Starting phenix.real_space_refine on Thu Mar 21 10:57:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxm_32184/03_2024/7vxm_32184.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxm_32184/03_2024/7vxm_32184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxm_32184/03_2024/7vxm_32184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxm_32184/03_2024/7vxm_32184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxm_32184/03_2024/7vxm_32184.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxm_32184/03_2024/7vxm_32184.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.151 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 142 5.16 5 C 19101 2.51 5 N 4984 2.21 5 O 5674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29901 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8301 Classifications: {'peptide': 1059} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1006} Chain breaks: 6 Time building chain proxies: 14.80, per 1000 atoms: 0.49 Number of scatterers: 29901 At special positions: 0 Unit cell: (161.764, 151.927, 263.413, 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 142 16.00 O 5674 8.00 N 4984 7.00 C 19101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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 C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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 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: 9.96 Conformation dependent library (CDL) restraints added in 4.9 seconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 47 sheets defined 31.7% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.582A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.939A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.743A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.744A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.529A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.557A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.540A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.233A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.703A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.940A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.649A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.538A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1152 removed outlier: 4.005A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 3.921A pdb=" N HIS A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A1160 " --> pdb=" O PHE A1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 4.055A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.746A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.935A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 88 " --> pdb=" O LEU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.040A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.946A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.832A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.790A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.604A pdb=" N ARG C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.650A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.809A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 250 removed outlier: 3.960A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.822A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 293 through 301 removed outlier: 3.754A pdb=" N ASP C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 removed outlier: 4.030A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.618A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.686A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.564A pdb=" N VAL C 404 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 412 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.772A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.626A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.008A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.891A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.109A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 503' Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.534A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 530 " --> pdb=" O GLN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.630A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.541A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.594A pdb=" N PHE C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.672A pdb=" N TRP C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.533A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.213A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 782 removed outlier: 3.967A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 removed outlier: 4.025A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.112A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.632A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.724A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.776A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.109A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1161 removed outlier: 3.860A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D1154 " --> pdb=" O GLU D1150 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR D1155 " --> pdb=" O GLU D1151 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE D1156 " --> pdb=" O LEU D1152 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D1157 " --> pdb=" O ASP D1153 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D1158 " --> pdb=" O LYS D1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.520A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.295A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.575A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.622A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.653A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.973A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.854A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 4.379A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.510A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.091A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.169A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.955A 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.234A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.697A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1125 through 1129' Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 4.286A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.784A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.237A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.532A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.910A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.501A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.998A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.796A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.624A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 672 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.612A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.627A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.320A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.554A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.573A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.046A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.538A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.798A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 31 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 194 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS D 187 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 48 through 55 removed outlier: 4.133A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.531A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D 104 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.277A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 325 through 328 removed outlier: 3.795A pdb=" N ASN D 542 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 328 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 576 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.291A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.976A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.560A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.606A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.823A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.740A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.682A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 101 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.682A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.585A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.476A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AE4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.872A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 8.119A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.043A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.575A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.677A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.284A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'B' and resid 1094 through 1097 1078 hydrogen bonds defined for protein. 3066 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: 11.88 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9649 1.34 - 1.46: 7530 1.46 - 1.58: 13246 1.58 - 1.70: 0 1.70 - 1.83: 193 Bond restraints: 30618 Sorted by residual: bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.437 -0.103 2.34e-02 1.83e+03 1.95e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.426 -0.092 2.34e-02 1.83e+03 1.54e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.80e+00 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.50e+00 bond pdb=" C LEU D 229 " pdb=" N PRO D 230 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.19e+00 ... (remaining 30613 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 747 105.97 - 112.98: 16186 112.98 - 119.99: 10163 119.99 - 127.00: 14226 127.00 - 134.01: 310 Bond angle restraints: 41632 Sorted by residual: angle pdb=" N ALA A 292 " pdb=" CA ALA A 292 " pdb=" C ALA A 292 " ideal model delta sigma weight residual 110.80 98.96 11.84 2.13e+00 2.20e-01 3.09e+01 angle pdb=" N CYS D 291 " pdb=" CA CYS D 291 " pdb=" C CYS D 291 " ideal model delta sigma weight residual 108.73 117.23 -8.50 1.63e+00 3.76e-01 2.72e+01 angle pdb=" N CYS A 291 " pdb=" CA CYS A 291 " pdb=" C CYS A 291 " ideal model delta sigma weight residual 108.73 116.32 -7.59 1.63e+00 3.76e-01 2.17e+01 angle pdb=" CA LEU B 492 " pdb=" C LEU B 492 " pdb=" N GLN B 493 " ideal model delta sigma weight residual 114.17 120.92 -6.75 1.45e+00 4.76e-01 2.17e+01 angle pdb=" N ALA D 292 " pdb=" CA ALA D 292 " pdb=" C ALA D 292 " ideal model delta sigma weight residual 110.80 101.51 9.29 2.13e+00 2.20e-01 1.90e+01 ... (remaining 41627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 17759 16.09 - 32.19: 309 32.19 - 48.28: 109 48.28 - 64.38: 21 64.38 - 80.47: 8 Dihedral angle restraints: 18206 sinusoidal: 7153 harmonic: 11053 Sorted by residual: dihedral pdb=" CA GLY B 142 " pdb=" C GLY B 142 " pdb=" N VAL B 143 " pdb=" CA VAL B 143 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 55.59 37.41 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -123.03 37.03 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 18203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4053 0.060 - 0.119: 566 0.119 - 0.179: 25 0.179 - 0.239: 2 0.239 - 0.298: 2 Chirality restraints: 4648 Sorted by residual: chirality pdb=" CA CYS D 291 " pdb=" N CYS D 291 " pdb=" C CYS D 291 " pdb=" CB CYS D 291 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA CYS A 291 " pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CB CYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ALA A 292 " pdb=" N ALA A 292 " pdb=" C ALA A 292 " pdb=" CB ALA A 292 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4645 not shown) Planarity restraints: 5393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 290 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C ASP A 290 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP A 290 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 291 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 290 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C ASP D 290 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP D 290 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS D 291 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 295 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.031 5.00e-02 4.00e+02 ... (remaining 5390 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 711 2.71 - 3.26: 28521 3.26 - 3.80: 44723 3.80 - 4.35: 59366 4.35 - 4.90: 98480 Nonbonded interactions: 231801 Sorted by model distance: nonbonded pdb=" OG1 THR D 108 " pdb=" O ASN D 234 " model vdw 2.159 2.440 nonbonded pdb=" CZ PHE B 140 " pdb=" CB SER B 244 " model vdw 2.214 3.740 nonbonded pdb=" NE ARG B 102 " pdb=" CG1 ILE B 243 " model vdw 2.215 3.520 nonbonded pdb=" O GLN A 755 " pdb=" OG SER D 968 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.256 2.520 ... (remaining 231796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 470 or resid 491 through 1161)) selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.710 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 72.510 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 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 : 0.002 0.103 30618 Z= 0.137 Angle : 0.508 11.839 41632 Z= 0.304 Chirality : 0.041 0.298 4648 Planarity : 0.004 0.056 5393 Dihedral : 7.685 80.472 10976 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -2.41 (0.11), residues: 3747 helix: -3.35 (0.09), residues: 975 sheet: -0.40 (0.17), residues: 654 loop : -1.05 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 436 HIS 0.006 0.000 HIS A 242 PHE 0.015 0.001 PHE A 32 TYR 0.016 0.001 TYR A 495 ARG 0.002 0.000 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 881 time to evaluate : 3.268 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 1029 MET cc_start: 0.7832 (tpp) cc_final: 0.7387 (tpt) REVERT: A 1037 SER cc_start: 0.8775 (t) cc_final: 0.8432 (p) REVERT: C 303 ASP cc_start: 0.5418 (p0) cc_final: 0.4959 (t0) REVERT: C 535 HIS cc_start: 0.2760 (m-70) cc_final: 0.2360 (t70) REVERT: D 177 MET cc_start: 0.1932 (ttm) cc_final: -0.0504 (mtp) REVERT: D 858 LEU cc_start: 0.6847 (mp) cc_final: 0.6557 (mp) REVERT: D 929 SER cc_start: 0.7551 (m) cc_final: 0.7325 (t) REVERT: B 695 TYR cc_start: 0.6318 (p90) cc_final: 0.5950 (p90) outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.4288 time to fit residues: 594.8637 Evaluate side-chains 422 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 7.9990 chunk 284 optimal weight: 0.0770 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 219 optimal weight: 0.2980 chunk 341 optimal weight: 2.9990 overall best weight: 1.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1088 HIS A1106 GLN A1159 HIS C 325 GLN C 417 HIS D 394 ASN ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN D 907 ASN D 913 GLN D 920 GLN D 949 GLN D1054 GLN D1106 GLN B 66 HIS B 137 ASN B 146 HIS B 148 ASN B 239 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 394 ASN B 439 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30618 Z= 0.227 Angle : 0.612 11.838 41632 Z= 0.320 Chirality : 0.044 0.210 4648 Planarity : 0.005 0.094 5393 Dihedral : 3.906 20.071 4060 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.92 % Allowed : 9.30 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.94 (0.12), residues: 3747 helix: -0.58 (0.14), residues: 1000 sheet: -0.06 (0.18), residues: 642 loop : -0.77 (0.12), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 473 HIS 0.006 0.001 HIS A 242 PHE 0.029 0.002 PHE D 643 TYR 0.021 0.002 TYR A 37 ARG 0.008 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 437 time to evaluate : 3.195 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: A 516 GLU cc_start: 0.1321 (OUTLIER) cc_final: 0.0927 (mp0) REVERT: A 1037 SER cc_start: 0.8816 (t) cc_final: 0.8453 (p) REVERT: C 323 MET cc_start: 0.2617 (mmm) cc_final: 0.1771 (mtt) REVERT: C 332 MET cc_start: 0.1305 (ttt) cc_final: -0.0303 (tmm) REVERT: C 383 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4392 (ppp) REVERT: C 535 HIS cc_start: 0.2477 (m-70) cc_final: 0.1862 (t70) REVERT: D 153 MET cc_start: 0.1722 (ttt) cc_final: 0.1328 (ttt) REVERT: D 966 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7585 (mm) REVERT: B 1118 ASP cc_start: 0.6300 (p0) cc_final: 0.6026 (p0) outliers start: 97 outliers final: 60 residues processed: 508 average time/residue: 0.3717 time to fit residues: 312.8446 Evaluate side-chains 391 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 328 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 750 SER Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 966 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 0.0670 chunk 369 optimal weight: 8.9990 chunk 304 optimal weight: 0.5980 chunk 339 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 overall best weight: 2.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 81 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 ASN C 524 GLN D 655 HIS D 955 ASN B 165 ASN B 439 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30618 Z= 0.298 Angle : 0.656 12.258 41632 Z= 0.340 Chirality : 0.046 0.225 4648 Planarity : 0.005 0.060 5393 Dihedral : 4.383 25.601 4060 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.76 % Allowed : 11.13 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.47 (0.13), residues: 3747 helix: 0.37 (0.16), residues: 1016 sheet: 0.07 (0.18), residues: 684 loop : -0.75 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 163 HIS 0.008 0.002 HIS A1064 PHE 0.025 0.002 PHE D 643 TYR 0.029 0.002 TYR D 145 ARG 0.010 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 368 time to evaluate : 3.537 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 119 ILE cc_start: 0.5181 (OUTLIER) cc_final: 0.4719 (mp) REVERT: A 153 MET cc_start: 0.1845 (mtt) cc_final: 0.0525 (ppp) REVERT: A 516 GLU cc_start: 0.1532 (OUTLIER) cc_final: 0.1069 (mp0) REVERT: A 900 MET cc_start: 0.7377 (mmm) cc_final: 0.7125 (mpp) REVERT: A 922 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 1037 SER cc_start: 0.8878 (t) cc_final: 0.8381 (p) REVERT: A 1128 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8546 (p) REVERT: C 535 HIS cc_start: 0.2513 (m-70) cc_final: 0.2074 (t-170) REVERT: D 153 MET cc_start: 0.1794 (ttt) cc_final: 0.1567 (ttt) REVERT: D 1037 SER cc_start: 0.8676 (t) cc_final: 0.8373 (p) REVERT: B 379 CYS cc_start: 0.3542 (OUTLIER) cc_final: 0.2850 (p) REVERT: B 870 ILE cc_start: 0.8814 (mm) cc_final: 0.8415 (mt) REVERT: B 1045 LYS cc_start: 0.7247 (mttm) cc_final: 0.7031 (ttmt) REVERT: B 1118 ASP cc_start: 0.6221 (p0) cc_final: 0.6000 (p0) outliers start: 125 outliers final: 72 residues processed: 466 average time/residue: 0.3785 time to fit residues: 294.0934 Evaluate side-chains 355 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 278 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 913 GLN Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 0.7980 chunk 257 optimal weight: 0.7980 chunk 177 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 229 optimal weight: 0.8980 chunk 343 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 325 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1088 HIS ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN B 165 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30618 Z= 0.152 Angle : 0.528 9.188 41632 Z= 0.272 Chirality : 0.043 0.178 4648 Planarity : 0.004 0.045 5393 Dihedral : 3.986 22.466 4060 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.50 % Allowed : 13.00 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.12 (0.13), residues: 3747 helix: 0.86 (0.16), residues: 1020 sheet: 0.15 (0.18), residues: 679 loop : -0.60 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.005 0.001 HIS A 242 PHE 0.026 0.001 PHE B 823 TYR 0.018 0.001 TYR D 145 ARG 0.009 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 324 time to evaluate : 3.345 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 153 MET cc_start: 0.1563 (mtt) cc_final: 0.0409 (ppp) REVERT: A 291 CYS cc_start: 0.4746 (OUTLIER) cc_final: 0.4244 (m) REVERT: A 753 LEU cc_start: 0.7743 (tp) cc_final: 0.7530 (tp) REVERT: A 1037 SER cc_start: 0.8779 (t) cc_final: 0.8367 (m) REVERT: A 1039 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8199 (mtp180) REVERT: C 135 PRO cc_start: 0.0951 (Cg_exo) cc_final: 0.0686 (Cg_endo) REVERT: C 323 MET cc_start: 0.3803 (mmm) cc_final: 0.1381 (mtm) REVERT: C 332 MET cc_start: -0.2069 (OUTLIER) cc_final: -0.2412 (mtp) REVERT: D 1037 SER cc_start: 0.8586 (t) cc_final: 0.8382 (p) REVERT: D 1071 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: B 379 CYS cc_start: 0.3417 (OUTLIER) cc_final: 0.2985 (p) outliers start: 83 outliers final: 53 residues processed: 383 average time/residue: 0.3820 time to fit residues: 241.4573 Evaluate side-chains 333 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 276 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 698 SER Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 745 ASP Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1071 GLN Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1097 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 8.9990 chunk 206 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 270 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1048 HIS A1108 ASN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS C 373 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 HIS C 572 ASN D 784 GLN D1048 HIS ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN B 321 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 30618 Z= 0.469 Angle : 0.784 12.754 41632 Z= 0.410 Chirality : 0.049 0.166 4648 Planarity : 0.006 0.088 5393 Dihedral : 5.119 23.933 4060 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.06 % Allowed : 12.58 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.61 (0.13), residues: 3747 helix: 0.49 (0.16), residues: 1036 sheet: -0.11 (0.18), residues: 722 loop : -0.99 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 353 HIS 0.011 0.002 HIS B1064 PHE 0.036 0.003 PHE B 823 TYR 0.031 0.003 TYR A 279 ARG 0.009 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 284 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2338 (mtt) cc_final: 0.1114 (pmm) REVERT: A 318 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.6896 (p90) REVERT: A 392 PHE cc_start: 0.1963 (OUTLIER) cc_final: 0.1289 (m-80) REVERT: A 598 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7900 (mp) REVERT: A 868 GLU cc_start: 0.8284 (tp30) cc_final: 0.7939 (tm-30) REVERT: A 1029 MET cc_start: 0.8848 (tpp) cc_final: 0.8627 (tpp) REVERT: A 1128 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 135 PRO cc_start: 0.0654 (Cg_exo) cc_final: 0.0374 (Cg_endo) REVERT: C 332 MET cc_start: -0.2289 (OUTLIER) cc_final: -0.2585 (mtp) REVERT: C 429 GLN cc_start: 0.4612 (OUTLIER) cc_final: 0.4029 (tp40) REVERT: D 823 PHE cc_start: 0.7430 (t80) cc_final: 0.7217 (t80) REVERT: D 955 ASN cc_start: 0.8227 (t0) cc_final: 0.8001 (t0) REVERT: D 1037 SER cc_start: 0.8734 (t) cc_final: 0.8493 (p) REVERT: B 379 CYS cc_start: 0.3889 (OUTLIER) cc_final: 0.2959 (p) outliers start: 135 outliers final: 85 residues processed: 395 average time/residue: 0.3863 time to fit residues: 257.6075 Evaluate side-chains 325 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 233 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 821 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 913 GLN Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 690 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN C 572 ASN D 779 GLN D 784 GLN D 856 ASN D1106 GLN B 218 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30618 Z= 0.167 Angle : 0.543 10.899 41632 Z= 0.280 Chirality : 0.043 0.162 4648 Planarity : 0.004 0.061 5393 Dihedral : 4.354 23.609 4060 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.14 % Allowed : 15.13 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.20 (0.13), residues: 3747 helix: 0.97 (0.16), residues: 1032 sheet: -0.03 (0.18), residues: 697 loop : -0.73 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.005 0.001 HIS A 242 PHE 0.026 0.001 PHE B 823 TYR 0.019 0.001 TYR D 204 ARG 0.005 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 281 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2010 (mtt) cc_final: 0.0824 (ppp) REVERT: A 177 MET cc_start: -0.0402 (tmm) cc_final: -0.0634 (tmm) REVERT: A 318 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6296 (p90) REVERT: A 368 LEU cc_start: 0.6534 (mt) cc_final: 0.6222 (pp) REVERT: A 1128 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8497 (p) REVERT: C 135 PRO cc_start: 0.1240 (Cg_exo) cc_final: 0.0970 (Cg_endo) REVERT: C 332 MET cc_start: -0.2459 (OUTLIER) cc_final: -0.2736 (mtp) REVERT: D 153 MET cc_start: 0.2353 (tpp) cc_final: 0.1776 (ttt) REVERT: D 950 ASP cc_start: 0.6198 (t70) cc_final: 0.5848 (t0) REVERT: B 379 CYS cc_start: 0.3585 (OUTLIER) cc_final: 0.3099 (p) REVERT: B 1084 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6853 (p0) outliers start: 71 outliers final: 48 residues processed: 334 average time/residue: 0.3965 time to fit residues: 222.4531 Evaluate side-chains 303 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 250 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 265 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 0.0870 chunk 203 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 167 optimal weight: 40.0000 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30618 Z= 0.154 Angle : 0.524 9.334 41632 Z= 0.269 Chirality : 0.042 0.162 4648 Planarity : 0.004 0.049 5393 Dihedral : 4.127 26.372 4060 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.08 % Allowed : 15.70 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.03 (0.13), residues: 3747 helix: 1.19 (0.16), residues: 1037 sheet: -0.00 (0.19), residues: 690 loop : -0.64 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 104 HIS 0.004 0.001 HIS A 242 PHE 0.039 0.001 PHE D 86 TYR 0.015 0.001 TYR B 265 ARG 0.005 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1868 (mtt) cc_final: 0.0730 (ppp) REVERT: A 177 MET cc_start: -0.0642 (tmm) cc_final: -0.0869 (tmm) REVERT: A 318 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6269 (p90) REVERT: A 368 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6279 (pp) REVERT: A 1128 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (p) REVERT: C 135 PRO cc_start: 0.1221 (Cg_exo) cc_final: 0.0960 (Cg_endo) REVERT: C 332 MET cc_start: -0.2604 (OUTLIER) cc_final: -0.2853 (mtp) REVERT: D 153 MET cc_start: 0.2416 (tpp) cc_final: 0.1823 (ttt) REVERT: D 950 ASP cc_start: 0.6227 (t70) cc_final: 0.5957 (t0) REVERT: B 379 CYS cc_start: 0.3543 (OUTLIER) cc_final: 0.3030 (p) outliers start: 69 outliers final: 50 residues processed: 320 average time/residue: 0.3483 time to fit residues: 188.3220 Evaluate side-chains 302 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 247 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 856 ASN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.7793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30618 Z= 0.281 Angle : 0.596 10.773 41632 Z= 0.308 Chirality : 0.044 0.243 4648 Planarity : 0.004 0.051 5393 Dihedral : 4.451 29.377 4060 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.44 % Allowed : 15.70 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.14 (0.13), residues: 3747 helix: 1.07 (0.16), residues: 1050 sheet: -0.07 (0.18), residues: 723 loop : -0.71 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 436 HIS 0.006 0.001 HIS C 378 PHE 0.032 0.002 PHE B 823 TYR 0.016 0.002 TYR C 279 ARG 0.006 0.001 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 257 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1572 (mtt) cc_final: 0.0993 (pmm) REVERT: A 318 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6198 (p90) REVERT: A 392 PHE cc_start: 0.2529 (OUTLIER) cc_final: 0.1520 (m-80) REVERT: A 1029 MET cc_start: 0.8729 (tpp) cc_final: 0.8111 (ttm) REVERT: A 1128 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8547 (p) REVERT: C 135 PRO cc_start: 0.0825 (Cg_exo) cc_final: 0.0587 (Cg_endo) REVERT: C 270 MET cc_start: 0.3179 (mtm) cc_final: 0.2970 (mtm) REVERT: C 332 MET cc_start: -0.2014 (OUTLIER) cc_final: -0.2250 (mtp) REVERT: C 429 GLN cc_start: 0.4745 (OUTLIER) cc_final: 0.4208 (tp40) REVERT: C 474 MET cc_start: 0.0463 (ttt) cc_final: 0.0099 (ttm) REVERT: D 775 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7185 (t0) REVERT: D 950 ASP cc_start: 0.6273 (t70) cc_final: 0.6011 (t0) REVERT: B 177 MET cc_start: 0.2465 (tmm) cc_final: 0.1706 (ttt) REVERT: B 379 CYS cc_start: 0.3974 (OUTLIER) cc_final: 0.3276 (p) REVERT: B 774 GLN cc_start: 0.7640 (mm110) cc_final: 0.7413 (mm110) outliers start: 81 outliers final: 61 residues processed: 316 average time/residue: 0.3653 time to fit residues: 195.5648 Evaluate side-chains 306 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 238 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 701 VAL Chi-restraints excluded: chain D residue 775 ASP Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 0.3980 chunk 347 optimal weight: 0.9980 chunk 316 optimal weight: 10.0000 chunk 337 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 703 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 957 GLN B1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30618 Z= 0.192 Angle : 0.538 10.448 41632 Z= 0.277 Chirality : 0.043 0.173 4648 Planarity : 0.004 0.047 5393 Dihedral : 4.282 29.767 4060 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.02 % Allowed : 16.28 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.02 (0.14), residues: 3747 helix: 1.25 (0.17), residues: 1036 sheet: 0.04 (0.19), residues: 713 loop : -0.69 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 168 HIS 0.008 0.001 HIS A 242 PHE 0.031 0.001 PHE D 275 TYR 0.016 0.001 TYR D 145 ARG 0.005 0.000 ARG C 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 265 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1530 (mtt) cc_final: 0.0970 (pmm) REVERT: A 318 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6278 (p90) REVERT: A 541 PHE cc_start: 0.6683 (p90) cc_final: 0.6452 (p90) REVERT: A 922 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7781 (mm) REVERT: A 1128 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 1144 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7634 (tt0) REVERT: C 135 PRO cc_start: 0.0915 (Cg_exo) cc_final: 0.0651 (Cg_endo) REVERT: C 152 MET cc_start: -0.2972 (mmt) cc_final: -0.3536 (mtt) REVERT: C 332 MET cc_start: -0.2072 (OUTLIER) cc_final: -0.2406 (mtp) REVERT: C 474 MET cc_start: 0.0493 (ttt) cc_final: -0.0211 (ttm) REVERT: D 950 ASP cc_start: 0.6231 (t70) cc_final: 0.6009 (t0) REVERT: B 64 TRP cc_start: 0.5557 (OUTLIER) cc_final: 0.4957 (m-10) REVERT: B 177 MET cc_start: 0.2296 (tmm) cc_final: 0.1569 (ttt) REVERT: B 379 CYS cc_start: 0.3840 (OUTLIER) cc_final: 0.3223 (p) outliers start: 67 outliers final: 53 residues processed: 313 average time/residue: 0.3644 time to fit residues: 192.3026 Evaluate side-chains 307 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 248 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.4980 chunk 357 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 248 optimal weight: 0.7980 chunk 374 optimal weight: 0.0770 chunk 344 optimal weight: 0.0060 chunk 298 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 30618 Z= 0.226 Angle : 0.664 59.199 41632 Z= 0.365 Chirality : 0.043 0.450 4648 Planarity : 0.004 0.054 5393 Dihedral : 4.310 35.504 4060 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.87 % Allowed : 16.49 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.01 (0.14), residues: 3747 helix: 1.26 (0.17), residues: 1036 sheet: 0.06 (0.19), residues: 701 loop : -0.68 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 104 HIS 0.022 0.001 HIS C 505 PHE 0.076 0.002 PHE D 186 TYR 0.031 0.002 TYR C 50 ARG 0.005 0.000 ARG A1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 251 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1635 (mtt) cc_final: 0.0981 (pmm) REVERT: A 318 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6267 (p90) REVERT: A 922 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 1128 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8493 (p) REVERT: A 1144 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7629 (tt0) REVERT: C 135 PRO cc_start: 0.0915 (Cg_exo) cc_final: 0.0642 (Cg_endo) REVERT: C 152 MET cc_start: -0.2997 (mmt) cc_final: -0.3546 (mtt) REVERT: C 474 MET cc_start: 0.0492 (ttt) cc_final: -0.0213 (ttm) REVERT: D 558 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6868 (mtmm) REVERT: D 950 ASP cc_start: 0.6226 (t70) cc_final: 0.6003 (t0) REVERT: B 64 TRP cc_start: 0.5548 (OUTLIER) cc_final: 0.4949 (m-10) REVERT: B 177 MET cc_start: 0.2283 (tmm) cc_final: 0.1553 (ttt) REVERT: B 234 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6724 (p0) REVERT: B 379 CYS cc_start: 0.3833 (OUTLIER) cc_final: 0.3217 (p) outliers start: 62 outliers final: 54 residues processed: 295 average time/residue: 0.3601 time to fit residues: 180.0469 Evaluate side-chains 306 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 245 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 558 LYS Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.8980 chunk 317 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 275 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 306 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.147703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.111461 restraints weight = 94284.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.112797 restraints weight = 57893.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.113576 restraints weight = 32329.195| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 30618 Z= 0.226 Angle : 0.664 59.199 41632 Z= 0.365 Chirality : 0.043 0.450 4648 Planarity : 0.004 0.054 5393 Dihedral : 4.310 35.504 4060 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 16.49 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.06 % 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: -0.01 (0.14), residues: 3747 helix: 1.26 (0.17), residues: 1036 sheet: 0.06 (0.19), residues: 701 loop : -0.68 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 104 HIS 0.022 0.001 HIS C 505 PHE 0.076 0.002 PHE D 186 TYR 0.031 0.002 TYR C 50 ARG 0.005 0.000 ARG A1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6333.78 seconds wall clock time: 115 minutes 4.02 seconds (6904.02 seconds total)