Starting phenix.real_space_refine on Thu Mar 21 10:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/03_2024/8wro_37784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/03_2024/8wro_37784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/03_2024/8wro_37784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/03_2024/8wro_37784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/03_2024/8wro_37784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wro_37784/03_2024/8wro_37784.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 19060 2.51 5 N 4969 2.21 5 O 5632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 982": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ASP 1136": "OD1" <-> "OD2" Residue "D GLU 430": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29807 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8364 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8295 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 57, 'TRANS': 1001} Chain breaks: 5 Chain: "C" Number of atoms: 8303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8303 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 57, 'TRANS': 1002} Chain breaks: 5 Chain: "D" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 15.64, per 1000 atoms: 0.52 Number of scatterers: 29807 At special positions: 0 Unit cell: (151.84, 164.32, 236.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 146 16.00 O 5632 8.00 N 4969 7.00 C 19060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.02 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 5.8 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7100 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 48 sheets defined 28.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.785A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE A 368 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.541A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 775 removed outlier: 4.312A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 938 removed outlier: 4.075A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 3.548A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.934A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 3.650A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1030 removed outlier: 3.601A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.521A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.952A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.536A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 774 removed outlier: 3.694A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.781A pdb=" N ASN B 853 " --> pdb=" O GLN B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.564A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.598A pdb=" N GLY B 905 " --> pdb=" O TYR B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.907A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.685A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 5.074A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.958A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.061A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.738A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.666A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.508A pdb=" N LYS C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN C 776 " --> pdb=" O ASP C 772 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 777 " --> pdb=" O LYS C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.638A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.704A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.939A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.734A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 961 removed outlier: 4.621A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS C 951 " --> pdb=" O ASP C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 965 Processing helix chain 'C' and resid 973 through 980 removed outlier: 3.809A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 985 Processing helix chain 'C' and resid 986 through 1030 removed outlier: 4.078A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.670A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.615A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.607A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.779A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.597A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.781A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 268 removed outlier: 3.988A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 331 removed outlier: 4.517A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.513A pdb=" N PHE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 412 removed outlier: 4.252A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.487A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.933A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.564A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 597 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.887A pdb=" N ASP A 50 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 270 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.988A pdb=" N THR A 60 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 264 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 262 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 200 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 224 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 128 removed outlier: 3.938A pdb=" N TRP A 101 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.745A pdb=" N GLY A 308 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 596 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 325 removed outlier: 3.717A pdb=" N VAL A 536 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 543 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.864A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A 427 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.864A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR A 427 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 431 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.238A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700 Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.851A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.851A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 732 removed outlier: 4.794A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1117 through 1120 Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.207A pdb=" N LEU B 81 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 234 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE B 103 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLN B 236 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP B 101 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 238 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 123 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 169 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 125 " --> pdb=" O TYR B 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 221 through 227 removed outlier: 6.455A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.966A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 324 removed outlier: 7.012A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 536 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.609A pdb=" N GLY B 428 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.652A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 592 through 595 Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.706A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.773A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.647A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.703A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD3, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.437A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 26 through 27 removed outlier: 4.019A pdb=" N THR C 26 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 59 " --> pdb=" O THR C 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 46 through 52 removed outlier: 3.803A pdb=" N HIS C 46 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 274 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 48 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.960A pdb=" N LEU C 81 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN C 236 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP C 101 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C 238 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.998A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 224 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.515A pdb=" N GLY C 308 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 647 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AE1, first strand: chain 'C' and resid 395 through 400 removed outlier: 4.122A pdb=" N ILE C 399 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 548 through 551 Processing sheet with id=AE4, first strand: chain 'C' and resid 661 through 662 removed outlier: 3.760A pdb=" N ILE C 661 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 716 removed outlier: 3.500A pdb=" N THR C 720 " --> pdb=" O HIS C1061 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 716 removed outlier: 6.058A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.481A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C1078 " --> pdb=" O HIS C1085 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.647A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.452A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.494A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2931 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: 12.09 Time building geometry restraints manager: 12.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8551 1.33 - 1.46: 8066 1.46 - 1.59: 13729 1.59 - 1.71: 1 1.71 - 1.84: 197 Bond restraints: 30544 Sorted by residual: bond pdb=" C PRO C 983 " pdb=" O PRO C 983 " ideal model delta sigma weight residual 1.240 1.208 0.032 1.12e-02 7.97e+03 8.17e+00 bond pdb=" N GLU C 985 " pdb=" CA GLU C 985 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.43e+00 bond pdb=" CB PRO C 334 " pdb=" CG PRO C 334 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" N ARG C 980 " pdb=" CA ARG C 980 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.70e+00 bond pdb=" N ASP C 982 " pdb=" CA ASP C 982 " ideal model delta sigma weight residual 1.451 1.487 -0.037 1.78e-02 3.16e+03 4.23e+00 ... (remaining 30539 not shown) Histogram of bond angle deviations from ideal: 95.07 - 102.92: 141 102.92 - 110.78: 9731 110.78 - 118.63: 14113 118.63 - 126.48: 17128 126.48 - 134.34: 447 Bond angle restraints: 41560 Sorted by residual: angle pdb=" CG1 ILE B 19 " pdb=" CB ILE B 19 " pdb=" CG2 ILE B 19 " ideal model delta sigma weight residual 110.70 95.07 15.63 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C GLU D 479 " pdb=" N MET D 480 " pdb=" CA MET D 480 " ideal model delta sigma weight residual 122.06 112.47 9.59 1.86e+00 2.89e-01 2.66e+01 angle pdb=" CB MET B 694 " pdb=" CG MET B 694 " pdb=" SD MET B 694 " ideal model delta sigma weight residual 112.70 127.22 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA MET A 150 " pdb=" CB MET A 150 " pdb=" CG MET A 150 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA PRO C 334 " pdb=" N PRO C 334 " pdb=" CD PRO C 334 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.21e+01 ... (remaining 41555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15311 18.00 - 36.00: 2114 36.00 - 53.99: 592 53.99 - 71.99: 123 71.99 - 89.99: 59 Dihedral angle restraints: 18199 sinusoidal: 7166 harmonic: 11033 Sorted by residual: dihedral pdb=" CB CYS C 735 " pdb=" SG CYS C 735 " pdb=" SG CYS C 757 " pdb=" CB CYS C 757 " ideal model delta sinusoidal sigma weight residual -86.00 0.25 -86.25 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 133 " pdb=" CB CYS C 133 " ideal model delta sinusoidal sigma weight residual 93.00 171.74 -78.74 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -162.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 ... (remaining 18196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4139 0.081 - 0.163: 475 0.163 - 0.244: 16 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 4633 Sorted by residual: chirality pdb=" CB ILE B 19 " pdb=" CA ILE B 19 " pdb=" CG1 ILE B 19 " pdb=" CG2 ILE B 19 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE A 98 " pdb=" CA ILE A 98 " pdb=" CG1 ILE A 98 " pdb=" CG2 ILE A 98 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU C 81 " pdb=" CB LEU C 81 " pdb=" CD1 LEU C 81 " pdb=" CD2 LEU C 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4630 not shown) Planarity restraints: 5380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 980 " 0.415 9.50e-02 1.11e+02 1.86e-01 2.12e+01 pdb=" NE ARG C 980 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG C 980 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 980 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 980 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.024 2.00e-02 2.50e+03 1.95e-02 9.47e+00 pdb=" CG TRP D 461 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 982 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO A 983 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.040 5.00e-02 4.00e+02 ... (remaining 5377 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5778 2.77 - 3.30: 28495 3.30 - 3.83: 51396 3.83 - 4.37: 54580 4.37 - 4.90: 93629 Nonbonded interactions: 233878 Sorted by model distance: nonbonded pdb=" O ASP A 933 " pdb=" OG SER A 937 " model vdw 2.237 2.440 nonbonded pdb=" O TYR C 310 " pdb=" OG SER C 593 " model vdw 2.243 2.440 nonbonded pdb=" O ASN A 436 " pdb=" OG SER A 440 " model vdw 2.258 2.440 nonbonded pdb=" O SER A 964 " pdb=" OG SER A 964 " model vdw 2.269 2.440 nonbonded pdb=" O SER A 24 " pdb=" OG1 THR A 60 " model vdw 2.277 2.440 ... (remaining 233873 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 140 or resid 149 through 824 or resid 847 throu \ gh 1137)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 824 or resid 847 through 1137)) } 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.230 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 81.050 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 30544 Z= 0.263 Angle : 0.791 15.632 41560 Z= 0.413 Chirality : 0.049 0.407 4633 Planarity : 0.006 0.186 5380 Dihedral : 18.348 89.988 10979 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 0.33 % Allowed : 34.33 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3742 helix: 0.45 (0.16), residues: 956 sheet: -1.36 (0.20), residues: 616 loop : -2.33 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 461 HIS 0.009 0.001 HIS C 336 PHE 0.036 0.002 PHE C 397 TYR 0.024 0.001 TYR C 362 ARG 0.006 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 464 time to evaluate : 3.292 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 38 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7816 (ttpt) REVERT: A 89 PHE cc_start: 0.8432 (t80) cc_final: 0.8001 (t80) REVERT: A 492 TYR cc_start: 0.1387 (OUTLIER) cc_final: 0.0988 (m-80) REVERT: A 694 MET cc_start: 0.7386 (mmt) cc_final: 0.7085 (tpt) REVERT: A 752 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8525 (mp10) REVERT: A 897 MET cc_start: 0.7268 (tpp) cc_final: 0.6933 (tpp) REVERT: A 987 GLU cc_start: 0.8359 (mp0) cc_final: 0.7899 (mp0) REVERT: B 272 PHE cc_start: 0.7340 (m-80) cc_final: 0.6543 (t80) REVERT: B 694 MET cc_start: 0.7498 (mmm) cc_final: 0.7104 (mmm) REVERT: B 737 MET cc_start: 0.7160 (tpp) cc_final: 0.6934 (mmm) REVERT: B 744 THR cc_start: 0.8649 (t) cc_final: 0.8116 (t) REVERT: B 748 ASN cc_start: 0.8940 (m110) cc_final: 0.8042 (m-40) REVERT: B 756 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 1046 LEU cc_start: 0.8415 (mt) cc_final: 0.7902 (tt) REVERT: B 1122 ASN cc_start: 0.6135 (p0) cc_final: 0.5789 (p0) REVERT: C 81 LEU cc_start: 0.8063 (tt) cc_final: 0.7105 (mm) REVERT: C 89 PHE cc_start: 0.7108 (t80) cc_final: 0.6513 (t80) REVERT: C 122 ASN cc_start: 0.8001 (m-40) cc_final: 0.7213 (p0) REVERT: C 392 VAL cc_start: 0.7276 (p) cc_final: 0.6971 (m) REVERT: C 420 TYR cc_start: 0.6532 (t80) cc_final: 0.6321 (t80) REVERT: C 539 ASN cc_start: 0.7935 (t0) cc_final: 0.7305 (p0) REVERT: C 870 TYR cc_start: 0.6829 (m-80) cc_final: 0.6502 (m-80) REVERT: C 884 THR cc_start: 0.7886 (p) cc_final: 0.7674 (t) REVERT: D 107 VAL cc_start: 0.7224 (t) cc_final: 0.6834 (t) REVERT: D 295 ASP cc_start: 0.8685 (t0) cc_final: 0.8344 (p0) REVERT: D 577 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8228 (tptt) outliers start: 11 outliers final: 3 residues processed: 472 average time/residue: 0.3754 time to fit residues: 287.5803 Evaluate side-chains 261 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 256 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain C residue 648 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.7980 chunk 284 optimal weight: 0.0020 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 192 optimal weight: 0.2980 chunk 152 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 0.2980 chunk 179 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 341 optimal weight: 50.0000 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN B 910 GLN B 946 GLN C 49 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN D 64 ASN D 188 ASN D 250 ASN D 429 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30544 Z= 0.158 Angle : 0.591 10.025 41560 Z= 0.300 Chirality : 0.043 0.190 4633 Planarity : 0.005 0.069 5380 Dihedral : 4.725 46.928 4067 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.65 % Favored : 93.24 % Rotamer: Outliers : 3.65 % Allowed : 33.60 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3742 helix: 1.09 (0.17), residues: 978 sheet: -1.34 (0.20), residues: 617 loop : -2.16 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 461 HIS 0.016 0.001 HIS A1080 PHE 0.026 0.001 PHE B 189 TYR 0.019 0.001 TYR C 914 ARG 0.007 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 280 time to evaluate : 3.258 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: A 38 LYS cc_start: 0.8121 (ttmm) cc_final: 0.7803 (ttpt) REVERT: A 321 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8853 (pm20) REVERT: A 402 ASN cc_start: 0.4201 (OUTLIER) cc_final: 0.3617 (p0) REVERT: A 694 MET cc_start: 0.7331 (mmt) cc_final: 0.7050 (tpt) REVERT: A 752 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8546 (mp10) REVERT: A 897 MET cc_start: 0.7275 (tpp) cc_final: 0.6996 (tpp) REVERT: B 272 PHE cc_start: 0.7131 (m-80) cc_final: 0.6348 (t80) REVERT: B 293 LEU cc_start: 0.8183 (tp) cc_final: 0.7930 (tt) REVERT: B 737 MET cc_start: 0.7193 (tpp) cc_final: 0.6884 (mmm) REVERT: B 744 THR cc_start: 0.8707 (t) cc_final: 0.8110 (t) REVERT: B 748 ASN cc_start: 0.8739 (m110) cc_final: 0.8082 (m-40) REVERT: B 1046 LEU cc_start: 0.8602 (mt) cc_final: 0.8078 (tt) REVERT: C 81 LEU cc_start: 0.7619 (tt) cc_final: 0.6819 (mm) REVERT: C 122 ASN cc_start: 0.7989 (m-40) cc_final: 0.7189 (p0) REVERT: C 420 TYR cc_start: 0.6598 (t80) cc_final: 0.6159 (t80) REVERT: C 521 VAL cc_start: 0.5976 (OUTLIER) cc_final: 0.5711 (t) REVERT: C 539 ASN cc_start: 0.7943 (t0) cc_final: 0.7304 (p0) REVERT: C 728 MET cc_start: 0.9037 (ppp) cc_final: 0.7244 (ppp) REVERT: C 897 MET cc_start: 0.6153 (mtt) cc_final: 0.5673 (mtp) REVERT: C 982 ASP cc_start: 0.8015 (p0) cc_final: 0.7602 (p0) REVERT: D 74 LYS cc_start: 0.5860 (tptt) cc_final: 0.5282 (tptt) REVERT: D 192 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7934 (tpm170) REVERT: D 295 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8386 (p0) REVERT: D 332 MET cc_start: -0.2064 (tmm) cc_final: -0.2923 (ptp) REVERT: D 526 GLN cc_start: 0.7136 (tp40) cc_final: 0.6796 (tm-30) REVERT: D 577 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8070 (tptt) outliers start: 121 outliers final: 42 residues processed: 384 average time/residue: 0.3811 time to fit residues: 243.5046 Evaluate side-chains 281 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1072 PHE Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 853 ASN Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 709 ILE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 803 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1135 TYR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 284 optimal weight: 0.0270 chunk 232 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 20.0000 chunk 369 optimal weight: 30.0000 chunk 304 optimal weight: 0.8980 chunk 339 optimal weight: 50.0000 chunk 116 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 242 HIS A 314 ASN A 748 ASN A1105 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 502 HIS B 748 ASN B 784 GLN B 853 ASN ** B 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 HIS B1085 HIS C 46 HIS C 66 HIS ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN C 910 GLN ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 HIS D 61 ASN D 64 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 30544 Z= 0.274 Angle : 0.669 10.717 41560 Z= 0.345 Chirality : 0.044 0.275 4633 Planarity : 0.005 0.094 5380 Dihedral : 4.683 27.546 4060 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.80 % Favored : 92.12 % Rotamer: Outliers : 5.43 % Allowed : 32.82 % Favored : 61.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3742 helix: 1.05 (0.17), residues: 999 sheet: -1.30 (0.21), residues: 573 loop : -2.15 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 477 HIS 0.015 0.001 HIS A1080 PHE 0.029 0.002 PHE B 397 TYR 0.044 0.002 TYR B 348 ARG 0.007 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 248 time to evaluate : 3.335 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 51 LEU cc_start: 0.8085 (mm) cc_final: 0.7288 (tp) REVERT: A 126 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7082 (tptt) REVERT: A 402 ASN cc_start: 0.4206 (OUTLIER) cc_final: 0.3559 (p0) REVERT: A 752 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8550 (mp10) REVERT: A 897 MET cc_start: 0.8200 (tpp) cc_final: 0.7944 (tpp) REVERT: B 198 PHE cc_start: 0.7708 (m-80) cc_final: 0.7495 (m-80) REVERT: B 272 PHE cc_start: 0.7490 (m-80) cc_final: 0.7080 (t80) REVERT: B 477 CYS cc_start: 0.2827 (OUTLIER) cc_final: 0.1240 (p) REVERT: B 744 THR cc_start: 0.8530 (t) cc_final: 0.8196 (t) REVERT: B 748 ASN cc_start: 0.8793 (m-40) cc_final: 0.8469 (m110) REVERT: B 897 MET cc_start: 0.8604 (tpp) cc_final: 0.8262 (tpp) REVERT: C 81 LEU cc_start: 0.7786 (tt) cc_final: 0.7107 (mm) REVERT: C 89 PHE cc_start: 0.7643 (t80) cc_final: 0.7287 (t80) REVERT: C 189 PHE cc_start: 0.7689 (m-80) cc_final: 0.7268 (m-10) REVERT: C 239 LEU cc_start: 0.8644 (mt) cc_final: 0.7970 (pt) REVERT: C 420 TYR cc_start: 0.6933 (t80) cc_final: 0.6259 (t80) REVERT: C 728 MET cc_start: 0.8898 (ppp) cc_final: 0.7167 (ppp) REVERT: C 748 ASN cc_start: 0.8755 (m-40) cc_final: 0.8527 (m110) REVERT: C 897 MET cc_start: 0.7635 (mtt) cc_final: 0.7225 (mtp) REVERT: C 1055 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6792 (m-70) REVERT: D 82 MET cc_start: 0.4853 (ppp) cc_final: 0.4579 (ppp) REVERT: D 190 MET cc_start: 0.2144 (ppp) cc_final: 0.1279 (ppp) REVERT: D 295 ASP cc_start: 0.8713 (t0) cc_final: 0.8346 (p0) REVERT: D 364 VAL cc_start: -0.0114 (OUTLIER) cc_final: -0.1255 (t) REVERT: D 476 LYS cc_start: -0.0234 (OUTLIER) cc_final: -0.0484 (tmmt) REVERT: D 480 MET cc_start: -0.0998 (ppp) cc_final: -0.1262 (ttp) REVERT: D 506 VAL cc_start: 0.3100 (OUTLIER) cc_final: 0.2854 (p) REVERT: D 526 GLN cc_start: 0.7086 (tp40) cc_final: 0.6758 (tm-30) REVERT: D 557 MET cc_start: 0.2258 (tmm) cc_final: 0.1896 (ttt) REVERT: D 577 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7941 (tptt) outliers start: 180 outliers final: 83 residues processed: 410 average time/residue: 0.3884 time to fit residues: 268.0279 Evaluate side-chains 296 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 207 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1055 HIS Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 363 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 325 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 279 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 923 GLN A 954 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 ASN B 748 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 869 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 330 ASN D 388 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 30544 Z= 0.481 Angle : 0.799 30.354 41560 Z= 0.410 Chirality : 0.047 0.306 4633 Planarity : 0.006 0.071 5380 Dihedral : 5.360 25.215 4060 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.11 % Favored : 90.78 % Rotamer: Outliers : 6.61 % Allowed : 32.40 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 3742 helix: 0.83 (0.17), residues: 988 sheet: -1.32 (0.21), residues: 530 loop : -2.37 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 69 HIS 0.075 0.003 HIS C1055 PHE 0.029 0.003 PHE C 512 TYR 0.028 0.002 TYR D 50 ARG 0.029 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 186 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8346 (mt) REVERT: A 282 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 359 VAL cc_start: 0.4603 (OUTLIER) cc_final: 0.4159 (t) REVERT: A 608 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9137 (pt) REVERT: A 954 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8676 (pp30) REVERT: A 987 GLU cc_start: 0.8910 (mp0) cc_final: 0.8327 (mp0) REVERT: B 201 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5671 (m-80) REVERT: B 477 CYS cc_start: 0.3219 (OUTLIER) cc_final: 0.1724 (p) REVERT: B 722 GLU cc_start: 0.8749 (pm20) cc_final: 0.8501 (pm20) REVERT: B 985 GLU cc_start: 0.9068 (tp30) cc_final: 0.8845 (tp30) REVERT: C 81 LEU cc_start: 0.8147 (tt) cc_final: 0.7473 (mm) REVERT: C 156 VAL cc_start: 0.4498 (OUTLIER) cc_final: 0.4115 (p) REVERT: C 420 TYR cc_start: 0.7094 (t80) cc_final: 0.6542 (t80) REVERT: C 694 MET cc_start: 0.9209 (mmm) cc_final: 0.8893 (tpt) REVERT: C 728 MET cc_start: 0.9202 (ppp) cc_final: 0.8039 (ppp) REVERT: C 784 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8072 (tp40) REVERT: C 951 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8315 (t-170) REVERT: C 1026 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8736 (tpp) REVERT: C 1047 MET cc_start: 0.8138 (mmm) cc_final: 0.7698 (mmm) REVERT: D 60 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6420 (pt0) REVERT: D 74 LYS cc_start: 0.6628 (tptt) cc_final: 0.5867 (tptt) REVERT: D 295 ASP cc_start: 0.8699 (t0) cc_final: 0.8352 (p0) REVERT: D 332 MET cc_start: -0.2445 (tmm) cc_final: -0.2956 (ptm) REVERT: D 364 VAL cc_start: 0.0238 (OUTLIER) cc_final: -0.0269 (t) REVERT: D 526 GLN cc_start: 0.7200 (tp40) cc_final: 0.6833 (tm-30) REVERT: D 577 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7645 (tptt) REVERT: D 581 VAL cc_start: -0.2204 (OUTLIER) cc_final: -0.2529 (p) outliers start: 219 outliers final: 129 residues processed: 394 average time/residue: 0.3614 time to fit residues: 238.6336 Evaluate side-chains 303 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 160 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 951 HIS Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 848 CYS Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 0 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1033 GLN B 134 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 869 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30544 Z= 0.188 Angle : 0.636 45.497 41560 Z= 0.304 Chirality : 0.043 0.238 4633 Planarity : 0.004 0.064 5380 Dihedral : 4.750 22.955 4060 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.11 % Favored : 92.78 % Rotamer: Outliers : 4.16 % Allowed : 34.78 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3742 helix: 1.17 (0.17), residues: 990 sheet: -1.38 (0.21), residues: 553 loop : -2.18 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 477 HIS 0.008 0.001 HIS C1055 PHE 0.025 0.001 PHE D 390 TYR 0.017 0.001 TYR A 492 ARG 0.004 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 166 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.9184 (t80) cc_final: 0.8961 (t80) REVERT: A 226 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 608 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9222 (pt) REVERT: A 694 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8329 (mmt) REVERT: A 735 CYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7286 (p) REVERT: A 954 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8787 (pp30) REVERT: A 987 GLU cc_start: 0.8910 (mp0) cc_final: 0.8374 (mp0) REVERT: B 150 MET cc_start: 0.6788 (mmp) cc_final: 0.6527 (mmt) REVERT: B 187 ARG cc_start: 0.8456 (mtt180) cc_final: 0.8150 (mtt180) REVERT: B 198 PHE cc_start: 0.8186 (m-80) cc_final: 0.7441 (m-80) REVERT: B 201 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: B 230 ILE cc_start: 0.4827 (OUTLIER) cc_final: 0.4538 (tt) REVERT: B 477 CYS cc_start: 0.2686 (OUTLIER) cc_final: 0.1014 (p) REVERT: B 584 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8057 (tp) REVERT: C 81 LEU cc_start: 0.8347 (tt) cc_final: 0.7608 (mm) REVERT: C 101 TRP cc_start: 0.5991 (m-10) cc_final: 0.5225 (m-90) REVERT: C 102 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7783 (tt) REVERT: C 156 VAL cc_start: 0.4582 (OUTLIER) cc_final: 0.4249 (p) REVERT: C 420 TYR cc_start: 0.7560 (t80) cc_final: 0.6450 (t80) REVERT: C 728 MET cc_start: 0.9365 (ppp) cc_final: 0.8059 (ppp) REVERT: C 951 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8230 (t-170) REVERT: C 1026 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7961 (ttp) REVERT: C 1047 MET cc_start: 0.7991 (mmm) cc_final: 0.7202 (tmm) REVERT: C 1089 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: D 74 LYS cc_start: 0.6611 (tptt) cc_final: 0.5895 (tptt) REVERT: D 82 MET cc_start: 0.5306 (ppp) cc_final: 0.5062 (ppp) REVERT: D 295 ASP cc_start: 0.8667 (t0) cc_final: 0.8338 (p0) REVERT: D 332 MET cc_start: -0.2274 (tmm) cc_final: -0.2785 (ptm) REVERT: D 526 GLN cc_start: 0.7224 (tp40) cc_final: 0.6841 (tm-30) REVERT: D 546 ASN cc_start: 0.4038 (OUTLIER) cc_final: 0.3730 (m-40) REVERT: D 557 MET cc_start: 0.2294 (tmm) cc_final: 0.1942 (ttt) REVERT: D 577 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7710 (tptt) REVERT: D 581 VAL cc_start: -0.2116 (OUTLIER) cc_final: -0.2466 (p) outliers start: 138 outliers final: 82 residues processed: 293 average time/residue: 0.3905 time to fit residues: 191.3254 Evaluate side-chains 251 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 153 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 461 TRP Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 89 optimal weight: 0.0000 chunk 363 optimal weight: 20.0000 chunk 301 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 0.0170 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.0028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN C 784 GLN ** C 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30544 Z= 0.240 Angle : 0.640 44.651 41560 Z= 0.308 Chirality : 0.043 0.182 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.665 35.535 4060 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.07 % Favored : 91.82 % Rotamer: Outliers : 5.07 % Allowed : 33.51 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3742 helix: 1.29 (0.17), residues: 989 sheet: -1.47 (0.21), residues: 561 loop : -2.13 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 101 HIS 0.006 0.001 HIS A 951 PHE 0.020 0.001 PHE C 368 TYR 0.029 0.001 TYR C 262 ARG 0.008 0.001 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 160 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (mmt) REVERT: A 728 MET cc_start: 0.8916 (ppp) cc_final: 0.8520 (ppp) REVERT: A 735 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7293 (p) REVERT: A 917 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: A 987 GLU cc_start: 0.8968 (mp0) cc_final: 0.8597 (mp0) REVERT: B 150 MET cc_start: 0.6977 (mmp) cc_final: 0.6640 (mmt) REVERT: B 187 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8264 (mtt180) REVERT: B 198 PHE cc_start: 0.8241 (m-80) cc_final: 0.7483 (m-80) REVERT: B 201 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5633 (m-80) REVERT: B 230 ILE cc_start: 0.4861 (OUTLIER) cc_final: 0.4640 (tt) REVERT: B 290 LEU cc_start: 0.8536 (tt) cc_final: 0.8224 (tt) REVERT: B 477 CYS cc_start: 0.2744 (OUTLIER) cc_final: 0.1163 (p) REVERT: B 584 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8196 (tp) REVERT: C 81 LEU cc_start: 0.8379 (tt) cc_final: 0.7561 (mm) REVERT: C 101 TRP cc_start: 0.5893 (m-10) cc_final: 0.5042 (m-90) REVERT: C 156 VAL cc_start: 0.4778 (OUTLIER) cc_final: 0.4471 (p) REVERT: C 420 TYR cc_start: 0.7609 (t80) cc_final: 0.6696 (t80) REVERT: C 694 MET cc_start: 0.9088 (mmm) cc_final: 0.8516 (tpt) REVERT: C 728 MET cc_start: 0.9349 (ppp) cc_final: 0.8030 (ppp) REVERT: C 756 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (t80) REVERT: C 951 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8235 (t-170) REVERT: C 1026 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8061 (ttp) REVERT: C 1047 MET cc_start: 0.8012 (mmm) cc_final: 0.7359 (tmm) REVERT: C 1089 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: D 82 MET cc_start: 0.5222 (ppp) cc_final: 0.4970 (ppp) REVERT: D 295 ASP cc_start: 0.8662 (t0) cc_final: 0.8336 (p0) REVERT: D 332 MET cc_start: -0.1869 (tmm) cc_final: -0.2469 (ptm) REVERT: D 526 GLN cc_start: 0.7254 (tp40) cc_final: 0.6864 (tm-30) REVERT: D 546 ASN cc_start: 0.4113 (OUTLIER) cc_final: 0.3798 (m-40) REVERT: D 577 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7625 (tptt) REVERT: D 581 VAL cc_start: -0.1993 (OUTLIER) cc_final: -0.2349 (p) outliers start: 168 outliers final: 107 residues processed: 314 average time/residue: 0.3768 time to fit residues: 197.7054 Evaluate side-chains 270 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 149 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 chunk 226 optimal weight: 0.2980 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 951 HIS B 952 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 539 ASN C 869 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30544 Z= 0.210 Angle : 0.626 43.543 41560 Z= 0.298 Chirality : 0.042 0.190 4633 Planarity : 0.004 0.061 5380 Dihedral : 4.556 22.648 4060 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.43 % Favored : 92.49 % Rotamer: Outliers : 4.25 % Allowed : 34.12 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3742 helix: 1.37 (0.17), residues: 995 sheet: -1.50 (0.21), residues: 564 loop : -2.07 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 461 HIS 0.008 0.001 HIS C 336 PHE 0.033 0.001 PHE B1072 TYR 0.044 0.001 TYR D 50 ARG 0.007 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 162 time to evaluate : 2.628 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: A 389 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: A 694 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8377 (mmt) REVERT: A 728 MET cc_start: 0.8944 (ppp) cc_final: 0.8498 (ppp) REVERT: A 735 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7271 (p) REVERT: A 866 MET cc_start: 0.8946 (mtt) cc_final: 0.8559 (mtt) REVERT: A 987 GLU cc_start: 0.8962 (mp0) cc_final: 0.8478 (mp0) REVERT: B 150 MET cc_start: 0.7062 (mmp) cc_final: 0.6792 (mmt) REVERT: B 198 PHE cc_start: 0.8277 (m-80) cc_final: 0.7535 (m-80) REVERT: B 201 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: B 230 ILE cc_start: 0.5072 (OUTLIER) cc_final: 0.4835 (tt) REVERT: B 477 CYS cc_start: 0.2581 (OUTLIER) cc_final: 0.1045 (p) REVERT: C 81 LEU cc_start: 0.8419 (tt) cc_final: 0.7715 (mm) REVERT: C 101 TRP cc_start: 0.6022 (m-10) cc_final: 0.4849 (m-90) REVERT: C 420 TYR cc_start: 0.7742 (t80) cc_final: 0.6302 (t80) REVERT: C 694 MET cc_start: 0.9058 (mmm) cc_final: 0.8361 (tpt) REVERT: C 728 MET cc_start: 0.9361 (ppp) cc_final: 0.8011 (ppp) REVERT: C 756 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7880 (t80) REVERT: C 951 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (t-170) REVERT: C 1026 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7946 (ttp) REVERT: C 1047 MET cc_start: 0.7971 (mmm) cc_final: 0.7306 (tmm) REVERT: C 1089 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8312 (mm-30) REVERT: D 82 MET cc_start: 0.5239 (ppp) cc_final: 0.4995 (ppp) REVERT: D 192 ARG cc_start: 0.8358 (mtm180) cc_final: 0.8098 (tpm170) REVERT: D 295 ASP cc_start: 0.8650 (t0) cc_final: 0.8323 (p0) REVERT: D 332 MET cc_start: -0.1866 (tmm) cc_final: -0.2466 (ptm) REVERT: D 526 GLN cc_start: 0.7183 (tp40) cc_final: 0.6787 (tm-30) REVERT: D 546 ASN cc_start: 0.4103 (OUTLIER) cc_final: 0.3781 (m-40) REVERT: D 577 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7557 (tptt) REVERT: D 581 VAL cc_start: -0.1675 (OUTLIER) cc_final: -0.2108 (p) outliers start: 141 outliers final: 107 residues processed: 287 average time/residue: 0.3901 time to fit residues: 184.0917 Evaluate side-chains 274 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 155 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 951 HIS Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 179 optimal weight: 0.0040 chunk 33 optimal weight: 40.0000 chunk 284 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30544 Z= 0.265 Angle : 0.648 41.041 41560 Z= 0.313 Chirality : 0.043 0.186 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.631 24.003 4060 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.66 % Favored : 91.26 % Rotamer: Outliers : 4.77 % Allowed : 33.33 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3742 helix: 1.34 (0.17), residues: 993 sheet: -1.59 (0.21), residues: 570 loop : -2.03 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 461 HIS 0.055 0.002 HIS B 951 PHE 0.029 0.001 PHE C1072 TYR 0.030 0.001 TYR D 50 ARG 0.014 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 153 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: A 494 PHE cc_start: 0.3397 (OUTLIER) cc_final: 0.2800 (m-80) REVERT: A 728 MET cc_start: 0.8881 (ppp) cc_final: 0.8432 (ppp) REVERT: A 735 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7327 (p) REVERT: B 198 PHE cc_start: 0.8274 (m-80) cc_final: 0.7519 (m-80) REVERT: B 201 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: B 272 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: B 477 CYS cc_start: 0.2743 (OUTLIER) cc_final: 0.1271 (p) REVERT: B 975 ASN cc_start: 0.8979 (m-40) cc_final: 0.8267 (t0) REVERT: C 81 LEU cc_start: 0.8547 (tt) cc_final: 0.7712 (mm) REVERT: C 101 TRP cc_start: 0.6462 (m-10) cc_final: 0.5005 (m-90) REVERT: C 156 VAL cc_start: 0.5416 (OUTLIER) cc_final: 0.5187 (p) REVERT: C 420 TYR cc_start: 0.7775 (t80) cc_final: 0.6312 (t80) REVERT: C 694 MET cc_start: 0.9082 (mmm) cc_final: 0.8828 (tpt) REVERT: C 728 MET cc_start: 0.9316 (ppp) cc_final: 0.8017 (ppp) REVERT: C 756 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7955 (t80) REVERT: C 1026 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8460 (tpp) REVERT: C 1047 MET cc_start: 0.8009 (mmm) cc_final: 0.7332 (tmm) REVERT: C 1089 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (mm-30) REVERT: D 82 MET cc_start: 0.5050 (ppp) cc_final: 0.4801 (ppp) REVERT: D 295 ASP cc_start: 0.8649 (t0) cc_final: 0.8321 (p0) REVERT: D 332 MET cc_start: -0.1899 (tmm) cc_final: -0.2494 (ptm) REVERT: D 523 PHE cc_start: 0.6088 (m-80) cc_final: 0.5849 (t80) REVERT: D 526 GLN cc_start: 0.7240 (tp40) cc_final: 0.6809 (tm-30) REVERT: D 546 ASN cc_start: 0.4264 (OUTLIER) cc_final: 0.3927 (m-40) REVERT: D 577 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7429 (tptt) REVERT: D 581 VAL cc_start: -0.1544 (OUTLIER) cc_final: -0.2041 (p) outliers start: 158 outliers final: 121 residues processed: 295 average time/residue: 0.3770 time to fit residues: 189.0721 Evaluate side-chains 281 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 148 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 7.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 337 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30544 Z= 0.215 Angle : 0.636 39.330 41560 Z= 0.303 Chirality : 0.042 0.186 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.535 22.825 4060 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 4.25 % Allowed : 33.97 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3742 helix: 1.37 (0.17), residues: 996 sheet: -1.52 (0.20), residues: 575 loop : -2.04 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 461 HIS 0.008 0.001 HIS C 336 PHE 0.021 0.001 PHE C1072 TYR 0.027 0.001 TYR D 50 ARG 0.005 0.000 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 159 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: A 494 PHE cc_start: 0.2879 (OUTLIER) cc_final: 0.2337 (m-80) REVERT: A 728 MET cc_start: 0.8950 (ppp) cc_final: 0.8508 (ppp) REVERT: A 735 CYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7320 (p) REVERT: B 150 MET cc_start: 0.6988 (mmp) cc_final: 0.6756 (mmt) REVERT: B 201 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: B 272 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: B 477 CYS cc_start: 0.2759 (OUTLIER) cc_final: 0.1290 (p) REVERT: B 648 ILE cc_start: 0.9418 (pt) cc_final: 0.9206 (pt) REVERT: B 975 ASN cc_start: 0.8994 (m-40) cc_final: 0.8312 (t0) REVERT: C 81 LEU cc_start: 0.8674 (tt) cc_final: 0.7844 (mm) REVERT: C 694 MET cc_start: 0.9092 (mmm) cc_final: 0.8875 (tpt) REVERT: C 728 MET cc_start: 0.9345 (ppp) cc_final: 0.8580 (ppp) REVERT: C 756 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7944 (t80) REVERT: C 951 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8241 (t-170) REVERT: C 1047 MET cc_start: 0.7987 (mmm) cc_final: 0.7437 (mmm) REVERT: D 82 MET cc_start: 0.5109 (ppp) cc_final: 0.4861 (ppp) REVERT: D 295 ASP cc_start: 0.8642 (t0) cc_final: 0.8290 (p0) REVERT: D 332 MET cc_start: -0.1870 (tmm) cc_final: -0.2465 (ptm) REVERT: D 546 ASN cc_start: 0.4278 (OUTLIER) cc_final: 0.3956 (m-40) REVERT: D 577 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7420 (tptt) REVERT: D 581 VAL cc_start: -0.1468 (OUTLIER) cc_final: -0.1970 (p) outliers start: 141 outliers final: 118 residues processed: 286 average time/residue: 0.3658 time to fit residues: 179.0886 Evaluate side-chains 276 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 148 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 951 HIS Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 344 CYS Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 3.9990 chunk 357 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1105 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.8626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30544 Z= 0.320 Angle : 0.690 36.814 41560 Z= 0.336 Chirality : 0.044 0.187 4633 Planarity : 0.005 0.057 5380 Dihedral : 4.785 24.806 4060 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.14 % Favored : 90.75 % Rotamer: Outliers : 4.13 % Allowed : 34.09 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3742 helix: 1.26 (0.17), residues: 987 sheet: -1.57 (0.21), residues: 560 loop : -2.10 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 101 HIS 0.017 0.001 HIS D 378 PHE 0.028 0.002 PHE D 523 TYR 0.027 0.002 TYR D 50 ARG 0.020 0.001 ARG C 631 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 152 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: A 494 PHE cc_start: 0.3343 (OUTLIER) cc_final: 0.2681 (m-80) REVERT: A 728 MET cc_start: 0.8932 (ppp) cc_final: 0.8436 (ppp) REVERT: A 735 CYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7338 (p) REVERT: A 917 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: B 150 MET cc_start: 0.7300 (mmp) cc_final: 0.7081 (mmt) REVERT: B 198 PHE cc_start: 0.8607 (m-80) cc_final: 0.7926 (m-80) REVERT: B 201 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: B 272 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: B 477 CYS cc_start: 0.2902 (OUTLIER) cc_final: 0.1591 (p) REVERT: B 570 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8799 (p) REVERT: B 975 ASN cc_start: 0.9092 (m-40) cc_final: 0.8457 (t0) REVERT: C 304 THR cc_start: 0.8811 (m) cc_final: 0.8569 (p) REVERT: C 631 ARG cc_start: 0.8109 (ptp90) cc_final: 0.7708 (ptp-170) REVERT: C 694 MET cc_start: 0.9136 (mmm) cc_final: 0.8551 (tpt) REVERT: C 728 MET cc_start: 0.9272 (ppp) cc_final: 0.8075 (ppp) REVERT: C 756 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7980 (t80) REVERT: C 1047 MET cc_start: 0.8019 (mmm) cc_final: 0.7450 (mmm) REVERT: D 74 LYS cc_start: 0.7353 (tptt) cc_final: 0.6935 (mmmt) REVERT: D 82 MET cc_start: 0.5214 (ppp) cc_final: 0.4955 (ppp) REVERT: D 295 ASP cc_start: 0.8536 (t0) cc_final: 0.8158 (p0) REVERT: D 332 MET cc_start: -0.1685 (tmm) cc_final: -0.2266 (ptm) REVERT: D 454 TYR cc_start: 0.5998 (t80) cc_final: 0.5535 (t80) REVERT: D 577 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7378 (tptt) outliers start: 137 outliers final: 114 residues processed: 278 average time/residue: 0.3854 time to fit residues: 184.4323 Evaluate side-chains 265 residues out of total 3315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 142 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 757 CYS Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1071 ASN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 757 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 336 HIS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 614 CYS Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 958 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 275 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 chunk 125 optimal weight: 0.0980 chunk 306 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 898 GLN C 962 GLN C1033 GLN C1051 GLN D 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.100432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.069585 restraints weight = 146728.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070131 restraints weight = 85745.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070631 restraints weight = 55708.104| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.8643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30544 Z= 0.162 Angle : 0.628 35.343 41560 Z= 0.300 Chirality : 0.043 0.179 4633 Planarity : 0.004 0.060 5380 Dihedral : 4.507 23.074 4060 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 2.93 % Allowed : 35.38 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3742 helix: 1.37 (0.17), residues: 989 sheet: -1.57 (0.20), residues: 581 loop : -2.03 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 461 HIS 0.013 0.001 HIS D 374 PHE 0.018 0.001 PHE B 372 TYR 0.023 0.001 TYR D 50 ARG 0.009 0.000 ARG C 631 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6086.76 seconds wall clock time: 111 minutes 50.55 seconds (6710.55 seconds total)