Starting phenix.real_space_refine on Sun Jul 5 12:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo5_33982/07_2026/7yo5_33982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo5_33982/07_2026/7yo5_33982.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 { model { file = "/net/cci-nas-00/data/ceres_data/7yo5_33982/07_2026/7yo5_33982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo5_33982/07_2026/7yo5_33982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yo5_33982/07_2026/7yo5_33982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo5_33982/07_2026/7yo5_33982.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 180 5.16 5 C 18104 2.51 5 N 4532 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27844 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6959 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 27, 'TRANS': 845} Chain breaks: 5 Chain: "B" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6959 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 27, 'TRANS': 845} Chain breaks: 5 Chain: "C" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6959 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 27, 'TRANS': 845} Chain breaks: 5 Chain: "D" Number of atoms: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6959 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 27, 'TRANS': 845} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 6.66, per 1000 atoms: 0.24 Number of scatterers: 27844 At special positions: 0 Unit cell: (141.432, 153.384, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 180 16.00 O 5020 8.00 N 4532 7.00 C 18104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 22 sheets defined 54.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 removed outlier: 3.896A pdb=" N TRP A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 109 through 135 removed outlier: 3.532A pdb=" N ARG A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 171 removed outlier: 3.752A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix removed outlier: 4.649A pdb=" N VAL A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.555A pdb=" N LEU A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.662A pdb=" N LEU A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.643A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.814A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.978A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 555 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.551A pdb=" N LEU A 561 " --> pdb=" O CYS A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.754A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.612A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 795 No H-bonds generated for 'chain 'A' and resid 793 through 795' Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 887 through 892 removed outlier: 4.027A pdb=" N LEU A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 892' Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 921 Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 930 through 942 removed outlier: 4.394A pdb=" N LEU A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.618A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 47 removed outlier: 3.848A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 109 through 135 Processing helix chain 'B' and resid 149 through 170 removed outlier: 3.787A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.636A pdb=" N LEU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix removed outlier: 4.001A pdb=" N TYR B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.965A pdb=" N LEU B 209 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.589A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.572A pdb=" N ASN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 328 Proline residue: B 320 - end of helix removed outlier: 3.837A pdb=" N ILE B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.818A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.860A pdb=" N ALA B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.036A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.964A pdb=" N PHE B 545 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 546 " --> pdb=" O SER B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 549 through 555 Processing helix chain 'B' and resid 556 through 562 removed outlier: 4.109A pdb=" N LYS B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.893A pdb=" N PHE B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 759 through 771 removed outlier: 3.626A pdb=" N LEU B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.555A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 918 through 921 Processing helix chain 'B' and resid 922 through 930 Processing helix chain 'B' and resid 930 through 941 removed outlier: 4.482A pdb=" N LEU B 934 " --> pdb=" O ASN B 930 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.527A pdb=" N ASP B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 988 removed outlier: 4.152A pdb=" N PHE B 987 " --> pdb=" O ASP B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'C' and resid 21 through 45 removed outlier: 3.514A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP C 43 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 95 through 104 removed outlier: 3.874A pdb=" N MET C 104 " --> pdb=" O TRP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 136 removed outlier: 3.508A pdb=" N ARG C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 171 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 181 through 200 Proline residue: C 191 - end of helix removed outlier: 4.065A pdb=" N VAL C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.873A pdb=" N LEU C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 224 removed outlier: 4.122A pdb=" N GLU C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 Proline residue: C 320 - end of helix removed outlier: 3.631A pdb=" N GLY C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.703A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.570A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.103A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 556 removed outlier: 3.923A pdb=" N LEU C 556 " --> pdb=" O THR C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 605 Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 733 through 739 removed outlier: 3.831A pdb=" N VAL C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET C 739 " --> pdb=" O ARG C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.506A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 768 removed outlier: 3.516A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.505A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.881A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.994A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 919 through 930 removed outlier: 4.279A pdb=" N LEU C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 929 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 942 removed outlier: 4.440A pdb=" N LEU C 934 " --> pdb=" O ASN C 930 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 972 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.156A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.554A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.992A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.550A pdb=" N SER D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 135 removed outlier: 3.851A pdb=" N VAL D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 170 removed outlier: 4.241A pdb=" N ILE D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 180 through 199 Proline residue: D 191 - end of helix removed outlier: 3.958A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.786A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 222 Processing helix chain 'D' and resid 229 through 259 removed outlier: 3.675A pdb=" N SER D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 318 Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 removed outlier: 3.505A pdb=" N HIS D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 463 through 470 Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.556A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.939A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.928A pdb=" N PHE D 545 " --> pdb=" O SER D 542 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 546 " --> pdb=" O SER D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 546' Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 601 through 611 removed outlier: 3.949A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.882A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 759 through 771 removed outlier: 4.712A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 817 through 829 removed outlier: 3.851A pdb=" N ILE D 821 " --> pdb=" O ASP D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 3.801A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 920 through 930 removed outlier: 3.749A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 941 removed outlier: 4.654A pdb=" N LEU D 934 " --> pdb=" O ASN D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 967 through 971 Processing helix chain 'D' and resid 986 through 991 removed outlier: 3.951A pdb=" N LEU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 141 removed outlier: 4.387A pdb=" N SER A 140 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 400 removed outlier: 6.309A pdb=" N ILE A 375 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 459 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 539 removed outlier: 4.263A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.290A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.563A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N HIS A 718 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS A 800 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 720 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE A 802 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS A 722 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER A 804 " --> pdb=" O CYS A 722 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 724 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 881 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER A 804 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 976 through 981 removed outlier: 4.318A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.610A pdb=" N SER B 140 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 399 removed outlier: 8.735A pdb=" N GLU B 399 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 375 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 539 removed outlier: 3.619A pdb=" N GLY B 595 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 566 " --> pdb=" O PHE B 596 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 776 through 779 removed outlier: 5.801A pdb=" N HIS B 718 " --> pdb=" O CYS B 797 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 799 " --> pdb=" O HIS B 718 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 804 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 977 through 981 removed outlier: 3.545A pdb=" N LEU B 980 " --> pdb=" O ILE B1049 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B1048 " --> pdb=" O ILE B1014 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE B1014 " --> pdb=" O LEU B1048 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE B1050 " --> pdb=" O PHE B1012 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.529A pdb=" N PHE C 377 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE C 345 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 346 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 535 through 539 removed outlier: 3.781A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.073A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.504A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS C 718 " --> pdb=" O ASP C 798 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS C 800 " --> pdb=" O HIS C 718 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 720 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE C 802 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS C 722 " --> pdb=" O ILE C 802 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER C 804 " --> pdb=" O CYS C 722 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE C 724 " --> pdb=" O SER C 804 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 881 " --> pdb=" O ILE C 802 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER C 804 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 977 through 981 removed outlier: 3.681A pdb=" N ALA C 978 " --> pdb=" O CYS C1051 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 139 through 140 removed outlier: 3.703A pdb=" N SER D 140 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 398 through 399 removed outlier: 3.607A pdb=" N GLU D 399 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 378 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 459 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 535 through 538 Processing sheet with id=AC2, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.454A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 962 " --> pdb=" O TYR D 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 776 through 779 removed outlier: 6.233A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS D 718 " --> pdb=" O ASP D 798 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N CYS D 800 " --> pdb=" O HIS D 718 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL D 720 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE D 802 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS D 722 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER D 804 " --> pdb=" O CYS D 722 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 724 " --> pdb=" O SER D 804 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER D 804 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 977 through 981 removed outlier: 6.622A pdb=" N LEU D1048 " --> pdb=" O ILE D1014 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE D1014 " --> pdb=" O LEU D1048 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE D1050 " --> pdb=" O PHE D1012 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU D1010 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3627 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: 5.88 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4468 1.32 - 1.44: 7869 1.44 - 1.57: 15871 1.57 - 1.69: 0 1.69 - 1.82: 272 Bond restraints: 28480 Sorted by residual: bond pdb=" CA SER C 286 " pdb=" CB SER C 286 " ideal model delta sigma weight residual 1.532 1.450 0.082 1.74e-02 3.30e+03 2.23e+01 bond pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.08e-02 8.57e+03 1.15e+01 bond pdb=" N THR A 297 " pdb=" CA THR A 297 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" C PRO A 947 " pdb=" O PRO A 947 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" N GLN B 108 " pdb=" CA GLN B 108 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 9.89e+00 ... (remaining 28475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 38200 2.67 - 5.34: 400 5.34 - 8.01: 45 8.01 - 10.69: 5 10.69 - 13.36: 2 Bond angle restraints: 38652 Sorted by residual: angle pdb=" N GLN B 108 " pdb=" CA GLN B 108 " pdb=" C GLN B 108 " ideal model delta sigma weight residual 111.36 122.13 -10.77 1.09e+00 8.42e-01 9.76e+01 angle pdb=" N SER C 286 " pdb=" CA SER C 286 " pdb=" C SER C 286 " ideal model delta sigma weight residual 113.17 102.75 10.42 1.26e+00 6.30e-01 6.84e+01 angle pdb=" N LEU B 110 " pdb=" CA LEU B 110 " pdb=" C LEU B 110 " ideal model delta sigma weight residual 111.71 103.63 8.08 1.15e+00 7.56e-01 4.94e+01 angle pdb=" C THR C 287 " pdb=" CA THR C 287 " pdb=" CB THR C 287 " ideal model delta sigma weight residual 110.35 123.71 -13.36 1.91e+00 2.74e-01 4.89e+01 angle pdb=" N TYR A 996 " pdb=" CA TYR A 996 " pdb=" C TYR A 996 " ideal model delta sigma weight residual 112.23 105.09 7.14 1.26e+00 6.30e-01 3.21e+01 ... (remaining 38647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15089 17.22 - 34.43: 1387 34.43 - 51.65: 220 51.65 - 68.86: 37 68.86 - 86.08: 19 Dihedral angle restraints: 16752 sinusoidal: 6540 harmonic: 10212 Sorted by residual: dihedral pdb=" C THR C 287 " pdb=" N THR C 287 " pdb=" CA THR C 287 " pdb=" CB THR C 287 " ideal model delta harmonic sigma weight residual -122.00 -142.36 20.36 0 2.50e+00 1.60e-01 6.64e+01 dihedral pdb=" N TRP B 263 " pdb=" C TRP B 263 " pdb=" CA TRP B 263 " pdb=" CB TRP B 263 " ideal model delta harmonic sigma weight residual 122.80 137.83 -15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" C TRP B 263 " pdb=" N TRP B 263 " pdb=" CA TRP B 263 " pdb=" CB TRP B 263 " ideal model delta harmonic sigma weight residual -122.60 -136.95 14.35 0 2.50e+00 1.60e-01 3.30e+01 ... (remaining 16749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4396 0.140 - 0.281: 39 0.281 - 0.421: 3 0.421 - 0.562: 1 0.562 - 0.702: 1 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA THR C 287 " pdb=" N THR C 287 " pdb=" C THR C 287 " pdb=" CB THR C 287 " both_signs ideal model delta sigma weight residual False 2.53 1.82 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA TRP B 263 " pdb=" N TRP B 263 " pdb=" C TRP B 263 " pdb=" CB TRP B 263 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.79e+00 chirality pdb=" CA GLN B 108 " pdb=" N GLN B 108 " pdb=" C GLN B 108 " pdb=" CB GLN B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 4437 not shown) Planarity restraints: 4832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 413 " -0.015 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ARG B 413 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG B 413 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL B 414 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 428 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C LYS A 428 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 428 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 429 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 554 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.37e+00 pdb=" C CYS D 554 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS D 554 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 555 " -0.017 2.00e-02 2.50e+03 ... (remaining 4829 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.98: 2 1.98 - 2.71: 813 2.71 - 3.44: 42651 3.44 - 4.17: 65864 4.17 - 4.90: 118757 Nonbonded interactions: 228087 Sorted by model distance: nonbonded pdb=" CE LYS C 606 " pdb=" CE2 PHE C 610 " model vdw 1.245 3.740 nonbonded pdb=" CE LYS C 606 " pdb=" CZ PHE C 610 " model vdw 1.884 3.740 nonbonded pdb=" O ASP C 892 " pdb="CA CA C1102 " model vdw 2.048 3.250 nonbonded pdb=" OG1 THR C 706 " pdb=" OE1 GLU C 709 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR D 538 " pdb=" ND2 ASN D 930 " model vdw 2.164 3.120 ... (remaining 228082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.510 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28480 Z= 0.190 Angle : 0.643 13.356 38652 Z= 0.382 Chirality : 0.048 0.702 4440 Planarity : 0.004 0.070 4832 Dihedral : 13.519 86.076 10136 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.29 % Allowed : 0.75 % Favored : 98.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3444 helix: 0.28 (0.13), residues: 1730 sheet: -0.12 (0.28), residues: 352 loop : -1.10 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 113 TYR 0.031 0.001 TYR D1039 PHE 0.037 0.001 PHE A 34 TRP 0.034 0.001 TRP B 263 HIS 0.003 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.19 (28480) covalent geometry : angle 0.64265 / 0.38 (38652) hydrogen bonds : bond 0.15481 / 10.33 ( 1280) hydrogen bonds : angle 6.48623 / 4.72 ( 3627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 780 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6260 (m-80) cc_final: 0.5898 (m-10) REVERT: A 120 PHE cc_start: 0.6218 (t80) cc_final: 0.5866 (t80) REVERT: A 180 GLU cc_start: 0.6618 (tt0) cc_final: 0.5840 (mm-30) REVERT: A 195 VAL cc_start: 0.7393 (p) cc_final: 0.7094 (t) REVERT: A 210 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7868 (mmt90) REVERT: A 252 PHE cc_start: 0.8083 (t80) cc_final: 0.7711 (t80) REVERT: A 309 LEU cc_start: 0.8803 (mp) cc_final: 0.8398 (mp) REVERT: A 409 HIS cc_start: 0.8380 (m-70) cc_final: 0.7824 (m90) REVERT: A 414 VAL cc_start: 0.8509 (m) cc_final: 0.8262 (t) REVERT: A 415 LYS cc_start: 0.8804 (mptt) cc_final: 0.8180 (mmtt) REVERT: A 536 MET cc_start: 0.7979 (tmm) cc_final: 0.6734 (tmm) REVERT: A 1009 MET cc_start: 0.5226 (mmp) cc_final: 0.4114 (mtt) REVERT: B 104 MET cc_start: 0.6420 (tpt) cc_final: 0.5581 (mtt) REVERT: B 154 MET cc_start: 0.6409 (tpp) cc_final: 0.5885 (tpt) REVERT: B 180 GLU cc_start: 0.7028 (tm-30) cc_final: 0.5403 (mm-30) REVERT: B 184 VAL cc_start: 0.7535 (t) cc_final: 0.7168 (t) REVERT: B 188 PHE cc_start: 0.7541 (m-80) cc_final: 0.6945 (m-80) REVERT: B 257 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 353 LEU cc_start: 0.8118 (tp) cc_final: 0.7876 (tt) REVERT: B 384 ASN cc_start: 0.3931 (t0) cc_final: 0.3196 (p0) REVERT: B 386 GLU cc_start: 0.6589 (mp0) cc_final: 0.5629 (tp30) REVERT: B 391 PHE cc_start: 0.5371 (m-10) cc_final: 0.5148 (m-80) REVERT: B 427 ASN cc_start: 0.7122 (t0) cc_final: 0.6666 (t0) REVERT: B 449 ASN cc_start: 0.7060 (t0) cc_final: 0.6858 (t0) REVERT: B 521 GLU cc_start: 0.7637 (pm20) cc_final: 0.7260 (tp30) REVERT: B 536 MET cc_start: 0.8482 (tmm) cc_final: 0.7971 (ttt) REVERT: B 768 GLU cc_start: 0.7089 (mp0) cc_final: 0.5547 (tt0) REVERT: B 817 ASP cc_start: 0.6844 (m-30) cc_final: 0.6580 (m-30) REVERT: B 884 ASN cc_start: 0.8779 (t0) cc_final: 0.8484 (t0) REVERT: B 948 GLU cc_start: 0.7962 (pt0) cc_final: 0.7759 (tt0) REVERT: B 1017 LEU cc_start: 0.7085 (mt) cc_final: 0.6864 (mt) REVERT: B 1053 MET cc_start: 0.6836 (ptm) cc_final: 0.6604 (ptm) REVERT: C 94 MET cc_start: 0.3812 (ptt) cc_final: 0.3383 (mmp) REVERT: C 142 GLN cc_start: 0.6264 (tt0) cc_final: 0.5884 (tm-30) REVERT: C 154 MET cc_start: 0.5763 (tpp) cc_final: 0.5492 (tpp) REVERT: C 159 PHE cc_start: 0.7857 (t80) cc_final: 0.7588 (t80) REVERT: C 388 GLU cc_start: 0.6850 (tt0) cc_final: 0.6630 (tt0) REVERT: C 399 GLU cc_start: 0.6506 (pt0) cc_final: 0.5627 (tp30) REVERT: C 404 SER cc_start: 0.7433 (t) cc_final: 0.6623 (p) REVERT: C 442 MET cc_start: 0.8438 (mmt) cc_final: 0.8230 (tpp) REVERT: C 466 LYS cc_start: 0.8106 (tttm) cc_final: 0.7804 (tptt) REVERT: C 516 PHE cc_start: 0.5007 (t80) cc_final: 0.4776 (t80) REVERT: C 739 MET cc_start: 0.8117 (mmm) cc_final: 0.7457 (mtm) REVERT: C 760 ILE cc_start: 0.8110 (tt) cc_final: 0.7862 (mt) REVERT: C 785 SER cc_start: 0.8964 (m) cc_final: 0.8594 (p) REVERT: C 816 GLN cc_start: 0.7730 (mm110) cc_final: 0.7271 (mp10) REVERT: C 952 LEU cc_start: 0.7933 (mm) cc_final: 0.7506 (mp) REVERT: D 142 GLN cc_start: 0.2567 (tp40) cc_final: 0.2266 (mm110) REVERT: D 153 ASP cc_start: 0.8231 (p0) cc_final: 0.7653 (t0) REVERT: D 252 PHE cc_start: 0.7545 (t80) cc_final: 0.7167 (m-80) REVERT: D 318 TYR cc_start: 0.6696 (m-10) cc_final: 0.6461 (m-80) REVERT: D 374 GLU cc_start: 0.6244 (tp30) cc_final: 0.5808 (tt0) REVERT: D 391 PHE cc_start: 0.7470 (m-80) cc_final: 0.6951 (m-10) REVERT: D 514 ARG cc_start: 0.6078 (mmm160) cc_final: 0.5746 (mmm160) REVERT: D 782 THR cc_start: 0.9151 (m) cc_final: 0.8923 (p) REVERT: D 1005 LYS cc_start: 0.7618 (pttp) cc_final: 0.7280 (mttp) REVERT: D 1044 VAL cc_start: 0.6399 (t) cc_final: 0.6175 (m) outliers start: 9 outliers final: 4 residues processed: 785 average time/residue: 0.1921 time to fit residues: 237.3098 Evaluate side-chains 422 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain D residue 984 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 HIS A 372 ASN A 449 ASN A 753 HIS A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 747 HIS C 753 HIS C1036 ASN C1054 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.132266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107335 restraints weight = 66245.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108032 restraints weight = 47890.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108712 restraints weight = 37771.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109199 restraints weight = 34895.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109391 restraints weight = 31833.629| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28480 Z= 0.134 Angle : 0.600 14.952 38652 Z= 0.303 Chirality : 0.043 0.248 4440 Planarity : 0.004 0.053 4832 Dihedral : 4.260 45.567 3735 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.89 % Allowed : 11.02 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3444 helix: 0.32 (0.12), residues: 1772 sheet: -0.05 (0.29), residues: 350 loop : -1.03 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 393 TYR 0.023 0.001 TYR B 163 PHE 0.031 0.002 PHE B 187 TRP 0.022 0.001 TRP A 477 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (28480) covalent geometry : angle 0.60026 / 0.30 (38652) hydrogen bonds : bond 0.04483 / 2.94 ( 1280) hydrogen bonds : angle 5.16289 / 3.74 ( 3627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 480 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7724 (mmm) cc_final: 0.6921 (ptt) REVERT: A 38 PHE cc_start: 0.6106 (m-80) cc_final: 0.5875 (m-10) REVERT: A 139 GLU cc_start: 0.3337 (mt-10) cc_final: 0.2707 (mp0) REVERT: A 180 GLU cc_start: 0.6602 (tt0) cc_final: 0.5693 (mm-30) REVERT: A 244 SER cc_start: 0.8351 (p) cc_final: 0.8115 (p) REVERT: A 252 PHE cc_start: 0.7740 (t80) cc_final: 0.7481 (t80) REVERT: A 304 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8578 (mmm) REVERT: A 309 LEU cc_start: 0.8981 (mp) cc_final: 0.8618 (mp) REVERT: A 321 GLU cc_start: 0.7492 (mp0) cc_final: 0.6653 (mt-10) REVERT: A 324 GLU cc_start: 0.6190 (pm20) cc_final: 0.5955 (mt-10) REVERT: A 409 HIS cc_start: 0.7956 (m-70) cc_final: 0.7659 (m90) REVERT: A 536 MET cc_start: 0.8009 (tmm) cc_final: 0.7791 (tmm) REVERT: A 1009 MET cc_start: 0.5303 (mmp) cc_final: 0.4273 (mtt) REVERT: B 94 MET cc_start: 0.0457 (tpp) cc_final: 0.0167 (tpp) REVERT: B 104 MET cc_start: 0.6293 (tpt) cc_final: 0.5803 (mtt) REVERT: B 130 TYR cc_start: 0.7853 (t80) cc_final: 0.7115 (t80) REVERT: B 154 MET cc_start: 0.5716 (tpp) cc_final: 0.5348 (tpt) REVERT: B 180 GLU cc_start: 0.6941 (tm-30) cc_final: 0.5277 (mm-30) REVERT: B 184 VAL cc_start: 0.7755 (t) cc_final: 0.7302 (t) REVERT: B 188 PHE cc_start: 0.7764 (m-80) cc_final: 0.7169 (m-80) REVERT: B 224 LEU cc_start: 0.4889 (mm) cc_final: 0.4646 (mt) REVERT: B 384 ASN cc_start: 0.4500 (t0) cc_final: 0.3239 (m-40) REVERT: B 391 PHE cc_start: 0.5634 (m-10) cc_final: 0.5303 (m-80) REVERT: B 392 LYS cc_start: 0.7464 (pttm) cc_final: 0.7060 (mmtm) REVERT: B 521 GLU cc_start: 0.7675 (pm20) cc_final: 0.7297 (tp30) REVERT: B 536 MET cc_start: 0.8431 (tmm) cc_final: 0.7987 (ttt) REVERT: B 556 LEU cc_start: 0.6807 (tp) cc_final: 0.6448 (tt) REVERT: B 685 LYS cc_start: 0.7577 (ttpp) cc_final: 0.6989 (mttp) REVERT: B 739 MET cc_start: 0.8524 (tpp) cc_final: 0.8181 (ttm) REVERT: B 897 ASP cc_start: 0.6849 (m-30) cc_final: 0.6611 (m-30) REVERT: B 948 GLU cc_start: 0.7716 (pt0) cc_final: 0.7510 (tp30) REVERT: B 1017 LEU cc_start: 0.7327 (mt) cc_final: 0.7093 (mt) REVERT: C 94 MET cc_start: 0.3929 (ptt) cc_final: 0.3503 (mmp) REVERT: C 203 TRP cc_start: 0.6551 (t60) cc_final: 0.6288 (t60) REVERT: C 332 TYR cc_start: 0.5463 (m-80) cc_final: 0.5135 (m-80) REVERT: C 399 GLU cc_start: 0.6629 (pt0) cc_final: 0.6057 (tp30) REVERT: C 404 SER cc_start: 0.7796 (t) cc_final: 0.7095 (p) REVERT: C 429 TYR cc_start: 0.7308 (m-80) cc_final: 0.6847 (m-80) REVERT: C 560 LYS cc_start: 0.5700 (pttp) cc_final: 0.5418 (ptpt) REVERT: C 739 MET cc_start: 0.8138 (mmm) cc_final: 0.7502 (mtm) REVERT: C 816 GLN cc_start: 0.8018 (mm110) cc_final: 0.7696 (mt0) REVERT: C 902 GLU cc_start: 0.7095 (tp30) cc_final: 0.6841 (tp30) REVERT: C 955 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: D 104 MET cc_start: 0.5417 (mmt) cc_final: 0.4799 (mmm) REVERT: D 142 GLN cc_start: 0.2493 (tp40) cc_final: 0.2059 (mm110) REVERT: D 153 ASP cc_start: 0.7899 (p0) cc_final: 0.7344 (t0) REVERT: D 366 LYS cc_start: 0.7477 (mmtm) cc_final: 0.7172 (tttt) REVERT: D 391 PHE cc_start: 0.7472 (m-80) cc_final: 0.6833 (m-10) REVERT: D 924 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8113 (ttm) REVERT: D 1005 LYS cc_start: 0.7574 (pttp) cc_final: 0.7241 (mttp) REVERT: D 1009 MET cc_start: 0.5179 (mmp) cc_final: 0.4954 (mmp) outliers start: 58 outliers final: 39 residues processed: 516 average time/residue: 0.1723 time to fit residues: 145.3184 Evaluate side-chains 423 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 381 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 955 GLU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 924 MET Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 187 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 289 optimal weight: 10.0000 chunk 287 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 ASN ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 772 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104810 restraints weight = 66361.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105630 restraints weight = 46991.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106342 restraints weight = 36906.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106677 restraints weight = 32266.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106790 restraints weight = 31031.821| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28480 Z= 0.141 Angle : 0.585 18.129 38652 Z= 0.295 Chirality : 0.043 0.216 4440 Planarity : 0.004 0.053 4832 Dihedral : 4.167 41.398 3734 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.00 % Allowed : 13.49 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3444 helix: 0.31 (0.12), residues: 1778 sheet: 0.22 (0.30), residues: 338 loop : -1.04 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 976 TYR 0.025 0.001 TYR D1015 PHE 0.029 0.002 PHE D1000 TRP 0.016 0.001 TRP D 263 HIS 0.006 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (28480) covalent geometry : angle 0.58534 / 0.29 (38652) hydrogen bonds : bond 0.04209 / 2.74 ( 1280) hydrogen bonds : angle 4.90322 / 3.54 ( 3627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 410 time to evaluate : 1.047 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 30 MET cc_start: 0.7631 (mmm) cc_final: 0.6842 (ptt) REVERT: A 38 PHE cc_start: 0.6080 (m-80) cc_final: 0.5811 (m-10) REVERT: A 120 PHE cc_start: 0.5686 (t80) cc_final: 0.5109 (t80) REVERT: A 180 GLU cc_start: 0.6690 (tt0) cc_final: 0.5733 (mm-30) REVERT: A 214 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8034 (tt) REVERT: A 244 SER cc_start: 0.8328 (p) cc_final: 0.8096 (p) REVERT: A 252 PHE cc_start: 0.7760 (t80) cc_final: 0.7516 (t80) REVERT: A 321 GLU cc_start: 0.7326 (mp0) cc_final: 0.6730 (mt-10) REVERT: A 409 HIS cc_start: 0.8055 (m-70) cc_final: 0.7669 (m90) REVERT: A 471 ASN cc_start: 0.6124 (m-40) cc_final: 0.5546 (m-40) REVERT: A 555 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7098 (mt-10) REVERT: A 1009 MET cc_start: 0.5368 (mmp) cc_final: 0.4171 (mtt) REVERT: B 33 PHE cc_start: 0.6604 (t80) cc_final: 0.6371 (t80) REVERT: B 94 MET cc_start: 0.0298 (tpp) cc_final: -0.0005 (tpp) REVERT: B 104 MET cc_start: 0.6343 (tpt) cc_final: 0.5839 (mtt) REVERT: B 130 TYR cc_start: 0.7844 (t80) cc_final: 0.7383 (t80) REVERT: B 180 GLU cc_start: 0.6863 (tm-30) cc_final: 0.5187 (mm-30) REVERT: B 184 VAL cc_start: 0.7611 (t) cc_final: 0.7039 (t) REVERT: B 188 PHE cc_start: 0.7970 (m-80) cc_final: 0.7392 (m-80) REVERT: B 391 PHE cc_start: 0.5703 (m-10) cc_final: 0.5345 (m-80) REVERT: B 392 LYS cc_start: 0.7542 (pttm) cc_final: 0.7111 (mmtm) REVERT: B 521 GLU cc_start: 0.7810 (pm20) cc_final: 0.7496 (tp30) REVERT: B 529 LEU cc_start: 0.8499 (mt) cc_final: 0.8210 (mt) REVERT: B 685 LYS cc_start: 0.7573 (ttpp) cc_final: 0.7022 (mttp) REVERT: C 94 MET cc_start: 0.4046 (ptt) cc_final: 0.3270 (mmp) REVERT: C 203 TRP cc_start: 0.6682 (t60) cc_final: 0.6273 (t60) REVERT: C 279 TYR cc_start: 0.8774 (t80) cc_final: 0.8440 (t80) REVERT: C 399 GLU cc_start: 0.6383 (pt0) cc_final: 0.6158 (tp30) REVERT: C 404 SER cc_start: 0.8021 (t) cc_final: 0.7391 (p) REVERT: C 429 TYR cc_start: 0.7440 (m-80) cc_final: 0.7004 (m-80) REVERT: C 739 MET cc_start: 0.8138 (mmm) cc_final: 0.7880 (mtm) REVERT: D 142 GLN cc_start: 0.2668 (tp40) cc_final: 0.2183 (mm110) REVERT: D 153 ASP cc_start: 0.8004 (p0) cc_final: 0.7431 (t0) REVERT: D 391 PHE cc_start: 0.7543 (m-80) cc_final: 0.6971 (m-10) REVERT: D 506 MET cc_start: 0.7525 (ppp) cc_final: 0.7226 (ttp) REVERT: D 892 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6462 (m-30) REVERT: D 984 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7046 (p0) REVERT: D 1009 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.4716 (mmp) outliers start: 92 outliers final: 62 residues processed: 472 average time/residue: 0.1538 time to fit residues: 121.3053 Evaluate side-chains 411 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 828 LYS Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1035 THR Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 133 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 80 optimal weight: 0.0370 chunk 185 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 179 optimal weight: 40.0000 chunk 105 optimal weight: 8.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS A 350 HIS A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103219 restraints weight = 66432.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103903 restraints weight = 49516.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104670 restraints weight = 40364.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104968 restraints weight = 35176.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105077 restraints weight = 32927.153| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28480 Z= 0.156 Angle : 0.583 17.650 38652 Z= 0.294 Chirality : 0.043 0.215 4440 Planarity : 0.004 0.054 4832 Dihedral : 4.155 42.064 3732 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.52 % Allowed : 15.55 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3444 helix: 0.35 (0.12), residues: 1748 sheet: -0.01 (0.27), residues: 388 loop : -1.07 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 213 TYR 0.024 0.002 TYR B 163 PHE 0.033 0.002 PHE D 120 TRP 0.016 0.001 TRP D 263 HIS 0.008 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (28480) covalent geometry : angle 0.58350 / 0.29 (38652) hydrogen bonds : bond 0.04204 / 2.73 ( 1280) hydrogen bonds : angle 4.87436 / 3.52 ( 3627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 386 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7607 (mmm) cc_final: 0.6880 (ptt) REVERT: A 38 PHE cc_start: 0.6040 (m-80) cc_final: 0.5760 (m-10) REVERT: A 180 GLU cc_start: 0.6606 (tt0) cc_final: 0.5740 (mm-30) REVERT: A 244 SER cc_start: 0.8336 (p) cc_final: 0.8121 (p) REVERT: A 252 PHE cc_start: 0.7830 (t80) cc_final: 0.7559 (t80) REVERT: A 409 HIS cc_start: 0.7933 (m-70) cc_final: 0.7623 (m90) REVERT: A 415 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8373 (mmtt) REVERT: A 513 MET cc_start: 0.7464 (tpt) cc_final: 0.6912 (tpt) REVERT: A 1008 ASN cc_start: 0.7451 (m110) cc_final: 0.7139 (m-40) REVERT: A 1009 MET cc_start: 0.5610 (mmp) cc_final: 0.4074 (mtt) REVERT: A 1036 ASN cc_start: 0.5787 (t0) cc_final: 0.5505 (t0) REVERT: A 1053 MET cc_start: 0.6080 (mmm) cc_final: 0.5677 (mmp) REVERT: B 94 MET cc_start: 0.0082 (tpp) cc_final: -0.0190 (tpp) REVERT: B 104 MET cc_start: 0.6242 (tpt) cc_final: 0.5960 (mtt) REVERT: B 130 TYR cc_start: 0.7845 (t80) cc_final: 0.7161 (t80) REVERT: B 180 GLU cc_start: 0.6819 (tm-30) cc_final: 0.5203 (mm-30) REVERT: B 264 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: B 285 MET cc_start: 0.8050 (mmt) cc_final: 0.7685 (mmt) REVERT: B 392 LYS cc_start: 0.7543 (pttm) cc_final: 0.7120 (mmtm) REVERT: B 521 GLU cc_start: 0.7830 (pm20) cc_final: 0.7553 (tp30) REVERT: B 685 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7032 (mttp) REVERT: B 739 MET cc_start: 0.8448 (tpp) cc_final: 0.8207 (ttm) REVERT: C 94 MET cc_start: 0.3867 (ptt) cc_final: 0.3064 (mmp) REVERT: C 151 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: C 203 TRP cc_start: 0.6748 (t60) cc_final: 0.6264 (t60) REVERT: C 279 TYR cc_start: 0.8848 (t80) cc_final: 0.8542 (t80) REVERT: C 399 GLU cc_start: 0.6467 (pt0) cc_final: 0.6174 (tp30) REVERT: C 404 SER cc_start: 0.8067 (t) cc_final: 0.7444 (p) REVERT: C 429 TYR cc_start: 0.7353 (m-80) cc_final: 0.7023 (m-80) REVERT: C 605 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7348 (p) REVERT: C 739 MET cc_start: 0.8021 (mmm) cc_final: 0.7737 (mtm) REVERT: D 142 GLN cc_start: 0.2576 (tp40) cc_final: 0.2098 (mm110) REVERT: D 150 LEU cc_start: 0.5669 (mt) cc_final: 0.5012 (mt) REVERT: D 153 ASP cc_start: 0.8144 (p0) cc_final: 0.7550 (t0) REVERT: D 391 PHE cc_start: 0.7492 (m-80) cc_final: 0.6896 (m-10) REVERT: D 892 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6385 (m-30) REVERT: D 984 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7267 (p0) REVERT: D 1009 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.4796 (mmp) outliers start: 108 outliers final: 75 residues processed: 460 average time/residue: 0.1620 time to fit residues: 125.1800 Evaluate side-chains 431 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 350 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 828 LYS Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 760 ILE Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1035 THR Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 268 optimal weight: 0.0470 chunk 110 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 135 optimal weight: 0.3980 chunk 234 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 394 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS D 407 ASN D 887 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103812 restraints weight = 66458.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103521 restraints weight = 52133.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104609 restraints weight = 42760.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105041 restraints weight = 36356.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105167 restraints weight = 33696.518| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28480 Z= 0.134 Angle : 0.569 16.328 38652 Z= 0.285 Chirality : 0.042 0.213 4440 Planarity : 0.004 0.054 4832 Dihedral : 4.073 42.378 3732 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.29 % Allowed : 17.21 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3444 helix: 0.42 (0.12), residues: 1750 sheet: -0.04 (0.27), residues: 394 loop : -1.06 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 213 TYR 0.037 0.001 TYR B 163 PHE 0.030 0.002 PHE D 120 TRP 0.016 0.001 TRP D 263 HIS 0.016 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (28480) covalent geometry : angle 0.56944 / 0.28 (38652) hydrogen bonds : bond 0.04019 / 2.60 ( 1280) hydrogen bonds : angle 4.78485 / 3.46 ( 3627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 383 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7629 (mmm) cc_final: 0.6732 (ptt) REVERT: A 38 PHE cc_start: 0.6002 (m-80) cc_final: 0.5766 (m-10) REVERT: A 120 PHE cc_start: 0.5821 (t80) cc_final: 0.5113 (t80) REVERT: A 180 GLU cc_start: 0.6483 (tt0) cc_final: 0.5650 (mm-30) REVERT: A 244 SER cc_start: 0.8373 (p) cc_final: 0.8166 (p) REVERT: A 252 PHE cc_start: 0.7793 (t80) cc_final: 0.7502 (t80) REVERT: A 303 PHE cc_start: 0.7221 (t80) cc_final: 0.7020 (t80) REVERT: A 309 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8614 (mp) REVERT: A 332 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.4926 (t80) REVERT: A 409 HIS cc_start: 0.7926 (m-70) cc_final: 0.7607 (m90) REVERT: A 415 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8370 (mmmt) REVERT: A 513 MET cc_start: 0.7466 (tpt) cc_final: 0.6921 (tpt) REVERT: A 1008 ASN cc_start: 0.7488 (m110) cc_final: 0.7137 (m-40) REVERT: A 1009 MET cc_start: 0.5501 (mmp) cc_final: 0.4056 (mtt) REVERT: A 1036 ASN cc_start: 0.5777 (t0) cc_final: 0.5458 (t0) REVERT: A 1053 MET cc_start: 0.6039 (mmm) cc_final: 0.5632 (mmp) REVERT: B 104 MET cc_start: 0.6372 (tpt) cc_final: 0.6089 (mtt) REVERT: B 130 TYR cc_start: 0.7826 (t80) cc_final: 0.6961 (t80) REVERT: B 180 GLU cc_start: 0.6717 (tm-30) cc_final: 0.5347 (mm-30) REVERT: B 392 LYS cc_start: 0.7528 (pttm) cc_final: 0.7161 (mmtm) REVERT: B 521 GLU cc_start: 0.7852 (pm20) cc_final: 0.7537 (tp30) REVERT: B 685 LYS cc_start: 0.7524 (ttpp) cc_final: 0.7008 (mttp) REVERT: B 739 MET cc_start: 0.8475 (tpp) cc_final: 0.8240 (ttm) REVERT: B 897 ASP cc_start: 0.7127 (m-30) cc_final: 0.6855 (m-30) REVERT: B 1009 MET cc_start: 0.5706 (mmp) cc_final: 0.5052 (mmt) REVERT: C 94 MET cc_start: 0.3719 (ptt) cc_final: 0.2867 (mmp) REVERT: C 151 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6416 (pm20) REVERT: C 203 TRP cc_start: 0.6805 (t60) cc_final: 0.6299 (t60) REVERT: C 279 TYR cc_start: 0.8823 (t80) cc_final: 0.8572 (t80) REVERT: C 399 GLU cc_start: 0.6477 (pt0) cc_final: 0.6171 (tp30) REVERT: C 404 SER cc_start: 0.8051 (t) cc_final: 0.7451 (p) REVERT: C 429 TYR cc_start: 0.7358 (m-80) cc_final: 0.7006 (m-80) REVERT: C 605 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7363 (p) REVERT: C 739 MET cc_start: 0.8076 (mmm) cc_final: 0.7791 (mtm) REVERT: D 142 GLN cc_start: 0.2672 (tp40) cc_final: 0.2106 (mm110) REVERT: D 153 ASP cc_start: 0.8256 (p0) cc_final: 0.7672 (t0) REVERT: D 391 PHE cc_start: 0.7477 (m-80) cc_final: 0.6926 (m-10) REVERT: D 892 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6315 (m-30) REVERT: D 984 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7222 (p0) REVERT: D 1009 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4938 (mmp) outliers start: 101 outliers final: 72 residues processed: 456 average time/residue: 0.1573 time to fit residues: 120.8936 Evaluate side-chains 417 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 338 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 46 optimal weight: 10.0000 chunk 184 optimal weight: 30.0000 chunk 279 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 324 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103389 restraints weight = 66653.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103516 restraints weight = 51966.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104428 restraints weight = 42365.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104831 restraints weight = 36069.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104936 restraints weight = 34497.826| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28480 Z= 0.129 Angle : 0.562 14.076 38652 Z= 0.282 Chirality : 0.042 0.222 4440 Planarity : 0.004 0.057 4832 Dihedral : 4.005 41.964 3730 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.55 % Allowed : 17.80 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3444 helix: 0.42 (0.12), residues: 1766 sheet: -0.01 (0.27), residues: 394 loop : -1.00 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.020 0.001 TYR A 996 PHE 0.033 0.002 PHE D 120 TRP 0.019 0.001 TRP D 263 HIS 0.007 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (28480) covalent geometry : angle 0.56156 / 0.28 (38652) hydrogen bonds : bond 0.03929 / 2.54 ( 1280) hydrogen bonds : angle 4.73596 / 3.42 ( 3627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 380 time to evaluate : 1.090 Fit side-chains REVERT: A 30 MET cc_start: 0.7664 (mmm) cc_final: 0.6716 (ptt) REVERT: A 38 PHE cc_start: 0.6132 (m-80) cc_final: 0.5743 (m-10) REVERT: A 120 PHE cc_start: 0.5853 (t80) cc_final: 0.5077 (t80) REVERT: A 176 TRP cc_start: 0.6229 (m100) cc_final: 0.5581 (m100) REVERT: A 179 LEU cc_start: 0.7083 (mp) cc_final: 0.6864 (mt) REVERT: A 180 GLU cc_start: 0.6503 (tt0) cc_final: 0.5676 (mm-30) REVERT: A 252 PHE cc_start: 0.7811 (t80) cc_final: 0.7559 (t80) REVERT: A 309 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8690 (mp) REVERT: A 332 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.4859 (t80) REVERT: A 409 HIS cc_start: 0.7864 (m-70) cc_final: 0.7576 (m90) REVERT: A 415 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8378 (mmmt) REVERT: A 513 MET cc_start: 0.7565 (tpt) cc_final: 0.7001 (tpt) REVERT: A 1036 ASN cc_start: 0.5773 (t0) cc_final: 0.5413 (t0) REVERT: B 104 MET cc_start: 0.6423 (tpt) cc_final: 0.6157 (mtt) REVERT: B 130 TYR cc_start: 0.7836 (t80) cc_final: 0.7229 (t80) REVERT: B 136 ASN cc_start: 0.6674 (t0) cc_final: 0.6180 (m-40) REVERT: B 180 GLU cc_start: 0.6820 (tm-30) cc_final: 0.5555 (mm-30) REVERT: B 391 PHE cc_start: 0.5745 (m-10) cc_final: 0.5369 (m-80) REVERT: B 392 LYS cc_start: 0.7561 (pttm) cc_final: 0.7198 (mmtm) REVERT: B 521 GLU cc_start: 0.7842 (pm20) cc_final: 0.7502 (tp30) REVERT: B 685 LYS cc_start: 0.7475 (ttpp) cc_final: 0.6937 (mttp) REVERT: B 739 MET cc_start: 0.8484 (tpp) cc_final: 0.8249 (ttm) REVERT: B 830 MET cc_start: 0.8283 (tpp) cc_final: 0.7757 (tpp) REVERT: B 902 GLU cc_start: 0.7243 (tp30) cc_final: 0.6730 (tp30) REVERT: B 930 ASN cc_start: 0.8032 (t0) cc_final: 0.7779 (t0) REVERT: C 23 TRP cc_start: 0.6330 (t60) cc_final: 0.6121 (t-100) REVERT: C 94 MET cc_start: 0.3762 (ptt) cc_final: 0.2840 (mmp) REVERT: C 151 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: C 168 PHE cc_start: 0.5649 (t80) cc_final: 0.5224 (t80) REVERT: C 203 TRP cc_start: 0.6833 (t60) cc_final: 0.6282 (t60) REVERT: C 279 TYR cc_start: 0.8853 (t80) cc_final: 0.8613 (t80) REVERT: C 404 SER cc_start: 0.8081 (t) cc_final: 0.7477 (p) REVERT: C 429 TYR cc_start: 0.7361 (m-80) cc_final: 0.7011 (m-80) REVERT: C 518 LYS cc_start: 0.6580 (ptpt) cc_final: 0.6362 (mmmt) REVERT: C 605 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7355 (p) REVERT: C 739 MET cc_start: 0.8050 (mmm) cc_final: 0.7833 (mtm) REVERT: D 142 GLN cc_start: 0.2739 (tp40) cc_final: 0.2235 (mm110) REVERT: D 153 ASP cc_start: 0.8181 (p0) cc_final: 0.7587 (t0) REVERT: D 391 PHE cc_start: 0.7464 (m-80) cc_final: 0.6922 (m-10) REVERT: D 799 MET cc_start: 0.8608 (tpt) cc_final: 0.8377 (tpt) REVERT: D 892 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6253 (m-30) REVERT: D 1009 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.4996 (mmp) outliers start: 109 outliers final: 80 residues processed: 453 average time/residue: 0.1539 time to fit residues: 118.5824 Evaluate side-chains 438 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 352 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1035 THR Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 284 optimal weight: 0.9980 chunk 341 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 337 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 282 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.104846 restraints weight = 66057.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105401 restraints weight = 48346.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106113 restraints weight = 40486.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106466 restraints weight = 35670.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106570 restraints weight = 33349.009| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28480 Z= 0.110 Angle : 0.555 12.888 38652 Z= 0.275 Chirality : 0.041 0.204 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.823 20.475 3728 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.93 % Allowed : 18.90 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3444 helix: 0.51 (0.12), residues: 1766 sheet: 0.05 (0.27), residues: 398 loop : -0.92 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 368 TYR 0.028 0.001 TYR A 996 PHE 0.030 0.001 PHE D 120 TRP 0.013 0.001 TRP A 477 HIS 0.028 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (28480) covalent geometry : angle 0.55456 / 0.28 (38652) hydrogen bonds : bond 0.03714 / 2.41 ( 1280) hydrogen bonds : angle 4.64083 / 3.36 ( 3627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 389 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7481 (mmm) cc_final: 0.6675 (ptt) REVERT: A 38 PHE cc_start: 0.5999 (m-80) cc_final: 0.5651 (m-10) REVERT: A 120 PHE cc_start: 0.5800 (t80) cc_final: 0.5111 (t80) REVERT: A 180 GLU cc_start: 0.6565 (tt0) cc_final: 0.5732 (mm-30) REVERT: A 252 PHE cc_start: 0.7760 (t80) cc_final: 0.7463 (t80) REVERT: A 321 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: A 332 TYR cc_start: 0.5692 (OUTLIER) cc_final: 0.4852 (t80) REVERT: A 409 HIS cc_start: 0.7816 (m-70) cc_final: 0.7543 (m90) REVERT: A 415 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8374 (mmmt) REVERT: A 513 MET cc_start: 0.7592 (tpt) cc_final: 0.7056 (tpt) REVERT: A 999 LEU cc_start: 0.8310 (mp) cc_final: 0.7913 (tp) REVERT: A 1002 LYS cc_start: 0.8257 (mppt) cc_final: 0.7938 (mmmt) REVERT: A 1036 ASN cc_start: 0.5689 (t0) cc_final: 0.5433 (t0) REVERT: B 104 MET cc_start: 0.6671 (tpt) cc_final: 0.6438 (mtm) REVERT: B 136 ASN cc_start: 0.6674 (t0) cc_final: 0.6243 (m-40) REVERT: B 180 GLU cc_start: 0.6880 (tm-30) cc_final: 0.5658 (mm-30) REVERT: B 391 PHE cc_start: 0.5683 (m-10) cc_final: 0.5325 (m-80) REVERT: B 392 LYS cc_start: 0.7530 (pttm) cc_final: 0.7138 (mmtm) REVERT: B 521 GLU cc_start: 0.7781 (pm20) cc_final: 0.7518 (tp30) REVERT: B 685 LYS cc_start: 0.7486 (ttpp) cc_final: 0.6938 (mttp) REVERT: B 739 MET cc_start: 0.8526 (tpp) cc_final: 0.8252 (ttm) REVERT: B 897 ASP cc_start: 0.7007 (m-30) cc_final: 0.6728 (m-30) REVERT: B 902 GLU cc_start: 0.7182 (tp30) cc_final: 0.6763 (tp30) REVERT: B 930 ASN cc_start: 0.7916 (t0) cc_final: 0.7652 (t0) REVERT: B 1009 MET cc_start: 0.5595 (mmp) cc_final: 0.4764 (mmt) REVERT: B 1056 ASP cc_start: 0.6203 (m-30) cc_final: 0.5767 (m-30) REVERT: C 23 TRP cc_start: 0.6313 (t60) cc_final: 0.6086 (t-100) REVERT: C 94 MET cc_start: 0.3837 (ptt) cc_final: 0.2789 (mmp) REVERT: C 151 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: C 168 PHE cc_start: 0.5818 (t80) cc_final: 0.5308 (t80) REVERT: C 203 TRP cc_start: 0.6751 (t60) cc_final: 0.6266 (t60) REVERT: C 279 TYR cc_start: 0.8825 (t80) cc_final: 0.8597 (t80) REVERT: C 404 SER cc_start: 0.8124 (t) cc_final: 0.7557 (p) REVERT: C 429 TYR cc_start: 0.7304 (m-80) cc_final: 0.6941 (m-80) REVERT: C 605 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7432 (p) REVERT: C 1000 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5609 (p90) REVERT: D 142 GLN cc_start: 0.2461 (tp40) cc_final: 0.1990 (mm110) REVERT: D 153 ASP cc_start: 0.8099 (p0) cc_final: 0.7499 (t0) REVERT: D 391 PHE cc_start: 0.7389 (m-80) cc_final: 0.6876 (m-10) REVERT: D 799 MET cc_start: 0.8529 (tpt) cc_final: 0.8157 (tpt) REVERT: D 892 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6172 (m-30) REVERT: D 1009 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.5064 (mmp) outliers start: 90 outliers final: 67 residues processed: 452 average time/residue: 0.1526 time to fit residues: 116.5808 Evaluate side-chains 435 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 361 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 82 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 317 optimal weight: 0.2980 chunk 159 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 263 optimal weight: 0.2980 chunk 147 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS A 932 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103447 restraints weight = 66685.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102865 restraints weight = 48771.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103976 restraints weight = 42946.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104296 restraints weight = 36748.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104476 restraints weight = 34765.685| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28480 Z= 0.145 Angle : 0.591 13.426 38652 Z= 0.294 Chirality : 0.042 0.239 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.937 22.194 3728 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.16 % Allowed : 19.39 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3444 helix: 0.43 (0.12), residues: 1766 sheet: 0.04 (0.27), residues: 398 loop : -0.96 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.030 0.001 TYR B 163 PHE 0.032 0.002 PHE D 120 TRP 0.021 0.001 TRP D 263 HIS 0.019 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (28480) covalent geometry : angle 0.59111 / 0.29 (38652) hydrogen bonds : bond 0.03950 / 2.56 ( 1280) hydrogen bonds : angle 4.70540 / 3.40 ( 3627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 373 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7528 (mmm) cc_final: 0.6561 (ptt) REVERT: A 38 PHE cc_start: 0.5975 (m-80) cc_final: 0.5552 (m-10) REVERT: A 120 PHE cc_start: 0.5844 (t80) cc_final: 0.5043 (t80) REVERT: A 179 LEU cc_start: 0.7074 (mt) cc_final: 0.6872 (mp) REVERT: A 180 GLU cc_start: 0.6649 (tt0) cc_final: 0.5727 (mm-30) REVERT: A 252 PHE cc_start: 0.7780 (t80) cc_final: 0.7467 (t80) REVERT: A 321 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: A 332 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.4869 (t80) REVERT: A 409 HIS cc_start: 0.7811 (m-70) cc_final: 0.7572 (m90) REVERT: A 415 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8410 (mmmt) REVERT: A 513 MET cc_start: 0.7613 (tpt) cc_final: 0.7030 (tpt) REVERT: A 918 SER cc_start: 0.8671 (p) cc_final: 0.8219 (t) REVERT: A 999 LEU cc_start: 0.8363 (mp) cc_final: 0.7959 (tp) REVERT: A 1002 LYS cc_start: 0.8223 (mppt) cc_final: 0.7893 (mmmt) REVERT: A 1036 ASN cc_start: 0.5701 (t0) cc_final: 0.5424 (t0) REVERT: B 104 MET cc_start: 0.6682 (tpt) cc_final: 0.6452 (mtm) REVERT: B 136 ASN cc_start: 0.6768 (t0) cc_final: 0.6300 (m-40) REVERT: B 391 PHE cc_start: 0.5770 (m-10) cc_final: 0.5391 (m-80) REVERT: B 392 LYS cc_start: 0.7588 (pttm) cc_final: 0.7200 (mmtm) REVERT: B 521 GLU cc_start: 0.7763 (pm20) cc_final: 0.7464 (tp30) REVERT: B 685 LYS cc_start: 0.7509 (ttpp) cc_final: 0.6921 (mttp) REVERT: B 739 MET cc_start: 0.8487 (tpp) cc_final: 0.8197 (ttm) REVERT: B 902 GLU cc_start: 0.7206 (tp30) cc_final: 0.6755 (tp30) REVERT: B 930 ASN cc_start: 0.8035 (t0) cc_final: 0.7773 (t0) REVERT: B 1056 ASP cc_start: 0.5801 (m-30) cc_final: 0.5552 (m-30) REVERT: C 23 TRP cc_start: 0.6290 (t60) cc_final: 0.6036 (t-100) REVERT: C 94 MET cc_start: 0.3821 (ptt) cc_final: 0.2727 (mmp) REVERT: C 151 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: C 168 PHE cc_start: 0.5955 (t80) cc_final: 0.5448 (t80) REVERT: C 203 TRP cc_start: 0.6861 (t60) cc_final: 0.6319 (t60) REVERT: C 279 TYR cc_start: 0.8825 (t80) cc_final: 0.8579 (t80) REVERT: C 404 SER cc_start: 0.8113 (t) cc_final: 0.7534 (p) REVERT: C 605 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7463 (p) REVERT: C 1000 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5739 (p90) REVERT: D 142 GLN cc_start: 0.2600 (tp40) cc_final: 0.2169 (mm110) REVERT: D 153 ASP cc_start: 0.8175 (p0) cc_final: 0.7548 (t0) REVERT: D 391 PHE cc_start: 0.7444 (m-80) cc_final: 0.6910 (m-10) REVERT: D 529 LEU cc_start: 0.8392 (mt) cc_final: 0.7762 (tt) REVERT: D 892 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6350 (m-30) REVERT: D 1009 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.5102 (mmp) outliers start: 97 outliers final: 75 residues processed: 438 average time/residue: 0.1556 time to fit residues: 114.9628 Evaluate side-chains 437 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 355 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 107 optimal weight: 0.4980 chunk 324 optimal weight: 10.0000 chunk 287 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 286 optimal weight: 0.0070 chunk 152 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.129555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104914 restraints weight = 66243.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105458 restraints weight = 48694.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106247 restraints weight = 40390.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106576 restraints weight = 35419.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106666 restraints weight = 33276.324| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28480 Z= 0.112 Angle : 0.578 12.682 38652 Z= 0.284 Chirality : 0.042 0.276 4440 Planarity : 0.004 0.057 4832 Dihedral : 3.849 22.286 3728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.77 % Allowed : 20.01 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3444 helix: 0.51 (0.12), residues: 1778 sheet: 0.08 (0.27), residues: 398 loop : -0.95 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.039 0.001 TYR B 163 PHE 0.029 0.001 PHE C 395 TRP 0.014 0.001 TRP D 263 HIS 0.014 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28480) covalent geometry : angle 0.57762 / 0.28 (38652) hydrogen bonds : bond 0.03696 / 2.39 ( 1280) hydrogen bonds : angle 4.61276 / 3.33 ( 3627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 372 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7372 (mmm) cc_final: 0.6593 (ptt) REVERT: A 38 PHE cc_start: 0.5922 (m-80) cc_final: 0.5532 (m-10) REVERT: A 120 PHE cc_start: 0.5641 (t80) cc_final: 0.5010 (t80) REVERT: A 176 TRP cc_start: 0.6257 (m100) cc_final: 0.5609 (m100) REVERT: A 179 LEU cc_start: 0.7114 (mt) cc_final: 0.6910 (mp) REVERT: A 180 GLU cc_start: 0.6749 (tt0) cc_final: 0.5829 (mm-30) REVERT: A 252 PHE cc_start: 0.7783 (t80) cc_final: 0.7484 (t80) REVERT: A 321 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: A 332 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.4810 (t80) REVERT: A 409 HIS cc_start: 0.7792 (m-70) cc_final: 0.7548 (m90) REVERT: A 415 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8402 (mmtt) REVERT: A 513 MET cc_start: 0.7572 (tpt) cc_final: 0.6980 (tpt) REVERT: A 918 SER cc_start: 0.8589 (p) cc_final: 0.8140 (t) REVERT: A 1002 LYS cc_start: 0.8188 (mppt) cc_final: 0.7878 (mmmt) REVERT: A 1036 ASN cc_start: 0.5740 (t0) cc_final: 0.5450 (t0) REVERT: B 21 MET cc_start: 0.6064 (tpt) cc_final: 0.5591 (mtt) REVERT: B 136 ASN cc_start: 0.6740 (t0) cc_final: 0.6313 (m-40) REVERT: B 391 PHE cc_start: 0.5660 (m-10) cc_final: 0.5348 (m-80) REVERT: B 392 LYS cc_start: 0.7555 (pttm) cc_final: 0.7175 (mmtm) REVERT: B 521 GLU cc_start: 0.7760 (pm20) cc_final: 0.7424 (tp30) REVERT: B 685 LYS cc_start: 0.7439 (ttpp) cc_final: 0.6887 (mttp) REVERT: B 739 MET cc_start: 0.8496 (tpp) cc_final: 0.8198 (ttm) REVERT: B 930 ASN cc_start: 0.7945 (t0) cc_final: 0.7657 (t0) REVERT: C 23 TRP cc_start: 0.6346 (t60) cc_final: 0.6031 (t-100) REVERT: C 94 MET cc_start: 0.3795 (ptt) cc_final: 0.2669 (mmp) REVERT: C 130 TYR cc_start: 0.7309 (t80) cc_final: 0.7078 (t80) REVERT: C 151 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: C 168 PHE cc_start: 0.5740 (t80) cc_final: 0.5279 (t80) REVERT: C 203 TRP cc_start: 0.6794 (t60) cc_final: 0.6241 (t60) REVERT: C 279 TYR cc_start: 0.8766 (t80) cc_final: 0.8535 (t80) REVERT: C 404 SER cc_start: 0.8140 (t) cc_final: 0.7573 (p) REVERT: C 605 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7443 (p) REVERT: C 1000 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5895 (p90) REVERT: D 142 GLN cc_start: 0.2383 (tp40) cc_final: 0.2025 (mm110) REVERT: D 153 ASP cc_start: 0.8095 (p0) cc_final: 0.7459 (t0) REVERT: D 391 PHE cc_start: 0.7373 (m-80) cc_final: 0.6849 (m-10) REVERT: D 529 LEU cc_start: 0.8388 (mt) cc_final: 0.7794 (tt) REVERT: D 892 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6161 (m-30) REVERT: D 1009 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.5133 (mmp) outliers start: 85 outliers final: 67 residues processed: 430 average time/residue: 0.1593 time to fit residues: 115.6981 Evaluate side-chains 433 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 359 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 160 optimal weight: 0.0050 chunk 338 optimal weight: 10.0000 chunk 237 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104588 restraints weight = 66632.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105135 restraints weight = 47617.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106021 restraints weight = 38943.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106332 restraints weight = 33997.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106494 restraints weight = 32082.422| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28480 Z= 0.116 Angle : 0.583 12.994 38652 Z= 0.287 Chirality : 0.042 0.265 4440 Planarity : 0.004 0.069 4832 Dihedral : 3.845 25.977 3728 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.38 % Allowed : 20.57 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3444 helix: 0.53 (0.12), residues: 1778 sheet: 0.11 (0.27), residues: 398 loop : -0.94 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.027 0.001 TYR B 163 PHE 0.030 0.001 PHE C 395 TRP 0.024 0.001 TRP B 100 HIS 0.003 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (28480) covalent geometry : angle 0.58265 / 0.29 (38652) hydrogen bonds : bond 0.03707 / 2.40 ( 1280) hydrogen bonds : angle 4.59495 / 3.32 ( 3627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 358 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7329 (mmm) cc_final: 0.6545 (ptt) REVERT: A 38 PHE cc_start: 0.5860 (m-80) cc_final: 0.5463 (m-10) REVERT: A 120 PHE cc_start: 0.5677 (t80) cc_final: 0.5006 (t80) REVERT: A 176 TRP cc_start: 0.6254 (m100) cc_final: 0.5610 (m100) REVERT: A 179 LEU cc_start: 0.6922 (mt) cc_final: 0.6692 (mp) REVERT: A 180 GLU cc_start: 0.6867 (tt0) cc_final: 0.5840 (mm-30) REVERT: A 252 PHE cc_start: 0.7751 (t80) cc_final: 0.7410 (t80) REVERT: A 321 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: A 332 TYR cc_start: 0.5609 (OUTLIER) cc_final: 0.4845 (t80) REVERT: A 409 HIS cc_start: 0.7797 (m-70) cc_final: 0.7558 (m90) REVERT: A 415 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8417 (mmmt) REVERT: A 513 MET cc_start: 0.7553 (tpt) cc_final: 0.6979 (tpt) REVERT: A 918 SER cc_start: 0.8596 (p) cc_final: 0.8130 (t) REVERT: A 999 LEU cc_start: 0.8098 (mp) cc_final: 0.7695 (tp) REVERT: A 1002 LYS cc_start: 0.8180 (mppt) cc_final: 0.7883 (mmmt) REVERT: A 1036 ASN cc_start: 0.5748 (t0) cc_final: 0.5461 (t0) REVERT: B 21 MET cc_start: 0.6136 (tpt) cc_final: 0.5591 (mtt) REVERT: B 136 ASN cc_start: 0.6626 (t0) cc_final: 0.6199 (m-40) REVERT: B 231 ASN cc_start: 0.7685 (m-40) cc_final: 0.6776 (p0) REVERT: B 391 PHE cc_start: 0.5630 (m-10) cc_final: 0.5367 (m-80) REVERT: B 460 MET cc_start: 0.7832 (mmt) cc_final: 0.7567 (mmt) REVERT: B 521 GLU cc_start: 0.7821 (pm20) cc_final: 0.7408 (tp30) REVERT: B 685 LYS cc_start: 0.7425 (ttpp) cc_final: 0.6877 (mttp) REVERT: B 739 MET cc_start: 0.8494 (tpp) cc_final: 0.8221 (ttm) REVERT: B 930 ASN cc_start: 0.7924 (t0) cc_final: 0.7669 (t0) REVERT: C 23 TRP cc_start: 0.6343 (t60) cc_final: 0.6006 (t-100) REVERT: C 94 MET cc_start: 0.3729 (ptt) cc_final: 0.2576 (mmp) REVERT: C 151 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: C 168 PHE cc_start: 0.5733 (t80) cc_final: 0.5283 (t80) REVERT: C 203 TRP cc_start: 0.6730 (t60) cc_final: 0.6208 (t60) REVERT: C 279 TYR cc_start: 0.8803 (t80) cc_final: 0.8559 (t80) REVERT: C 404 SER cc_start: 0.8073 (t) cc_final: 0.7509 (p) REVERT: C 605 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7422 (p) REVERT: D 142 GLN cc_start: 0.2413 (tp40) cc_final: 0.2055 (mm110) REVERT: D 153 ASP cc_start: 0.8097 (p0) cc_final: 0.7452 (t0) REVERT: D 391 PHE cc_start: 0.7371 (m-80) cc_final: 0.6761 (m-10) REVERT: D 529 LEU cc_start: 0.8380 (mt) cc_final: 0.7808 (tt) REVERT: D 892 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6224 (m-30) REVERT: D 1009 MET cc_start: 0.5483 (OUTLIER) cc_final: 0.5132 (mmp) outliers start: 73 outliers final: 63 residues processed: 412 average time/residue: 0.1528 time to fit residues: 107.0165 Evaluate side-chains 415 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 289 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 345 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 284 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 234 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS D 887 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.129808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105099 restraints weight = 66797.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104416 restraints weight = 48425.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105396 restraints weight = 41022.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105718 restraints weight = 36041.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105954 restraints weight = 33618.651| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28480 Z= 0.121 Angle : 0.596 13.500 38652 Z= 0.292 Chirality : 0.042 0.251 4440 Planarity : 0.004 0.063 4832 Dihedral : 3.879 24.082 3728 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.54 % Allowed : 20.57 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3444 helix: 0.56 (0.13), residues: 1762 sheet: 0.12 (0.27), residues: 398 loop : -0.89 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 210 TYR 0.041 0.001 TYR B 163 PHE 0.030 0.001 PHE C 395 TRP 0.024 0.001 TRP B 100 HIS 0.004 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (28480) covalent geometry : angle 0.59596 / 0.29 (38652) hydrogen bonds : bond 0.03751 / 2.43 ( 1280) hydrogen bonds : angle 4.60048 / 3.31 ( 3627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4280.10 seconds wall clock time: 75 minutes 13.46 seconds (4513.46 seconds total)