.2989 time to fit residues: 1216.9792 Evaluate side-chains 399 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 351 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 214 ASN Chi-restraints excluded: chain j residue 106 LEU Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 200 VAL Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 366 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 433 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1005 GLN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35944 Z= 0.273 Angle : 0.557 11.033 48911 Z= 0.297 Chirality : 0.044 0.215 5529 Planarity : 0.004 0.073 6330 Dihedral : 5.385 59.375 4901 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.93 % Allowed : 12.48 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.04 (0.12), residues: 4515 helix: 1.26 (0.20), residues: 706 sheet: 0.24 (0.13), residues: 1467 loop : -0.55 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 161 HIS 0.004 0.001 HIS B 655 PHE 0.040 0.002 PHE l 153 TYR 0.020 0.002 TYR C1067 ARG 0.009 0.000 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 366 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 92 VAL cc_start: 0.7809 (t) cc_final: 0.7396 (p) REVERT: A 196 ASN cc_start: 0.7140 (t0) cc_final: 0.6811 (t0) REVERT: A 224 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6705 (mp0) REVERT: A 319 ARG cc_start: 0.7759 (ptm160) cc_final: 0.7362 (ttm110) REVERT: A 349 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7323 (p) REVERT: A 646 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7702 (mtm180) REVERT: A 661 GLU cc_start: 0.8129 (tt0) cc_final: 0.7759 (pm20) REVERT: A 697 MET cc_start: 0.8804 (ptm) cc_final: 0.8567 (ptm) REVERT: A 773 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7459 (tt0) REVERT: A 796 ASP cc_start: 0.6672 (p0) cc_final: 0.6343 (t0) REVERT: A 814 LYS cc_start: 0.7588 (mttt) cc_final: 0.7107 (mtmt) REVERT: A 824 ASN cc_start: 0.8029 (m-40) cc_final: 0.7603 (m110) REVERT: A 868 GLU cc_start: 0.8199 (tt0) cc_final: 0.7900 (tt0) REVERT: A 957 GLN cc_start: 0.8292 (tt0) cc_final: 0.8023 (tp-100) REVERT: A 1038 LYS cc_start: 0.7949 (mttt) cc_final: 0.7641 (mppt) REVERT: A 1045 LYS cc_start: 0.8393 (mttt) cc_final: 0.8167 (ttpt) REVERT: A 1100 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7267 (p) REVERT: B 48 SER cc_start: 0.7439 (m) cc_final: 0.7142 (p) REVERT: B 177 MET cc_start: -0.0606 (ttm) cc_final: -0.1379 (tpp) REVERT: B 542 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6818 (p0) REVERT: B 613 GLN cc_start: 0.8237 (mt0) cc_final: 0.7838 (mt0) REVERT: B 646 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7517 (mpp-170) REVERT: B 773 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: B 804 GLN cc_start: 0.8253 (mt0) cc_final: 0.7972 (mm110) REVERT: B 855 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.5576 (t80) REVERT: B 868 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7137 (pt0) REVERT: B 936 ASP cc_start: 0.7646 (m-30) cc_final: 0.7426 (m-30) REVERT: B 1038 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8105 (mppt) REVERT: B 1045 LYS cc_start: 0.8598 (mttt) cc_final: 0.8150 (ttpt) REVERT: B 1073 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7917 (mmtp) REVERT: C 43 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7778 (mtpp) REVERT: C 177 MET cc_start: 0.1298 (mtp) cc_final: 0.0465 (mtp) REVERT: C 206 LYS cc_start: 0.7463 (tttt) cc_final: 0.7188 (tttp) REVERT: C 586 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6849 (t0) REVERT: C 646 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7562 (tmt170) REVERT: C 735 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7886 (p) REVERT: C 740 MET cc_start: 0.8193 (ttt) cc_final: 0.7903 (ttm) REVERT: C 794 ILE cc_start: 0.7132 (mt) cc_final: 0.6894 (mp) REVERT: C 796 ASP cc_start: 0.6710 (t0) cc_final: 0.6122 (p0) REVERT: C 931 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 1002 GLN cc_start: 0.8300 (tt0) cc_final: 0.7972 (tp-100) REVERT: C 1019 ARG cc_start: 0.8389 (ttt180) cc_final: 0.8030 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8708 (mttt) cc_final: 0.8172 (tmmt) REVERT: C 1092 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: j 3 GLN cc_start: 0.8079 (tt0) cc_final: 0.7539 (tp-100) REVERT: g 33 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8123 (m110) REVERT: g 47 LYS cc_start: 0.7233 (tttt) cc_final: 0.6450 (mtmm) REVERT: g 55 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7189 (mtpp) REVERT: l 87 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6540 (mtm180) REVERT: l 215 ASP cc_start: 0.6083 (t0) cc_final: 0.5449 (m-30) outliers start: 76 outliers final: 45 residues processed: 422 average time/residue: 2.2955 time to fit residues: 1198.8009 Evaluate side-chains 411 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 352 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 106 LEU Chi-restraints excluded: chain g residue 33 ASN Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain k residue 90 CYS Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain k residue 200 VAL Chi-restraints excluded: chain l residue 69 THR Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 130 optimal weight: 50.0000 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 chunk 214 optimal weight: 50.0000 chunk 40 optimal weight: 0.0040 chunk 340 optimal weight: 30.0000 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 914 ASN A1002 GLN A1005 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN B1005 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1005 GLN C1113 GLN ** i 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 141 ASN j 171 HIS ** k 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35944 Z= 0.200 Angle : 0.528 9.663 48911 Z= 0.280 Chirality : 0.043 0.182 5529 Planarity : 0.004 0.049 6330 Dihedral : 5.193 59.793 4901 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.78 % Allowed : 12.68 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.10 (0.12), residues: 4515 helix: 1.50 (0.20), residues: 699 sheet: 0.30 (0.13), residues: 1455 loop : -0.47 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP l 161 HIS 0.003 0.001 HIS B 655 PHE 0.033 0.001 PHE l 153 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG i 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 370 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7809 (m) REVERT: A 92 VAL cc_start: 0.7798 (t) cc_final: 0.7384 (p) REVERT: A 196 ASN cc_start: 0.7262 (t0) cc_final: 0.7021 (t0) REVERT: A 224 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6710 (mp0) REVERT: A 319 ARG cc_start: 0.7703 (ptm160) cc_final: 0.7291 (ttp-110) REVERT: A 349 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7279 (p) REVERT: A 646 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7692 (mtm180) REVERT: A 661 GLU cc_start: 0.8122 (tt0) cc_final: 0.7760 (pm20) REVERT: A 697 MET cc_start: 0.8797 (ptm) cc_final: 0.8552 (ptm) REVERT: A 764 ASN cc_start: 0.8707 (m-40) cc_final: 0.8241 (m110) REVERT: A 773 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7456 (tt0) REVERT: A 796 ASP cc_start: 0.6687 (p0) cc_final: 0.6350 (t0) REVERT: A 814 LYS cc_start: 0.7504 (mttt) cc_final: 0.7068 (mtmt) REVERT: A 824 ASN cc_start: 0.8010 (m-40) cc_final: 0.7630 (m110) REVERT: A 868 GLU cc_start: 0.8163 (tt0) cc_final: 0.7882 (tt0) REVERT: A 957 GLN cc_start: 0.8211 (tt0) cc_final: 0.7942 (tp-100) REVERT: A 1038 LYS cc_start: 0.7932 (mttt) cc_final: 0.7555 (mmtp) REVERT: A 1045 LYS cc_start: 0.8365 (mttt) cc_final: 0.8162 (ttpt) REVERT: A 1100 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.7199 (p) REVERT: B 48 SER cc_start: 0.7381 (m) cc_final: 0.7091 (p) REVERT: B 177 MET cc_start: -0.0547 (ttm) cc_final: -0.1267 (tpp) REVERT: B 542 ASN cc_start: 0.7055 (OUTLIER) cc_final: 0.6762 (p0) REVERT: B 613 GLN cc_start: 0.8195 (mt0) cc_final: 0.7866 (mt0) REVERT: B 646 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7545 (mpp-170) REVERT: B 804 GLN cc_start: 0.8187 (mt0) cc_final: 0.7916 (mm110) REVERT: B 855 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.5551 (t80) REVERT: B 868 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7101 (pt0) REVERT: B 1038 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8013 (mmtp) REVERT: B 1045 LYS cc_start: 0.8595 (mttt) cc_final: 0.8164 (ttpt) REVERT: B 1073 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7892 (mmtp) REVERT: C 43 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7794 (mtpp) REVERT: C 177 MET cc_start: 0.1495 (mtp) cc_final: 0.0521 (mtp) REVERT: C 206 LYS cc_start: 0.7432 (tttt) cc_final: 0.7160 (tttp) REVERT: C 427 ASP cc_start: 0.8086 (m-30) cc_final: 0.7277 (p0) REVERT: C 646 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7564 (tmt170) REVERT: C 735 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 740 MET cc_start: 0.8180 (ttt) cc_final: 0.7893 (ttm) REVERT: C 794 ILE cc_start: 0.7112 (mt) cc_final: 0.6870 (mp) REVERT: C 796 ASP cc_start: 0.6692 (t0) cc_final: 0.6112 (p0) REVERT: C 931 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 1002 GLN cc_start: 0.8281 (tt0) cc_final: 0.7972 (tp-100) REVERT: C 1019 ARG cc_start: 0.8390 (ttt180) cc_final: 0.8020 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8686 (mttt) cc_final: 0.8168 (tmmt) REVERT: C 1092 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: j 3 GLN cc_start: 0.8084 (tt0) cc_final: 0.7565 (tp-100) REVERT: j 16 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7407 (mmp80) REVERT: g 47 LYS cc_start: 0.7239 (tttt) cc_final: 0.6473 (mtmm) REVERT: h 73 ASP cc_start: 0.8008 (t0) cc_final: 0.7783 (t0) REVERT: l 87 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6562 (mtm180) REVERT: l 215 ASP cc_start: 0.6151 (t0) cc_final: 0.5504 (m-30) outliers start: 70 outliers final: 44 residues processed: 420 average time/residue: 2.2989 time to fit residues: 1198.9578 Evaluate side-chains 405 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 350 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain j residue 106 LEU Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain k residue 90 CYS Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 87 ARG Chi-restraints excluded: chain l residue 153 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 3.9990 chunk 415 optimal weight: 3.9990 chunk 379 optimal weight: 20.0000 chunk 404 optimal weight: 0.0070 chunk 243 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 317 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 365 optimal weight: 0.9990 chunk 382 optimal weight: 7.9990 chunk 402 optimal weight: 3.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A1005 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1005 GLN i 81 GLN j 171 HIS k 142 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35944 Z= 0.200 Angle : 0.522 9.847 48911 Z= 0.276 Chirality : 0.043 0.168 5529 Planarity : 0.004 0.068 6330 Dihedral : 5.073 59.473 4901 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.67 % Allowed : 13.17 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.14 (0.12), residues: 4515 helix: 1.53 (0.20), residues: 711 sheet: 0.31 (0.13), residues: 1464 loop : -0.45 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP l 161 HIS 0.003 0.001 HIS B 655 PHE 0.025 0.001 PHE l 153 TYR 0.018 0.001 TYR B 904 ARG 0.013 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 363 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7807 (m) REVERT: A 92 VAL cc_start: 0.7794 (t) cc_final: 0.7373 (p) REVERT: A 224 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6730 (mp0) REVERT: A 319 ARG cc_start: 0.7669 (ptm160) cc_final: 0.7260 (ttp-110) REVERT: A 349 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7273 (p) REVERT: A 646 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7697 (mtm180) REVERT: A 661 GLU cc_start: 0.8125 (tt0) cc_final: 0.7759 (pm20) REVERT: A 697 MET cc_start: 0.8796 (ptm) cc_final: 0.8554 (ptm) REVERT: A 764 ASN cc_start: 0.8724 (m-40) cc_final: 0.8263 (m110) REVERT: A 773 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7483 (tt0) REVERT: A 796 ASP cc_start: 0.6695 (p0) cc_final: 0.6358 (t0) REVERT: A 814 LYS cc_start: 0.7508 (mttt) cc_final: 0.7074 (mtmt) REVERT: A 824 ASN cc_start: 0.7985 (m-40) cc_final: 0.7596 (m110) REVERT: A 868 GLU cc_start: 0.8154 (tt0) cc_final: 0.7855 (tt0) REVERT: A 957 GLN cc_start: 0.8193 (tt0) cc_final: 0.7927 (tp-100) REVERT: A 1038 LYS cc_start: 0.7927 (mttt) cc_final: 0.7548 (mmtp) REVERT: A 1100 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7215 (p) REVERT: B 48 SER cc_start: 0.7392 (m) cc_final: 0.7104 (p) REVERT: B 177 MET cc_start: -0.0587 (ttm) cc_final: -0.1078 (tpp) REVERT: B 542 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6830 (p0) REVERT: B 613 GLN cc_start: 0.8196 (mt0) cc_final: 0.7864 (mt0) REVERT: B 646 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7548 (mpp-170) REVERT: B 804 GLN cc_start: 0.8176 (mt0) cc_final: 0.7898 (mm110) REVERT: B 855 PHE cc_start: 0.5950 (OUTLIER) cc_final: 0.5555 (t80) REVERT: B 868 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7098 (pt0) REVERT: B 1038 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8034 (mmtp) REVERT: B 1045 LYS cc_start: 0.8605 (mttt) cc_final: 0.8172 (ttpt) REVERT: B 1073 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7905 (mmtp) REVERT: C 43 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: C 177 MET cc_start: 0.1442 (mtp) cc_final: 0.0579 (mtp) REVERT: C 206 LYS cc_start: 0.7384 (tttt) cc_final: 0.7118 (tttp) REVERT: C 427 ASP cc_start: 0.8058 (m-30) cc_final: 0.7205 (p0) REVERT: C 586 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6742 (t0) REVERT: C 646 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7570 (tmt170) REVERT: C 735 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7889 (p) REVERT: C 740 MET cc_start: 0.8167 (ttt) cc_final: 0.7894 (ttm) REVERT: C 780 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: C 794 ILE cc_start: 0.7096 (mt) cc_final: 0.6851 (mp) REVERT: C 796 ASP cc_start: 0.6693 (t0) cc_final: 0.6109 (p0) REVERT: C 931 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 1002 GLN cc_start: 0.8255 (tt0) cc_final: 0.7973 (tp-100) REVERT: C 1019 ARG cc_start: 0.8358 (ttt180) cc_final: 0.8007 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8676 (mttt) cc_final: 0.8150 (tmmt) REVERT: C 1092 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: j 3 GLN cc_start: 0.8090 (tt0) cc_final: 0.7536 (tp-100) REVERT: j 16 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7477 (mmp80) REVERT: g 47 LYS cc_start: 0.7256 (tttt) cc_final: 0.6454 (mtmm) REVERT: h 73 ASP cc_start: 0.7988 (t0) cc_final: 0.7777 (t0) REVERT: h 215 ASP cc_start: 0.6240 (m-30) cc_final: 0.5801 (t0) REVERT: l 87 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6544 (mtm180) REVERT: l 215 ASP cc_start: 0.6156 (t0) cc_final: 0.5461 (m-30) outliers start: 66 outliers final: 40 residues processed: 412 average time/residue: 2.2652 time to fit residues: 1161.8679 Evaluate side-chains 406 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 353 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 145 LEU Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain k residue 90 CYS Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 54 ASP Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 0.9990 chunk 427 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 297 optimal weight: 0.9980 chunk 448 optimal weight: 20.0000 chunk 412 optimal weight: 0.6980 chunk 356 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A1005 GLN A1106 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1005 GLN k 142 ASN l 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35944 Z= 0.245 Angle : 0.536 9.889 48911 Z= 0.284 Chirality : 0.043 0.173 5529 Planarity : 0.004 0.048 6330 Dihedral : 5.070 59.949 4901 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.52 % Allowed : 13.50 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.11 (0.12), residues: 4515 helix: 1.49 (0.20), residues: 712 sheet: 0.30 (0.13), residues: 1450 loop : -0.46 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP l 161 HIS 0.004 0.001 HIS B 655 PHE 0.024 0.002 PHE B 898 TYR 0.019 0.001 TYR C1067 ARG 0.011 0.000 ARG k 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9030 Ramachandran restraints generated. 4515 Oldfield, 0 Emsley, 4515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7815 (m) REVERT: A 92 VAL cc_start: 0.7801 (t) cc_final: 0.7445 (p) REVERT: A 155 MET cc_start: 0.0795 (pmm) cc_final: 0.0289 (pmt) REVERT: A 224 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6706 (mp0) REVERT: A 319 ARG cc_start: 0.7590 (ptm160) cc_final: 0.7252 (ttp-110) REVERT: A 349 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.7317 (p) REVERT: A 646 ARG cc_start: 0.8398 (mtt90) cc_final: 0.7708 (mtm180) REVERT: A 661 GLU cc_start: 0.8131 (tt0) cc_final: 0.7761 (pm20) REVERT: A 697 MET cc_start: 0.8799 (ptm) cc_final: 0.8559 (ptm) REVERT: A 764 ASN cc_start: 0.8768 (m-40) cc_final: 0.8317 (m110) REVERT: A 773 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7476 (tt0) REVERT: A 796 ASP cc_start: 0.6668 (p0) cc_final: 0.6350 (t0) REVERT: A 814 LYS cc_start: 0.7518 (mttt) cc_final: 0.7086 (mtmt) REVERT: A 824 ASN cc_start: 0.8012 (m-40) cc_final: 0.7622 (m110) REVERT: A 868 GLU cc_start: 0.8178 (tt0) cc_final: 0.7891 (tt0) REVERT: A 957 GLN cc_start: 0.8276 (tt0) cc_final: 0.7998 (tp-100) REVERT: A 1038 LYS cc_start: 0.7904 (mttt) cc_final: 0.7542 (mmtp) REVERT: A 1100 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7205 (p) REVERT: B 48 SER cc_start: 0.7400 (m) cc_final: 0.7111 (p) REVERT: B 177 MET cc_start: -0.0596 (ttm) cc_final: -0.1106 (tpp) REVERT: B 542 ASN cc_start: 0.7118 (OUTLIER) cc_final: 0.6813 (p0) REVERT: B 646 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7561 (mpp-170) REVERT: B 804 GLN cc_start: 0.8183 (mt0) cc_final: 0.7912 (mm110) REVERT: B 855 PHE cc_start: 0.5954 (OUTLIER) cc_final: 0.5580 (t80) REVERT: B 868 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7109 (pt0) REVERT: B 1038 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8044 (mmtp) REVERT: B 1045 LYS cc_start: 0.8601 (mttt) cc_final: 0.8170 (ttpt) REVERT: B 1073 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7898 (mmtp) REVERT: C 43 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7771 (mtpp) REVERT: C 177 MET cc_start: 0.1401 (mtp) cc_final: 0.0496 (mtp) REVERT: C 206 LYS cc_start: 0.7401 (tttt) cc_final: 0.7127 (tttp) REVERT: C 269 TYR cc_start: 0.6860 (m-80) cc_final: 0.6629 (m-80) REVERT: C 271 GLN cc_start: 0.7999 (mp10) cc_final: 0.7636 (mp10) REVERT: C 586 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6704 (t0) REVERT: C 646 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7579 (tmt170) REVERT: C 735 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7881 (p) REVERT: C 740 MET cc_start: 0.8190 (ttt) cc_final: 0.7911 (ttm) REVERT: C 780 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: C 794 ILE cc_start: 0.7095 (mt) cc_final: 0.6845 (mp) REVERT: C 796 ASP cc_start: 0.6701 (t0) cc_final: 0.6104 (p0) REVERT: C 931 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8347 (mp) REVERT: C 1002 GLN cc_start: 0.8263 (tt0) cc_final: 0.7965 (tp-100) REVERT: C 1019 ARG cc_start: 0.8377 (ttt180) cc_final: 0.8031 (ttp-110) REVERT: C 1045 LYS cc_start: 0.8690 (mttt) cc_final: 0.8173 (tmmt) REVERT: C 1092 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: j 3 GLN cc_start: 0.8089 (tt0) cc_final: 0.7545 (tp-100) REVERT: j 16 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7506 (mmp80) REVERT: g 47 LYS cc_start: 0.7275 (tttt) cc_final: 0.6465 (mtmm) REVERT: h 73 ASP cc_start: 0.7945 (t0) cc_final: 0.7717 (t0) REVERT: h 215 ASP cc_start: 0.6255 (m-30) cc_final: 0.5807 (t0) REVERT: l 87 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6662 (mtm180) REVERT: l 215 ASP cc_start: 0.6168 (t0) cc_final: 0.5464 (m-30) outliers start: 60 outliers final: 36 residues processed: 411 average time/residue: 2.3221 time to fit residues: 1195.5783 Evaluate side-chains 406 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 357 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 22 CYS Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain k residue 90 CYS Chi-restraints excluded: chain k residue 93 LEU Chi-restraints excluded: chain l residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 0.5980 chunk 380 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 367 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A1005 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C1005 GLN ** g 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 142 ASN l 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.195277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140640 restraints weight = 144376.634| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.07 r_work: 0.3544 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 35944 Z= 0.370 Angle : 0.589 10.091 48911 Z= 0.314 Chirality : 0.045 0.240 5529 Planarity : 0.004 0.060 6330 Dihedral : 5.248 59.202 4901 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.60 % Allowed : 13.55 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.13 (0.12), residues: 4515 helix: 1.17 (0.19), residues: 714 sheet: 0.18 (0.13), residues: 1458 loop : -0.61 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP l 161 HIS 0.005 0.001 HIS B1101 PHE 0.031 0.002 PHE B 898 TYR 0.023 0.002 TYR C1067 ARG 0.010 0.001 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21704.29 seconds wall clock time: 373 minutes 42.83 seconds (22422.83 seconds total)