Starting phenix.real_space_refine on Tue Mar 19 17:07:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk3_32557/03_2024/7wk3_32557.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk3_32557/03_2024/7wk3_32557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk3_32557/03_2024/7wk3_32557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk3_32557/03_2024/7wk3_32557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk3_32557/03_2024/7wk3_32557.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk3_32557/03_2024/7wk3_32557.pdb" } resolution = 3.4 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15874 2.51 5 N 4133 2.21 5 O 4684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24805 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Time building chain proxies: 13.06, per 1000 atoms: 0.53 Number of scatterers: 24805 At special positions: 0 Unit cell: (147.555, 144.276, 196.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4684 8.00 N 4133 7.00 C 15874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.53 Conformation dependent library (CDL) restraints added in 4.6 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 47 sheets defined 23.3% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.767A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.772A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 782 removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.932A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.685A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.078A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.768A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.229A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.912A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.783A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.983A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.861A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.536A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.187A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.734A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.693A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.704A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.621A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.722A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.683A 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 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.785A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.095A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 4.147A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.385A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.827A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.960A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 4.055A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.587A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.717A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.707A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.502A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.659A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.765A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.257A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.968A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.951A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.538A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.170A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.994A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.926A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.675A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.648A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.181A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.415A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.912A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.517A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.066A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.682A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.653A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.625A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.500A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.648A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.478A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.478A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.246A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 3.642A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.960A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.760A pdb=" N PHE C 186 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN C 188 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR C 208 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.688A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.540A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.019A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.527A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.108A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 359 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.868A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.235A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.814A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.814A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 968 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.55 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7967 1.35 - 1.46: 6235 1.46 - 1.58: 11038 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25384 Sorted by residual: bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.550 -0.216 2.34e-02 1.83e+03 8.53e+01 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.505 -0.171 2.34e-02 1.83e+03 5.35e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.497 -0.163 2.34e-02 1.83e+03 4.83e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.495 -0.161 2.34e-02 1.83e+03 4.76e+01 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.482 -0.148 2.34e-02 1.83e+03 4.01e+01 ... (remaining 25379 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.98: 776 106.98 - 113.76: 13790 113.76 - 120.54: 9683 120.54 - 127.31: 10033 127.31 - 134.09: 233 Bond angle restraints: 34515 Sorted by residual: angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 112.83 109.98 2.85 9.90e-01 1.02e+00 8.29e+00 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.01e+00 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 112.83 110.08 2.75 9.90e-01 1.02e+00 7.70e+00 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.45 113.82 -3.37 1.30e+00 5.92e-01 6.71e+00 ... (remaining 34510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 14828 15.83 - 31.66: 234 31.66 - 47.49: 81 47.49 - 63.32: 14 63.32 - 79.15: 1 Dihedral angle restraints: 15158 sinusoidal: 5944 harmonic: 9214 Sorted by residual: dihedral pdb=" CA LYS C 795 " pdb=" C LYS C 795 " pdb=" N TYR C 796 " pdb=" CA TYR C 796 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 0.00 21.91 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 795 " pdb=" C LYS A 795 " pdb=" N TYR A 796 " pdb=" CA TYR A 796 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2416 0.030 - 0.061: 991 0.061 - 0.091: 191 0.091 - 0.121: 270 0.121 - 0.152: 36 Chirality restraints: 3904 Sorted by residual: chirality pdb=" CA ILE C 410 " pdb=" N ILE C 410 " pdb=" C ILE C 410 " pdb=" CB ILE C 410 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 3901 not shown) Planarity restraints: 4462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 295 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 217 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 216 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 217 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " -0.023 5.00e-02 4.00e+02 ... (remaining 4459 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 184 2.58 - 3.16: 20884 3.16 - 3.74: 35661 3.74 - 4.32: 52838 4.32 - 4.90: 86686 Nonbonded interactions: 196253 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 1.998 2.440 nonbonded pdb=" O ASN A 978 " pdb=" OG SER A 982 " model vdw 2.013 2.440 nonbonded pdb=" OG SER B 813 " pdb=" OE2 GLU B 868 " model vdw 2.023 2.440 nonbonded pdb=" OH TYR A 674 " pdb=" OE1 GLN A 690 " model vdw 2.046 2.440 nonbonded pdb=" OG SER C 813 " pdb=" OE2 GLU C 868 " model vdw 2.061 2.440 ... (remaining 196248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.560 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 70.560 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 25384 Z= 0.245 Angle : 0.564 7.403 34515 Z= 0.352 Chirality : 0.043 0.152 3904 Planarity : 0.003 0.049 4462 Dihedral : 7.179 79.153 9105 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 3114 helix: -2.17 (0.16), residues: 646 sheet: -0.80 (0.16), residues: 670 loop : -1.39 (0.12), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.003 0.001 HIS C1048 PHE 0.018 0.001 PHE B 718 TYR 0.016 0.001 TYR C 707 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 791 time to evaluate : 2.541 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: A 34 ARG cc_start: 0.6932 (mtt-85) cc_final: 0.6374 (ttp80) REVERT: A 578 ASP cc_start: 0.2983 (t70) cc_final: 0.1219 (t0) REVERT: A 756 TYR cc_start: 0.6677 (m-80) cc_final: 0.6253 (m-80) REVERT: B 315 THR cc_start: 0.7102 (m) cc_final: 0.6523 (m) REVERT: B 535 LYS cc_start: 0.7362 (mttt) cc_final: 0.7151 (mttp) REVERT: B 537 LYS cc_start: 0.6839 (ttmt) cc_final: 0.6628 (mtpp) REVERT: B 581 THR cc_start: 0.4450 (p) cc_final: 0.2476 (m) REVERT: B 737 ASP cc_start: 0.6361 (t0) cc_final: 0.5845 (t0) REVERT: C 553 THR cc_start: 0.4797 (p) cc_final: 0.4313 (m) REVERT: C 737 ASP cc_start: 0.6897 (t0) cc_final: 0.6565 (t70) REVERT: C 800 PHE cc_start: 0.6037 (m-10) cc_final: 0.5823 (m-80) outliers start: 0 outliers final: 0 residues processed: 791 average time/residue: 0.4081 time to fit residues: 480.5816 Evaluate side-chains 529 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 949 GLN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1101 HIS C 30 ASN C 134 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 613 GLN C 641 ASN C 895 GLN C 901 GLN C 954 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1088 HIS C1113 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5996 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25384 Z= 0.345 Angle : 0.685 10.351 34515 Z= 0.363 Chirality : 0.048 0.234 3904 Planarity : 0.005 0.056 4462 Dihedral : 4.643 24.571 3391 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.49 % Allowed : 9.06 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.95 (0.13), residues: 3114 helix: 0.31 (0.20), residues: 659 sheet: -0.28 (0.17), residues: 640 loop : -1.12 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 436 HIS 0.014 0.002 HIS B 954 PHE 0.052 0.003 PHE A 92 TYR 0.036 0.002 TYR A 91 ARG 0.011 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 580 time to evaluate : 2.702 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: A 267 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7544 (t) REVERT: A 552 LEU cc_start: 0.7005 (mt) cc_final: 0.6769 (mp) REVERT: A 578 ASP cc_start: 0.4047 (t70) cc_final: 0.2909 (t0) REVERT: A 935 GLN cc_start: 0.8006 (pp30) cc_final: 0.7796 (tm-30) REVERT: A 1002 GLN cc_start: 0.6974 (tp40) cc_final: 0.6744 (tp40) REVERT: B 528 LYS cc_start: 0.6091 (ttpt) cc_final: 0.4328 (ttpp) REVERT: C 710 ASN cc_start: 0.7604 (p0) cc_final: 0.7355 (p0) REVERT: C 819 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6747 (mt-10) REVERT: C 947 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6802 (mttm) REVERT: C 970 PHE cc_start: 0.7548 (m-10) cc_final: 0.7332 (m-80) outliers start: 69 outliers final: 43 residues processed: 612 average time/residue: 0.3813 time to fit residues: 353.2874 Evaluate side-chains 525 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 480 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 285 optimal weight: 0.3980 chunk 308 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 283 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 229 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 690 GLN A 787 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 245 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 717 ASN B 901 GLN B 913 GLN C 52 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1119 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25384 Z= 0.207 Angle : 0.579 10.030 34515 Z= 0.302 Chirality : 0.044 0.181 3904 Planarity : 0.004 0.042 4462 Dihedral : 4.267 21.152 3391 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.71 % Allowed : 11.81 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.38 (0.14), residues: 3114 helix: 1.10 (0.20), residues: 651 sheet: 0.15 (0.18), residues: 629 loop : -0.92 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 64 HIS 0.006 0.001 HIS B 954 PHE 0.028 0.002 PHE B 342 TYR 0.023 0.001 TYR A 265 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 510 time to evaluate : 2.700 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: A 267 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7469 (t) REVERT: A 567 ARG cc_start: 0.6615 (ptp-110) cc_final: 0.6383 (ptp90) REVERT: A 578 ASP cc_start: 0.4002 (t70) cc_final: 0.2844 (t0) REVERT: A 935 GLN cc_start: 0.8026 (pp30) cc_final: 0.7778 (tm-30) REVERT: A 964 LYS cc_start: 0.7905 (mmmm) cc_final: 0.7647 (mmmm) REVERT: B 528 LYS cc_start: 0.5957 (ttpt) cc_final: 0.4870 (mmtp) REVERT: C 710 ASN cc_start: 0.7546 (p0) cc_final: 0.7332 (p0) REVERT: C 776 LYS cc_start: 0.8175 (tppp) cc_final: 0.7945 (tppp) REVERT: C 947 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6914 (mttm) outliers start: 75 outliers final: 44 residues processed: 546 average time/residue: 0.3985 time to fit residues: 330.1438 Evaluate side-chains 513 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 467 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 303 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 914 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 563 GLN B 580 GLN B 658 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25384 Z= 0.368 Angle : 0.653 9.973 34515 Z= 0.345 Chirality : 0.047 0.203 3904 Planarity : 0.004 0.060 4462 Dihedral : 4.675 24.399 3391 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.04 % Allowed : 11.52 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.39 (0.14), residues: 3114 helix: 1.10 (0.20), residues: 646 sheet: 0.21 (0.19), residues: 660 loop : -0.95 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 64 HIS 0.009 0.002 HIS C1064 PHE 0.040 0.002 PHE B 342 TYR 0.025 0.002 TYR A 265 ARG 0.011 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 502 time to evaluate : 2.785 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: A 236 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7414 (t) REVERT: A 581 THR cc_start: 0.4660 (p) cc_final: 0.3480 (p) REVERT: A 692 ILE cc_start: 0.8267 (mt) cc_final: 0.8038 (mt) REVERT: A 935 GLN cc_start: 0.7950 (pp30) cc_final: 0.7720 (tm-30) REVERT: A 964 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7665 (mmmm) REVERT: A 1002 GLN cc_start: 0.7027 (tp40) cc_final: 0.6797 (tp40) REVERT: B 331 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.6776 (p0) REVERT: B 592 PHE cc_start: 0.4246 (OUTLIER) cc_final: 0.3684 (p90) REVERT: B 888 PHE cc_start: 0.8039 (p90) cc_final: 0.7824 (p90) REVERT: C 48 LEU cc_start: 0.8098 (mm) cc_final: 0.7520 (mp) REVERT: C 52 GLN cc_start: 0.6410 (tp40) cc_final: 0.6199 (tp40) REVERT: C 804 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6991 (mm-40) REVERT: C 902 MET cc_start: 0.7564 (mmt) cc_final: 0.7096 (mmt) REVERT: C 947 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6953 (mttm) outliers start: 112 outliers final: 69 residues processed: 563 average time/residue: 0.3737 time to fit residues: 322.4815 Evaluate side-chains 526 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 453 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 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 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 914 ASN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 271 GLN B 542 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25384 Z= 0.256 Angle : 0.589 8.671 34515 Z= 0.310 Chirality : 0.044 0.174 3904 Planarity : 0.004 0.058 4462 Dihedral : 4.546 25.260 3391 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.18 % Allowed : 13.90 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.26 (0.14), residues: 3114 helix: 1.29 (0.21), residues: 652 sheet: 0.26 (0.19), residues: 670 loop : -0.91 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.006 0.001 HIS A 207 PHE 0.046 0.002 PHE B 342 TYR 0.023 0.002 TYR C 707 ARG 0.012 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 480 time to evaluate : 2.992 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: A 153 MET cc_start: 0.4517 (pmm) cc_final: 0.4265 (pmm) REVERT: A 655 TYR cc_start: 0.7083 (t80) cc_final: 0.6858 (t80) REVERT: A 902 MET cc_start: 0.7616 (mmm) cc_final: 0.7303 (mmp) REVERT: A 964 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7701 (mmmm) REVERT: A 1002 GLN cc_start: 0.6995 (tp40) cc_final: 0.6490 (tp40) REVERT: B 592 PHE cc_start: 0.4340 (OUTLIER) cc_final: 0.3920 (p90) REVERT: B 664 ILE cc_start: 0.7648 (mp) cc_final: 0.7437 (mt) REVERT: B 888 PHE cc_start: 0.8165 (p90) cc_final: 0.7937 (p90) REVERT: B 935 GLN cc_start: 0.7425 (tt0) cc_final: 0.7144 (tt0) REVERT: B 964 LYS cc_start: 0.8309 (tppp) cc_final: 0.7931 (tppp) REVERT: B 1002 GLN cc_start: 0.6383 (tp40) cc_final: 0.6000 (tp40) REVERT: C 48 LEU cc_start: 0.7938 (mm) cc_final: 0.7723 (mp) REVERT: C 710 ASN cc_start: 0.7927 (p0) cc_final: 0.7690 (p0) REVERT: C 804 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6871 (mm-40) REVERT: C 947 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6853 (mttm) REVERT: C 1002 GLN cc_start: 0.6936 (tp40) cc_final: 0.6712 (tp40) outliers start: 88 outliers final: 61 residues processed: 528 average time/residue: 0.3927 time to fit residues: 313.6838 Evaluate side-chains 517 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 454 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.6980 chunk 273 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 252 optimal weight: 40.0000 chunk 140 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 913 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 657 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25384 Z= 0.205 Angle : 0.585 12.291 34515 Z= 0.303 Chirality : 0.044 0.190 3904 Planarity : 0.004 0.059 4462 Dihedral : 4.402 22.603 3391 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.92 % Allowed : 15.16 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.16 (0.14), residues: 3114 helix: 1.35 (0.21), residues: 668 sheet: 0.33 (0.19), residues: 665 loop : -0.86 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 64 HIS 0.005 0.001 HIS A 207 PHE 0.050 0.002 PHE B 342 TYR 0.022 0.001 TYR C1138 ARG 0.012 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 478 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8338 (t) cc_final: 0.8131 (p) REVERT: A 964 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7731 (mmmm) REVERT: A 1002 GLN cc_start: 0.6696 (tp40) cc_final: 0.6351 (tp40) REVERT: A 1017 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6115 (tp30) REVERT: B 664 ILE cc_start: 0.7665 (mp) cc_final: 0.7463 (mt) REVERT: B 765 ARG cc_start: 0.6117 (tmm-80) cc_final: 0.5592 (ttm-80) REVERT: B 964 LYS cc_start: 0.8268 (tppp) cc_final: 0.7964 (tppp) REVERT: B 1002 GLN cc_start: 0.6246 (tp40) cc_final: 0.5879 (tp40) REVERT: C 281 GLU cc_start: 0.5656 (pp20) cc_final: 0.5446 (pp20) REVERT: C 586 ASP cc_start: 0.6319 (p0) cc_final: 0.5812 (p0) REVERT: C 710 ASN cc_start: 0.7993 (p0) cc_final: 0.7723 (p0) REVERT: C 804 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6853 (mm-40) REVERT: C 947 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6820 (mttm) outliers start: 81 outliers final: 57 residues processed: 523 average time/residue: 0.3910 time to fit residues: 310.0500 Evaluate side-chains 514 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 456 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 221 optimal weight: 0.3980 chunk 171 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 271 GLN B 657 ASN B1002 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25384 Z= 0.231 Angle : 0.592 9.518 34515 Z= 0.309 Chirality : 0.044 0.152 3904 Planarity : 0.004 0.058 4462 Dihedral : 4.383 22.686 3391 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.07 % Allowed : 15.70 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.17 (0.15), residues: 3114 helix: 1.28 (0.21), residues: 678 sheet: 0.37 (0.19), residues: 660 loop : -0.87 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.005 0.001 HIS C1064 PHE 0.048 0.002 PHE B 342 TYR 0.025 0.001 TYR B 660 ARG 0.012 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 480 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8364 (t) cc_final: 0.8010 (p) REVERT: A 1002 GLN cc_start: 0.6918 (tp-100) cc_final: 0.6202 (tp40) REVERT: B 271 GLN cc_start: 0.6714 (mm110) cc_final: 0.6512 (mm-40) REVERT: B 964 LYS cc_start: 0.8219 (tppp) cc_final: 0.7925 (tppp) REVERT: C 710 ASN cc_start: 0.8059 (p0) cc_final: 0.7787 (p0) REVERT: C 804 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6630 (mm-40) REVERT: C 947 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6788 (mttm) REVERT: C 1019 ARG cc_start: 0.6546 (ttp80) cc_final: 0.6116 (ttp80) outliers start: 85 outliers final: 68 residues processed: 527 average time/residue: 0.4029 time to fit residues: 323.1379 Evaluate side-chains 533 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 464 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN A1119 ASN B 657 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 25384 Z= 0.352 Angle : 0.655 9.568 34515 Z= 0.344 Chirality : 0.046 0.174 3904 Planarity : 0.004 0.058 4462 Dihedral : 4.692 24.157 3391 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.47 % Allowed : 15.60 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.33 (0.15), residues: 3114 helix: 1.12 (0.21), residues: 680 sheet: 0.27 (0.19), residues: 695 loop : -0.97 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.008 0.001 HIS C1064 PHE 0.053 0.002 PHE B 342 TYR 0.025 0.002 TYR C 707 ARG 0.012 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 473 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8444 (t) cc_final: 0.8009 (p) REVERT: A 96 GLU cc_start: 0.4949 (tp30) cc_final: 0.4664 (mt-10) REVERT: A 239 GLN cc_start: 0.6202 (tp40) cc_final: 0.5736 (mm-40) REVERT: B 572 THR cc_start: 0.8179 (p) cc_final: 0.7798 (t) REVERT: B 964 LYS cc_start: 0.8241 (tppp) cc_final: 0.7891 (ttmm) REVERT: B 1002 GLN cc_start: 0.7104 (tp40) cc_final: 0.6679 (tp40) REVERT: C 195 LYS cc_start: 0.6424 (pttp) cc_final: 0.6220 (pttp) REVERT: C 804 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6912 (mm-40) REVERT: C 947 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6890 (mttm) REVERT: C 957 GLN cc_start: 0.7131 (tt0) cc_final: 0.6839 (tt0) outliers start: 96 outliers final: 75 residues processed: 525 average time/residue: 0.4023 time to fit residues: 318.5031 Evaluate side-chains 534 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 458 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 0.9980 chunk 289 optimal weight: 0.3980 chunk 264 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 266 optimal weight: 0.9980 chunk 281 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 913 GLN A 914 ASN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 544 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 25384 Z= 0.217 Angle : 0.616 9.717 34515 Z= 0.321 Chirality : 0.044 0.286 3904 Planarity : 0.004 0.059 4462 Dihedral : 4.523 22.753 3391 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.89 % Allowed : 16.68 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.22 (0.15), residues: 3114 helix: 1.27 (0.21), residues: 679 sheet: 0.37 (0.19), residues: 683 loop : -0.94 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.004 0.001 HIS C1064 PHE 0.057 0.002 PHE A 981 TYR 0.020 0.001 TYR C 707 ARG 0.013 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 473 time to evaluate : 2.853 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: A 45 SER cc_start: 0.8364 (t) cc_final: 0.8122 (p) REVERT: A 96 GLU cc_start: 0.4826 (tp30) cc_final: 0.4366 (mt-10) REVERT: A 239 GLN cc_start: 0.6065 (tp40) cc_final: 0.5641 (mm-40) REVERT: A 655 TYR cc_start: 0.7181 (t80) cc_final: 0.6946 (t80) REVERT: B 572 THR cc_start: 0.8094 (p) cc_final: 0.7752 (t) REVERT: B 964 LYS cc_start: 0.8213 (tppp) cc_final: 0.7826 (ttmm) REVERT: C 710 ASN cc_start: 0.8074 (p0) cc_final: 0.7837 (p0) REVERT: C 804 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6833 (mm-40) REVERT: C 947 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6796 (mttm) outliers start: 80 outliers final: 74 residues processed: 520 average time/residue: 0.3987 time to fit residues: 312.4490 Evaluate side-chains 537 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 462 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 192 optimal weight: 0.0370 chunk 152 optimal weight: 0.5980 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 787 GLN A 913 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 544 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 641 ASN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 25384 Z= 0.228 Angle : 0.626 10.157 34515 Z= 0.325 Chirality : 0.044 0.188 3904 Planarity : 0.004 0.050 4462 Dihedral : 4.497 22.665 3391 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.96 % Allowed : 17.04 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -0.23 (0.15), residues: 3114 helix: 1.27 (0.21), residues: 678 sheet: 0.38 (0.19), residues: 683 loop : -0.96 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.004 0.001 HIS C1064 PHE 0.055 0.002 PHE B 342 TYR 0.020 0.001 TYR C 707 ARG 0.011 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 478 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8349 (t) cc_final: 0.8092 (p) REVERT: A 96 GLU cc_start: 0.4775 (tp30) cc_final: 0.4287 (mt-10) REVERT: A 239 GLN cc_start: 0.6110 (tp40) cc_final: 0.5680 (mm-40) REVERT: A 655 TYR cc_start: 0.7173 (t80) cc_final: 0.6927 (t80) REVERT: B 572 THR cc_start: 0.8105 (p) cc_final: 0.7727 (t) REVERT: B 964 LYS cc_start: 0.8223 (tppp) cc_final: 0.7842 (ttmm) REVERT: C 710 ASN cc_start: 0.8091 (p0) cc_final: 0.7861 (p0) REVERT: C 804 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6809 (mm-40) REVERT: C 947 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6808 (mttm) outliers start: 82 outliers final: 73 residues processed: 523 average time/residue: 0.4105 time to fit residues: 324.2179 Evaluate side-chains 540 residues out of total 2770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 466 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 229 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 256 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121492 restraints weight = 47612.853| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.00 r_work: 0.3431 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 25384 Z= 0.322 Angle : 1.004 59.198 34515 Z= 0.598 Chirality : 0.048 0.780 3904 Planarity : 0.005 0.122 4462 Dihedral : 4.576 39.070 3391 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.64 % Allowed : 17.51 % Favored : 79.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3114 helix: 1.26 (0.21), residues: 678 sheet: 0.41 (0.19), residues: 671 loop : -0.98 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.023 0.001 HIS B1101 PHE 0.101 0.002 PHE B 140 TYR 0.019 0.001 TYR A 265 ARG 0.024 0.000 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6724.85 seconds wall clock time: 121 minutes 0.51 seconds (7260.51 seconds total)