Starting phenix.real_space_refine on Mon Aug 25 12:04:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo5_33982/08_2025/7yo5_33982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo5_33982/08_2025/7yo5_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_33982/08_2025/7yo5_33982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo5_33982/08_2025/7yo5_33982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yo5_33982/08_2025/7yo5_33982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo5_33982/08_2025/7yo5_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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.11, per 1000 atoms: 0.26 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.13 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: 5.94 Time building geometry restraints manager: 3.13 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 2.510 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: 0.03 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.970 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 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 aren 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 covalent geometry : bond 0.00319 (28480) covalent geometry : angle 0.64265 (38652) hydrogen bonds : bond 0.15481 ( 1280) hydrogen bonds : angle 6.48623 ( 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 : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.5868 (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: 0.7867 (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: 0.8397 (mp) REVERT: A 409 HIS cc_start: 0.8380 (m-70) cc_final: 0.7825 (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: 0.8179 (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: 0.5886 (tpt) REVERT: B 180 GLU cc_start: 0.7028 (tm-30) cc_final: 0.5406 (mm-30) REVERT: B 184 VAL cc_start: 0.7535 (t) cc_final: 0.7169 (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: 0.7875 (tt) REVERT: B 384 ASN cc_start: 0.3931 (t0) cc_final: 0.3195 (p0) REVERT: B 386 GLU cc_start: 0.6589 (mp0) cc_final: 0.5628 (tp30) REVERT: B 391 PHE cc_start: 0.5371 (m-10) cc_final: 0.5150 (m-80) REVERT: B 427 ASN cc_start: 0.7122 (t0) cc_final: 0.6669 (t0) REVERT: B 449 ASN cc_start: 0.7061 (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: 0.6843 (m-30) cc_final: 0.6579 (m-30) REVERT: B 884 ASN cc_start: 0.8779 (t0) cc_final: 0.8485 (t0) REVERT: B 948 GLU cc_start: 0.7962 (pt0) cc_final: 0.7758 (tt0) REVERT: B 1017 LEU cc_start: 0.7085 (mt) cc_final: 0.6865 (mt) REVERT: B 1053 MET cc_start: 0.6836 (ptm) cc_final: 0.6604 (ptm) REVERT: B 1056 ASP cc_start: 0.5854 (m-30) cc_final: 0.5650 (m-30) REVERT: C 94 MET cc_start: 0.3812 (ptt) cc_final: 0.3382 (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: 0.5491 (tpp) REVERT: C 159 PHE cc_start: 0.7857 (t80) cc_final: 0.7587 (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: 0.6624 (p) REVERT: C 442 MET cc_start: 0.8438 (mmt) cc_final: 0.8229 (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: 0.4777 (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: 0.7272 (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: 0.2265 (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: 0.5807 (tt0) REVERT: D 391 PHE cc_start: 0.7470 (m-80) cc_final: 0.6949 (m-10) REVERT: D 514 ARG cc_start: 0.6078 (mmm160) cc_final: 0.5853 (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: 0.6177 (m) outliers start: 9 outliers final: 4 residues processed: 785 average time/residue: 0.1980 time to fit residues: 243.7183 Evaluate side-chains 425 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 421 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: A 365 HIS A 449 ASN A 753 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** ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 747 HIS C 753 HIS C1036 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107203 restraints weight = 66102.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.107959 restraints weight = 47885.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108571 restraints weight = 36667.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109116 restraints weight = 35682.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109209 restraints weight = 31770.046| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2378 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= 0.134 Angle : 0.601 14.591 38652 Z= 0.303 Chirality : 0.043 0.211 4440 Planarity : 0.004 0.053 4832 Dihedral : 4.259 45.717 3735 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.83 % Allowed : 11.11 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.14), residues: 3444 helix: 0.31 (0.12), residues: 1784 sheet: -0.05 (0.29), residues: 350 loop : -1.08 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.022 0.002 TYR B 163 PHE 0.030 0.002 PHE B 187 TRP 0.021 0.001 TRP B 263 HIS 0.003 0.001 HIS D 753 Details of bonding type rmsd covalent geometry : bond 0.00289 (28480) covalent geometry : angle 0.60078 (38652) hydrogen bonds : bond 0.04528 ( 1280) hydrogen bonds : angle 5.18675 ( 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 532 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 476 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7743 (mmm) cc_final: 0.6936 (ptt) REVERT: A 38 PHE cc_start: 0.6078 (m-80) cc_final: 0.5855 (m-10) REVERT: A 139 GLU cc_start: 0.3334 (mt-10) cc_final: 0.2705 (mp0) REVERT: A 180 GLU cc_start: 0.6609 (tt0) cc_final: 0.5686 (mm-30) REVERT: A 195 VAL cc_start: 0.7503 (p) cc_final: 0.7287 (t) REVERT: A 244 SER cc_start: 0.8359 (p) cc_final: 0.8124 (p) REVERT: A 252 PHE cc_start: 0.7738 (t80) cc_final: 0.7478 (t80) REVERT: A 304 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8574 (mmm) REVERT: A 309 LEU cc_start: 0.8980 (mp) cc_final: 0.8632 (mp) REVERT: A 321 GLU cc_start: 0.7488 (mp0) cc_final: 0.6631 (mt-10) REVERT: A 324 GLU cc_start: 0.6199 (pm20) cc_final: 0.5945 (mt-10) REVERT: A 409 HIS cc_start: 0.7974 (m-70) cc_final: 0.7677 (m90) REVERT: A 536 MET cc_start: 0.7998 (tmm) cc_final: 0.7782 (tmm) REVERT: A 1009 MET cc_start: 0.5317 (mmp) cc_final: 0.4280 (mtt) REVERT: B 104 MET cc_start: 0.6315 (tpt) cc_final: 0.5824 (mtt) REVERT: B 130 TYR cc_start: 0.7951 (t80) cc_final: 0.7076 (t80) REVERT: B 154 MET cc_start: 0.5585 (tpp) cc_final: 0.5259 (tpt) REVERT: B 180 GLU cc_start: 0.6948 (tm-30) cc_final: 0.5268 (mm-30) REVERT: B 184 VAL cc_start: 0.7758 (t) cc_final: 0.7300 (t) REVERT: B 188 PHE cc_start: 0.7747 (m-80) cc_final: 0.7197 (m-80) REVERT: B 224 LEU cc_start: 0.4843 (mm) cc_final: 0.4609 (mt) REVERT: B 384 ASN cc_start: 0.4499 (t0) cc_final: 0.3236 (m-40) REVERT: B 391 PHE cc_start: 0.5576 (m-10) cc_final: 0.5256 (m-80) REVERT: B 392 LYS cc_start: 0.7464 (pttm) cc_final: 0.7060 (mmtm) REVERT: B 521 GLU cc_start: 0.7677 (pm20) cc_final: 0.7288 (tp30) REVERT: B 536 MET cc_start: 0.8512 (tmm) cc_final: 0.8067 (ttt) REVERT: B 685 LYS cc_start: 0.7579 (ttpp) cc_final: 0.6987 (mttp) REVERT: B 739 MET cc_start: 0.8557 (tpp) cc_final: 0.8220 (ttm) REVERT: B 799 MET cc_start: 0.8271 (tpp) cc_final: 0.7991 (tpp) REVERT: B 948 GLU cc_start: 0.7787 (pt0) cc_final: 0.7497 (tp30) REVERT: B 1017 LEU cc_start: 0.7331 (mt) cc_final: 0.7102 (mt) REVERT: C 94 MET cc_start: 0.3929 (ptt) cc_final: 0.3507 (mmp) REVERT: C 203 TRP cc_start: 0.6514 (t60) cc_final: 0.6243 (t60) REVERT: C 332 TYR cc_start: 0.5420 (m-80) cc_final: 0.5108 (m-80) REVERT: C 399 GLU cc_start: 0.6621 (pt0) cc_final: 0.6051 (tp30) REVERT: C 404 SER cc_start: 0.7757 (t) cc_final: 0.7056 (p) REVERT: C 429 TYR cc_start: 0.7298 (m-80) cc_final: 0.6834 (m-80) REVERT: C 560 LYS cc_start: 0.5662 (pttp) cc_final: 0.5356 (ptpt) REVERT: C 739 MET cc_start: 0.8139 (mmm) cc_final: 0.7504 (mtm) REVERT: C 816 GLN cc_start: 0.7990 (mm110) cc_final: 0.7705 (mt0) REVERT: C 902 GLU cc_start: 0.7135 (tp30) cc_final: 0.6876 (tp30) REVERT: C 955 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: D 104 MET cc_start: 0.5437 (mmt) cc_final: 0.4817 (mmm) REVERT: D 142 GLN cc_start: 0.2489 (tp40) cc_final: 0.2052 (mm110) REVERT: D 153 ASP cc_start: 0.7908 (p0) cc_final: 0.7357 (t0) REVERT: D 366 LYS cc_start: 0.7484 (mmtm) cc_final: 0.7171 (tttt) REVERT: D 391 PHE cc_start: 0.7459 (m-80) cc_final: 0.6813 (m-10) REVERT: D 924 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8132 (ttm) REVERT: D 950 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7948 (mt-10) REVERT: D 1005 LYS cc_start: 0.7558 (pttp) cc_final: 0.7224 (mttp) outliers start: 56 outliers final: 38 residues processed: 513 average time/residue: 0.1789 time to fit residues: 149.3028 Evaluate side-chains 424 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 383 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 154 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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 772 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105936 restraints weight = 66178.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106019 restraints weight = 49654.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106756 restraints weight = 39304.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107294 restraints weight = 37973.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.107455 restraints weight = 33895.054| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2908 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 : 0.574 17.367 38652 Z= 0.288 Chirality : 0.042 0.205 4440 Planarity : 0.004 0.054 4832 Dihedral : 4.132 41.799 3734 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.71 % Allowed : 13.27 % Favored : 84.03 % 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 aren not related in a simple way. whole: -0.31 (0.14), residues: 3444 helix: 0.37 (0.12), residues: 1774 sheet: 0.21 (0.30), residues: 338 loop : -1.00 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 213 TYR 0.022 0.001 TYR D1015 PHE 0.029 0.002 PHE D1000 TRP 0.015 0.001 TRP A 477 HIS 0.007 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00288 (28480) covalent geometry : angle 0.57395 (38652) hydrogen bonds : bond 0.04148 ( 1280) hydrogen bonds : angle 4.92534 ( 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 489 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 406 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7760 (mmm) cc_final: 0.6913 (ptt) REVERT: A 38 PHE cc_start: 0.6254 (m-80) cc_final: 0.5925 (m-10) REVERT: A 120 PHE cc_start: 0.5801 (t80) cc_final: 0.5173 (t80) REVERT: A 180 GLU cc_start: 0.6579 (tt0) cc_final: 0.5618 (mm-30) REVERT: A 213 ARG cc_start: 0.5256 (mtt90) cc_final: 0.4660 (ttm110) REVERT: A 244 SER cc_start: 0.8343 (p) cc_final: 0.8110 (p) REVERT: A 252 PHE cc_start: 0.7788 (t80) cc_final: 0.7536 (t80) REVERT: A 321 GLU cc_start: 0.7330 (mp0) cc_final: 0.6757 (mt-10) REVERT: A 409 HIS cc_start: 0.8041 (m-70) cc_final: 0.7657 (m90) REVERT: A 1009 MET cc_start: 0.5422 (mmp) cc_final: 0.4206 (mtt) REVERT: B 94 MET cc_start: 0.0212 (tpp) cc_final: -0.0184 (tpp) REVERT: B 104 MET cc_start: 0.6346 (tpt) cc_final: 0.5813 (mtt) REVERT: B 130 TYR cc_start: 0.7716 (t80) cc_final: 0.7233 (t80) REVERT: B 163 TYR cc_start: 0.8005 (t80) cc_final: 0.7795 (t80) REVERT: B 180 GLU cc_start: 0.6917 (tm-30) cc_final: 0.5153 (mm-30) REVERT: B 184 VAL cc_start: 0.7562 (t) cc_final: 0.7040 (t) REVERT: B 188 PHE cc_start: 0.7831 (m-80) cc_final: 0.7254 (m-80) REVERT: B 391 PHE cc_start: 0.5675 (m-10) cc_final: 0.5322 (m-80) REVERT: B 392 LYS cc_start: 0.7551 (pttm) cc_final: 0.7118 (mmtm) REVERT: B 521 GLU cc_start: 0.7744 (pm20) cc_final: 0.7396 (tp30) REVERT: B 529 LEU cc_start: 0.8651 (mt) cc_final: 0.8387 (mt) REVERT: B 685 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7031 (mttp) REVERT: B 1005 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7499 (pttt) REVERT: C 94 MET cc_start: 0.3754 (ptt) cc_final: 0.3088 (mmp) REVERT: C 203 TRP cc_start: 0.6711 (t60) cc_final: 0.6334 (t60) REVERT: C 279 TYR cc_start: 0.8734 (t80) cc_final: 0.8382 (t80) REVERT: C 399 GLU cc_start: 0.6372 (pt0) cc_final: 0.6102 (tp30) REVERT: C 404 SER cc_start: 0.7890 (t) cc_final: 0.7208 (p) REVERT: C 429 TYR cc_start: 0.7394 (m-80) cc_final: 0.6961 (m-80) REVERT: C 739 MET cc_start: 0.8185 (mmm) cc_final: 0.7863 (mtm) REVERT: D 142 GLN cc_start: 0.2556 (tp40) cc_final: 0.2107 (mm110) REVERT: D 153 ASP cc_start: 0.7991 (p0) cc_final: 0.7435 (t0) REVERT: D 391 PHE cc_start: 0.7524 (m-80) cc_final: 0.6950 (m-10) REVERT: D 506 MET cc_start: 0.7580 (ppp) cc_final: 0.7143 (ttp) REVERT: D 950 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7928 (mt-10) REVERT: D 984 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6991 (p0) REVERT: D 1005 LYS cc_start: 0.7623 (pttp) cc_final: 0.7179 (mttp) outliers start: 83 outliers final: 59 residues processed: 461 average time/residue: 0.1759 time to fit residues: 134.9056 Evaluate side-chains 419 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 359 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 281 LEU 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 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 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 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 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 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 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 1039 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 133 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 179 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS A 350 HIS A 771 HIS A 930 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 HIS C 402 GLN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.125869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100958 restraints weight = 66590.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100562 restraints weight = 49532.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101534 restraints weight = 43837.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101862 restraints weight = 37750.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102015 restraints weight = 35323.226| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28480 Z= 0.214 Angle : 0.671 19.065 38652 Z= 0.342 Chirality : 0.046 0.276 4440 Planarity : 0.005 0.055 4832 Dihedral : 4.540 40.669 3732 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.85 % Allowed : 15.65 % Favored : 80.51 % 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 aren not related in a simple way. whole: -0.62 (0.14), residues: 3444 helix: 0.12 (0.12), residues: 1764 sheet: 0.00 (0.27), residues: 384 loop : -1.15 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 213 TYR 0.034 0.002 TYR D1015 PHE 0.032 0.003 PHE D 120 TRP 0.019 0.002 TRP D 263 HIS 0.009 0.002 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00491 (28480) covalent geometry : angle 0.67076 (38652) hydrogen bonds : bond 0.04842 ( 1280) hydrogen bonds : angle 5.10234 ( 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 519 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 401 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6090 (m-80) cc_final: 0.5818 (m-10) REVERT: A 244 SER cc_start: 0.8328 (p) cc_final: 0.8114 (p) REVERT: A 409 HIS cc_start: 0.7963 (m-70) cc_final: 0.7649 (m90) REVERT: A 415 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8459 (mmmt) REVERT: A 513 MET cc_start: 0.7285 (tpt) cc_final: 0.6558 (tpt) REVERT: A 918 SER cc_start: 0.8550 (p) cc_final: 0.8094 (t) REVERT: A 1036 ASN cc_start: 0.5570 (t0) cc_final: 0.5288 (t0) REVERT: A 1053 MET cc_start: 0.6206 (mmm) cc_final: 0.5661 (mmp) REVERT: B 94 MET cc_start: 0.0801 (tpp) cc_final: 0.0226 (tpp) REVERT: B 104 MET cc_start: 0.6360 (tpt) cc_final: 0.5972 (mtt) REVERT: B 130 TYR cc_start: 0.8001 (t80) cc_final: 0.7024 (t80) REVERT: B 180 GLU cc_start: 0.6795 (tm-30) cc_final: 0.5121 (mm-30) REVERT: B 257 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 285 MET cc_start: 0.8002 (mmt) cc_final: 0.7745 (mmt) REVERT: B 392 LYS cc_start: 0.7603 (pttm) cc_final: 0.7209 (mmtm) REVERT: B 521 GLU cc_start: 0.7864 (pm20) cc_final: 0.7550 (tp30) REVERT: B 685 LYS cc_start: 0.7564 (ttpp) cc_final: 0.7023 (mttp) REVERT: B 739 MET cc_start: 0.8437 (tpp) cc_final: 0.8216 (ttm) REVERT: C 94 MET cc_start: 0.3843 (ptt) cc_final: 0.3030 (mmp) REVERT: C 151 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: C 203 TRP cc_start: 0.6753 (t60) cc_final: 0.6403 (t60) REVERT: C 307 PHE cc_start: 0.7471 (t80) cc_final: 0.7174 (t80) REVERT: C 399 GLU cc_start: 0.6522 (pt0) cc_final: 0.6193 (tp30) REVERT: C 404 SER cc_start: 0.8185 (t) cc_final: 0.7359 (p) REVERT: C 429 TYR cc_start: 0.7426 (m-80) cc_final: 0.7123 (m-80) REVERT: C 605 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7393 (p) REVERT: C 613 LYS cc_start: 0.5274 (mmtt) cc_final: 0.4932 (tppt) REVERT: C 990 LEU cc_start: 0.6495 (tp) cc_final: 0.5974 (mp) REVERT: D 142 GLN cc_start: 0.2678 (tp40) cc_final: 0.2127 (mm110) REVERT: D 150 LEU cc_start: 0.5805 (mt) cc_final: 0.5300 (mt) REVERT: D 153 ASP cc_start: 0.8207 (p0) cc_final: 0.7530 (t0) REVERT: D 212 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (mt) REVERT: D 391 PHE cc_start: 0.7470 (m-80) cc_final: 0.6871 (m-10) REVERT: D 892 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: D 984 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7234 (p0) outliers start: 118 outliers final: 74 residues processed: 485 average time/residue: 0.1675 time to fit residues: 136.5420 Evaluate side-chains 425 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 346 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 233 ILE 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 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 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 227 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 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 798 ASP Chi-restraints excluded: chain B residue 917 VAL 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 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 594 LEU Chi-restraints excluded: chain C residue 605 VAL 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 817 ASP 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 D residue 185 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 255 LEU 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 456 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 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 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: 2.9990 chunk 110 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 7.9990 chunk 135 optimal weight: 0.2980 chunk 234 optimal weight: 10.0000 chunk 71 optimal weight: 0.0020 chunk 74 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN A1054 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS D 407 ASN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 887 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104130 restraints weight = 66157.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104676 restraints weight = 47003.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105636 restraints weight = 37884.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105893 restraints weight = 32597.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106027 restraints weight = 31421.450| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28480 Z= 0.111 Angle : 0.560 15.023 38652 Z= 0.280 Chirality : 0.041 0.193 4440 Planarity : 0.004 0.055 4832 Dihedral : 4.089 42.939 3732 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.54 % Allowed : 18.06 % Favored : 79.40 % 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 aren not related in a simple way. whole: -0.27 (0.14), residues: 3444 helix: 0.49 (0.12), residues: 1736 sheet: 0.01 (0.27), residues: 390 loop : -1.04 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 213 TYR 0.024 0.001 TYR B 163 PHE 0.047 0.001 PHE B 391 TRP 0.017 0.001 TRP A 477 HIS 0.017 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00238 (28480) covalent geometry : angle 0.56019 (38652) hydrogen bonds : bond 0.03898 ( 1280) hydrogen bonds : angle 4.77925 ( 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 486 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 408 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7769 (mmm) cc_final: 0.6799 (ptt) REVERT: A 38 PHE cc_start: 0.6036 (m-80) cc_final: 0.5795 (m-10) REVERT: A 120 PHE cc_start: 0.5746 (t80) cc_final: 0.5078 (t80) REVERT: A 180 GLU cc_start: 0.6391 (tt0) cc_final: 0.5583 (mm-30) REVERT: A 309 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 332 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.4810 (t80) REVERT: A 409 HIS cc_start: 0.7865 (m-70) cc_final: 0.7539 (m90) REVERT: A 415 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8305 (mmmt) REVERT: A 513 MET cc_start: 0.7630 (tpt) cc_final: 0.7229 (tpt) REVERT: A 604 GLU cc_start: 0.7649 (mp0) cc_final: 0.7067 (mp0) REVERT: A 1009 MET cc_start: 0.5731 (mmp) cc_final: 0.4470 (mtt) REVERT: A 1036 ASN cc_start: 0.5721 (t0) cc_final: 0.5439 (t0) REVERT: B 94 MET cc_start: 0.0418 (tpp) cc_final: 0.0076 (tpp) REVERT: B 104 MET cc_start: 0.6322 (tpt) cc_final: 0.6076 (mtt) REVERT: B 130 TYR cc_start: 0.7815 (t80) cc_final: 0.7000 (t80) REVERT: B 180 GLU cc_start: 0.6630 (tm-30) cc_final: 0.5314 (mm-30) REVERT: B 257 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7457 (mm-30) REVERT: B 391 PHE cc_start: 0.5767 (m-80) cc_final: 0.5512 (m-80) REVERT: B 392 LYS cc_start: 0.7491 (pttm) cc_final: 0.7127 (mmtm) REVERT: B 521 GLU cc_start: 0.7839 (pm20) cc_final: 0.7532 (tp30) REVERT: B 685 LYS cc_start: 0.7501 (ttpp) cc_final: 0.7000 (mttp) REVERT: B 739 MET cc_start: 0.8483 (tpp) cc_final: 0.8215 (ttm) REVERT: B 902 GLU cc_start: 0.7112 (tp30) cc_final: 0.6603 (tp30) REVERT: B 948 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: C 94 MET cc_start: 0.3740 (ptt) cc_final: 0.2811 (mmp) REVERT: C 151 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: C 203 TRP cc_start: 0.6776 (t60) cc_final: 0.6330 (t60) REVERT: C 279 TYR cc_start: 0.8831 (t80) cc_final: 0.8533 (t80) REVERT: C 399 GLU cc_start: 0.6411 (pt0) cc_final: 0.6108 (tp30) REVERT: C 404 SER cc_start: 0.8118 (t) cc_final: 0.7526 (p) REVERT: C 429 TYR cc_start: 0.7279 (m-80) cc_final: 0.6918 (m-80) REVERT: C 605 VAL cc_start: 0.7663 (t) cc_final: 0.7422 (p) REVERT: D 142 GLN cc_start: 0.2677 (tp40) cc_final: 0.2149 (mm110) REVERT: D 153 ASP cc_start: 0.8123 (p0) cc_final: 0.7596 (t0) REVERT: D 212 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8369 (mt) REVERT: D 391 PHE cc_start: 0.7378 (m-80) cc_final: 0.6819 (m-10) REVERT: D 799 MET cc_start: 0.8552 (tpt) cc_final: 0.7986 (tpt) REVERT: D 892 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: D 984 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7160 (p0) REVERT: D 1009 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4809 (mmp) outliers start: 78 outliers final: 51 residues processed: 462 average time/residue: 0.1691 time to fit residues: 130.5161 Evaluate side-chains 413 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 354 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 309 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 372 ASN 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 917 VAL Chi-restraints excluded: chain A residue 987 PHE 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 293 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 727 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 B residue 948 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1005 LYS 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 405 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 594 LEU 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 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 253 ILE 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 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: 7.9990 chunk 184 optimal weight: 30.0000 chunk 279 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 105 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN 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 534 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 = 0.3808 r_free = 0.3808 target = 0.126612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101386 restraints weight = 66853.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101557 restraints weight = 52738.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102582 restraints weight = 42748.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102828 restraints weight = 36054.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102962 restraints weight = 33674.896| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28480 Z= 0.173 Angle : 0.616 15.378 38652 Z= 0.311 Chirality : 0.043 0.238 4440 Planarity : 0.004 0.057 4832 Dihedral : 4.229 41.578 3730 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.52 % Allowed : 18.84 % Favored : 77.64 % 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 aren not related in a simple way. whole: -0.44 (0.14), residues: 3444 helix: 0.31 (0.12), residues: 1760 sheet: -0.05 (0.27), residues: 390 loop : -1.09 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 210 TYR 0.025 0.002 TYR B 163 PHE 0.034 0.002 PHE D 120 TRP 0.018 0.001 TRP D 263 HIS 0.006 0.001 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00398 (28480) covalent geometry : angle 0.61628 (38652) hydrogen bonds : bond 0.04340 ( 1280) hydrogen bonds : angle 4.90055 ( 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 481 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 373 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7852 (mmm) cc_final: 0.6816 (ptt) REVERT: A 38 PHE cc_start: 0.6045 (m-80) cc_final: 0.5698 (m-10) REVERT: A 120 PHE cc_start: 0.5647 (t80) cc_final: 0.4888 (t80) REVERT: A 180 GLU cc_start: 0.6549 (tt0) cc_final: 0.5683 (mm-30) REVERT: A 309 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8767 (mp) REVERT: A 321 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7038 (mt-10) REVERT: A 332 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.5217 (t80) REVERT: A 409 HIS cc_start: 0.7834 (m-70) cc_final: 0.7560 (m90) REVERT: A 415 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8422 (mmmt) REVERT: A 513 MET cc_start: 0.7615 (tpt) cc_final: 0.7062 (tpt) REVERT: A 918 SER cc_start: 0.8689 (p) cc_final: 0.8238 (t) REVERT: A 1009 MET cc_start: 0.5685 (mmp) cc_final: 0.4568 (mtt) REVERT: A 1036 ASN cc_start: 0.5713 (t0) cc_final: 0.5411 (t0) REVERT: B 94 MET cc_start: 0.0634 (tpp) cc_final: 0.0359 (tpp) REVERT: B 104 MET cc_start: 0.6590 (tpt) cc_final: 0.6220 (mtm) REVERT: B 130 TYR cc_start: 0.7984 (t80) cc_final: 0.6889 (t80) REVERT: B 136 ASN cc_start: 0.6604 (t0) cc_final: 0.6330 (t0) REVERT: B 257 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 391 PHE cc_start: 0.5888 (m-80) cc_final: 0.5658 (m-80) REVERT: B 513 MET cc_start: 0.6353 (tpt) cc_final: 0.6015 (tpt) REVERT: B 521 GLU cc_start: 0.7833 (pm20) cc_final: 0.7537 (tp30) REVERT: B 685 LYS cc_start: 0.7588 (ttpp) cc_final: 0.7020 (mttp) REVERT: B 739 MET cc_start: 0.8450 (tpp) cc_final: 0.8248 (ttm) REVERT: B 905 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7895 (tt) REVERT: C 23 TRP cc_start: 0.6221 (t60) cc_final: 0.5963 (t-100) REVERT: C 94 MET cc_start: 0.3838 (ptt) cc_final: 0.2721 (mmp) REVERT: C 151 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6472 (pm20) REVERT: C 203 TRP cc_start: 0.6878 (t60) cc_final: 0.6406 (t60) REVERT: C 314 MET cc_start: 0.5911 (ttp) cc_final: 0.5056 (ttp) REVERT: C 404 SER cc_start: 0.8080 (t) cc_final: 0.7442 (p) REVERT: C 605 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7518 (p) REVERT: C 989 ASP cc_start: 0.6912 (p0) cc_final: 0.6683 (p0) REVERT: D 142 GLN cc_start: 0.2685 (tp40) cc_final: 0.2129 (mm110) REVERT: D 153 ASP cc_start: 0.8171 (p0) cc_final: 0.7545 (t0) REVERT: D 212 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8360 (mt) REVERT: D 391 PHE cc_start: 0.7462 (m-80) cc_final: 0.6910 (m-10) REVERT: D 529 LEU cc_start: 0.8435 (mt) cc_final: 0.7772 (tt) REVERT: D 892 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6969 (m-30) REVERT: D 1043 LEU cc_start: 0.5972 (mt) cc_final: 0.5757 (tp) outliers start: 108 outliers final: 81 residues processed: 442 average time/residue: 0.1667 time to fit residues: 124.7436 Evaluate side-chains 440 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 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 233 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 309 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 323 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 LEU 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 771 HIS Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 983 LEU 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 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ILE 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 365 HIS 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 760 ILE 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 B residue 1005 LYS 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 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 822 LEU 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 180 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 253 ILE 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 456 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 941 VAL 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: 2.9990 chunk 81 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 chunk 340 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 282 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.127954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103192 restraints weight = 66198.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103926 restraints weight = 48152.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104783 restraints weight = 39064.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105078 restraints weight = 33975.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105174 restraints weight = 31846.082| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28480 Z= 0.124 Angle : 0.576 13.827 38652 Z= 0.287 Chirality : 0.042 0.213 4440 Planarity : 0.004 0.057 4832 Dihedral : 4.005 21.376 3728 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.80 % Allowed : 19.72 % Favored : 77.48 % 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 aren not related in a simple way. whole: -0.29 (0.14), residues: 3444 helix: 0.47 (0.13), residues: 1750 sheet: -0.02 (0.28), residues: 384 loop : -1.04 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.042 0.001 TYR B 163 PHE 0.031 0.001 PHE D 120 TRP 0.015 0.001 TRP A 477 HIS 0.022 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00279 (28480) covalent geometry : angle 0.57636 (38652) hydrogen bonds : bond 0.03927 ( 1280) hydrogen bonds : angle 4.77569 ( 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 465 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 379 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7741 (mmm) cc_final: 0.6855 (ptt) REVERT: A 38 PHE cc_start: 0.6040 (m-80) cc_final: 0.5679 (m-10) REVERT: A 120 PHE cc_start: 0.5536 (t80) cc_final: 0.4879 (t80) REVERT: A 180 GLU cc_start: 0.6535 (tt0) cc_final: 0.5663 (mm-30) REVERT: A 321 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: A 332 TYR cc_start: 0.5730 (OUTLIER) cc_final: 0.5135 (t80) REVERT: A 409 HIS cc_start: 0.7768 (m-70) cc_final: 0.7489 (m90) REVERT: A 415 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8322 (mmmt) REVERT: A 513 MET cc_start: 0.7644 (tpt) cc_final: 0.7118 (tpt) REVERT: A 918 SER cc_start: 0.8622 (p) cc_final: 0.8192 (t) REVERT: A 1002 LYS cc_start: 0.8234 (mppt) cc_final: 0.7871 (mmmt) REVERT: A 1008 ASN cc_start: 0.7076 (m-40) cc_final: 0.6547 (m-40) REVERT: A 1009 MET cc_start: 0.5625 (mmp) cc_final: 0.4518 (mtt) REVERT: A 1036 ASN cc_start: 0.5759 (t0) cc_final: 0.5491 (t0) REVERT: B 94 MET cc_start: 0.0668 (tpp) cc_final: 0.0432 (tpp) REVERT: B 130 TYR cc_start: 0.7840 (t80) cc_final: 0.7071 (t80) REVERT: B 136 ASN cc_start: 0.6632 (t0) cc_final: 0.6193 (m-40) REVERT: B 391 PHE cc_start: 0.5763 (m-80) cc_final: 0.5461 (m-80) REVERT: B 392 LYS cc_start: 0.7483 (pttm) cc_final: 0.7086 (mmtm) REVERT: B 521 GLU cc_start: 0.7777 (pm20) cc_final: 0.7501 (tp30) REVERT: B 685 LYS cc_start: 0.7541 (ttpp) cc_final: 0.6980 (mttp) REVERT: B 739 MET cc_start: 0.8470 (tpp) cc_final: 0.8219 (ttm) REVERT: B 905 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7880 (tt) REVERT: C 23 TRP cc_start: 0.6033 (t60) cc_final: 0.5809 (t-100) REVERT: C 94 MET cc_start: 0.3788 (ptt) cc_final: 0.2597 (mmp) REVERT: C 151 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: C 203 TRP cc_start: 0.6845 (t60) cc_final: 0.6366 (t60) REVERT: C 404 SER cc_start: 0.8109 (t) cc_final: 0.7545 (p) REVERT: C 605 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7485 (p) REVERT: C 989 ASP cc_start: 0.6971 (p0) cc_final: 0.6739 (p0) REVERT: D 142 GLN cc_start: 0.2467 (tp40) cc_final: 0.2018 (mm110) REVERT: D 153 ASP cc_start: 0.8076 (p0) cc_final: 0.7427 (t0) REVERT: D 303 PHE cc_start: 0.6829 (t80) cc_final: 0.6609 (t80) REVERT: D 391 PHE cc_start: 0.7415 (m-80) cc_final: 0.6885 (m-10) REVERT: D 892 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6888 (m-30) outliers start: 86 outliers final: 61 residues processed: 437 average time/residue: 0.1671 time to fit residues: 123.3197 Evaluate side-chains 424 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 357 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 372 ASN Chi-restraints excluded: chain A residue 499 LEU 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 917 VAL Chi-restraints excluded: chain A residue 983 LEU 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 233 ILE Chi-restraints excluded: chain B residue 281 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 578 ARG Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 ILE 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 346 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 560 LYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 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 942 THR Chi-restraints excluded: chain C residue 1014 ILE 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 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 1039 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 82 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 263 optimal weight: 0.4980 chunk 147 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 887 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.127085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102125 restraints weight = 66657.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101992 restraints weight = 51119.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102723 restraints weight = 41658.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103385 restraints weight = 37042.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103467 restraints weight = 34334.702| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4548 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= 0.148 Angle : 0.595 13.947 38652 Z= 0.298 Chirality : 0.042 0.222 4440 Planarity : 0.004 0.059 4832 Dihedral : 4.051 22.306 3728 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.06 % Allowed : 19.82 % Favored : 77.12 % 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 aren not related in a simple way. whole: -0.36 (0.14), residues: 3444 helix: 0.40 (0.12), residues: 1774 sheet: -0.03 (0.28), residues: 380 loop : -1.08 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.020 0.002 TYR A 996 PHE 0.031 0.002 PHE D 120 TRP 0.017 0.001 TRP D 263 HIS 0.019 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00340 (28480) covalent geometry : angle 0.59490 (38652) hydrogen bonds : bond 0.04041 ( 1280) hydrogen bonds : angle 4.78965 ( 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 449 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 355 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7712 (mmm) cc_final: 0.6803 (ptt) REVERT: A 38 PHE cc_start: 0.6011 (m-80) cc_final: 0.5617 (m-10) REVERT: A 120 PHE cc_start: 0.5654 (t80) cc_final: 0.5016 (t80) REVERT: A 176 TRP cc_start: 0.6286 (m100) cc_final: 0.5579 (m100) REVERT: A 180 GLU cc_start: 0.6523 (tt0) cc_final: 0.5641 (mm-30) REVERT: A 332 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.5223 (t80) REVERT: A 409 HIS cc_start: 0.7781 (m-70) cc_final: 0.7548 (m90) REVERT: A 415 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8314 (mmmt) REVERT: A 513 MET cc_start: 0.7658 (tpt) cc_final: 0.7061 (tpt) REVERT: A 830 MET cc_start: 0.8422 (mtp) cc_final: 0.8083 (mtp) REVERT: A 918 SER cc_start: 0.8664 (p) cc_final: 0.8252 (t) REVERT: A 1008 ASN cc_start: 0.7067 (m-40) cc_final: 0.6589 (m-40) REVERT: A 1009 MET cc_start: 0.5606 (mmp) cc_final: 0.4627 (mtt) REVERT: A 1036 ASN cc_start: 0.5720 (t0) cc_final: 0.5438 (t0) REVERT: B 94 MET cc_start: 0.0786 (tpp) cc_final: 0.0573 (tpp) REVERT: B 130 TYR cc_start: 0.7871 (t80) cc_final: 0.7018 (t80) REVERT: B 136 ASN cc_start: 0.6677 (t0) cc_final: 0.6233 (m-40) REVERT: B 160 PHE cc_start: 0.5556 (m-80) cc_final: 0.5116 (m-80) REVERT: B 391 PHE cc_start: 0.5990 (m-80) cc_final: 0.5676 (m-80) REVERT: B 392 LYS cc_start: 0.7563 (pttm) cc_final: 0.7168 (mmtm) REVERT: B 521 GLU cc_start: 0.7810 (pm20) cc_final: 0.7465 (tp30) REVERT: B 685 LYS cc_start: 0.7559 (ttpp) cc_final: 0.6996 (mttp) REVERT: B 739 MET cc_start: 0.8483 (tpp) cc_final: 0.8274 (ttm) REVERT: B 902 GLU cc_start: 0.7229 (tp30) cc_final: 0.6669 (tp30) REVERT: C 23 TRP cc_start: 0.6052 (t60) cc_final: 0.5817 (t-100) REVERT: C 94 MET cc_start: 0.3758 (ptt) cc_final: 0.2454 (mmp) REVERT: C 151 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6502 (pm20) REVERT: C 168 PHE cc_start: 0.5848 (t80) cc_final: 0.5387 (t80) REVERT: C 203 TRP cc_start: 0.6845 (t60) cc_final: 0.6338 (t60) REVERT: C 404 SER cc_start: 0.8155 (t) cc_final: 0.7575 (p) REVERT: C 605 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7509 (p) REVERT: C 989 ASP cc_start: 0.6996 (p0) cc_final: 0.6767 (p0) REVERT: C 1000 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.6157 (p90) REVERT: C 1039 TYR cc_start: 0.6840 (t80) cc_final: 0.6145 (t80) REVERT: D 142 GLN cc_start: 0.2477 (tp40) cc_final: 0.2043 (mm110) REVERT: D 153 ASP cc_start: 0.8079 (p0) cc_final: 0.7402 (t0) REVERT: D 391 PHE cc_start: 0.7436 (m-80) cc_final: 0.6911 (m-10) REVERT: D 892 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.6969 (m-30) outliers start: 94 outliers final: 77 residues processed: 418 average time/residue: 0.1651 time to fit residues: 116.8492 Evaluate side-chains 424 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 342 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 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 332 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 553 VAL 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 732 ILE Chi-restraints excluded: chain A residue 771 HIS Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1035 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 239 LEU Chi-restraints excluded: chain B residue 281 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 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 760 ILE 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 B residue 1005 LYS 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 560 LYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 253 ILE 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 456 ILE Chi-restraints excluded: chain D residue 564 LEU 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 1039 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 287 optimal weight: 0.0970 chunk 9 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 286 optimal weight: 0.0770 chunk 152 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104365 restraints weight = 66042.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103953 restraints weight = 50836.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105158 restraints weight = 41770.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105517 restraints weight = 35838.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105644 restraints weight = 33747.029| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28480 Z= 0.110 Angle : 0.569 12.680 38652 Z= 0.282 Chirality : 0.041 0.198 4440 Planarity : 0.004 0.057 4832 Dihedral : 3.915 22.477 3728 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.67 % Allowed : 20.44 % 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 aren not related in a simple way. whole: -0.20 (0.14), residues: 3444 helix: 0.53 (0.13), residues: 1762 sheet: 0.06 (0.28), residues: 394 loop : -1.03 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.018 0.001 TYR A 996 PHE 0.029 0.001 PHE D 120 TRP 0.016 0.001 TRP B 100 HIS 0.027 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00243 (28480) covalent geometry : angle 0.56866 (38652) hydrogen bonds : bond 0.03718 ( 1280) hydrogen bonds : angle 4.65326 ( 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 451 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 369 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7450 (mmm) cc_final: 0.6675 (ptt) REVERT: A 38 PHE cc_start: 0.5995 (m-80) cc_final: 0.5603 (m-10) REVERT: A 120 PHE cc_start: 0.5663 (t80) cc_final: 0.5045 (t80) REVERT: A 176 TRP cc_start: 0.6289 (m100) cc_final: 0.5599 (m100) REVERT: A 180 GLU cc_start: 0.6398 (tt0) cc_final: 0.5573 (mm-30) REVERT: A 332 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.5093 (t80) REVERT: A 409 HIS cc_start: 0.7748 (m-70) cc_final: 0.7460 (m90) REVERT: A 415 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8333 (mmtt) REVERT: A 513 MET cc_start: 0.7582 (tpt) cc_final: 0.7002 (tpt) REVERT: A 830 MET cc_start: 0.8352 (mtp) cc_final: 0.8024 (mtp) REVERT: A 918 SER cc_start: 0.8627 (p) cc_final: 0.8174 (t) REVERT: A 1002 LYS cc_start: 0.8204 (mppt) cc_final: 0.7831 (mmmt) REVERT: A 1008 ASN cc_start: 0.6908 (m-40) cc_final: 0.6479 (m110) REVERT: A 1009 MET cc_start: 0.5538 (mmp) cc_final: 0.4343 (mtt) REVERT: A 1036 ASN cc_start: 0.5792 (t0) cc_final: 0.5507 (t0) REVERT: B 21 MET cc_start: 0.6054 (tpt) cc_final: 0.5522 (mtt) REVERT: B 130 TYR cc_start: 0.7767 (t80) cc_final: 0.7025 (t80) REVERT: B 136 ASN cc_start: 0.6708 (t0) cc_final: 0.6299 (m-40) REVERT: B 160 PHE cc_start: 0.5468 (m-80) cc_final: 0.4991 (m-80) REVERT: B 188 PHE cc_start: 0.7600 (m-80) cc_final: 0.7071 (m-80) REVERT: B 391 PHE cc_start: 0.5781 (m-80) cc_final: 0.5509 (m-80) REVERT: B 392 LYS cc_start: 0.7548 (pttm) cc_final: 0.7123 (mmtm) REVERT: B 513 MET cc_start: 0.6091 (tpt) cc_final: 0.5641 (tpt) REVERT: B 521 GLU cc_start: 0.7818 (pm20) cc_final: 0.7453 (tp30) REVERT: B 685 LYS cc_start: 0.7528 (ttpp) cc_final: 0.6997 (mttp) REVERT: B 739 MET cc_start: 0.8463 (tpp) cc_final: 0.8206 (ttm) REVERT: B 830 MET cc_start: 0.8359 (tpp) cc_final: 0.7795 (tpp) REVERT: B 930 ASN cc_start: 0.8056 (t0) cc_final: 0.7816 (t0) REVERT: C 94 MET cc_start: 0.3720 (ptt) cc_final: 0.2454 (mmp) REVERT: C 168 PHE cc_start: 0.5842 (t80) cc_final: 0.5394 (t80) REVERT: C 203 TRP cc_start: 0.6805 (t60) cc_final: 0.6293 (t60) REVERT: C 286 SER cc_start: 0.9055 (p) cc_final: 0.8689 (m) REVERT: C 404 SER cc_start: 0.8149 (t) cc_final: 0.7571 (p) REVERT: C 605 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7479 (p) REVERT: C 691 MET cc_start: 0.6859 (mmm) cc_final: 0.6587 (tpt) REVERT: C 989 ASP cc_start: 0.7081 (p0) cc_final: 0.6862 (p0) REVERT: C 1000 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6250 (p90) REVERT: C 1039 TYR cc_start: 0.6735 (t80) cc_final: 0.6106 (t80) REVERT: D 142 GLN cc_start: 0.2426 (tp40) cc_final: 0.2083 (mm110) REVERT: D 153 ASP cc_start: 0.8099 (p0) cc_final: 0.7447 (t0) REVERT: D 391 PHE cc_start: 0.7403 (m-80) cc_final: 0.6882 (m-10) REVERT: D 892 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: D 1009 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5120 (mmp) outliers start: 82 outliers final: 61 residues processed: 428 average time/residue: 0.1651 time to fit residues: 119.4899 Evaluate side-chains 414 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 319 VAL 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 396 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 499 LEU 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 917 VAL Chi-restraints excluded: chain A residue 983 LEU 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 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 546 VAL 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 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 B residue 1005 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL 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 560 LYS 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 720 VAL 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 1000 PHE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 PHE 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 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: 0.7980 chunk 41 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 101 optimal weight: 0.0470 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105442 restraints weight = 66163.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106304 restraints weight = 48458.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107060 restraints weight = 39391.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107375 restraints weight = 34099.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107510 restraints weight = 31961.509| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28480 Z= 0.107 Angle : 0.572 12.923 38652 Z= 0.282 Chirality : 0.041 0.215 4440 Planarity : 0.004 0.057 4832 Dihedral : 3.801 26.724 3728 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.05 % Allowed : 21.12 % Favored : 76.83 % 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 aren not related in a simple way. whole: -0.09 (0.14), residues: 3444 helix: 0.61 (0.13), residues: 1760 sheet: 0.10 (0.28), residues: 392 loop : -0.96 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.040 0.001 TYR B 163 PHE 0.041 0.001 PHE A1000 TRP 0.016 0.001 TRP B 100 HIS 0.004 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00232 (28480) covalent geometry : angle 0.57200 (38652) hydrogen bonds : bond 0.03575 ( 1280) hydrogen bonds : angle 4.56107 ( 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 435 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 372 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7301 (mmm) cc_final: 0.6682 (ptt) REVERT: A 38 PHE cc_start: 0.5956 (m-80) cc_final: 0.5568 (m-10) REVERT: A 120 PHE cc_start: 0.5589 (t80) cc_final: 0.5002 (t80) REVERT: A 176 TRP cc_start: 0.6249 (m100) cc_final: 0.5528 (m100) REVERT: A 180 GLU cc_start: 0.6372 (tt0) cc_final: 0.5501 (mm-30) REVERT: A 332 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5050 (t80) REVERT: A 409 HIS cc_start: 0.7730 (m-70) cc_final: 0.7409 (m90) REVERT: A 415 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8313 (mmtt) REVERT: A 513 MET cc_start: 0.7553 (tpt) cc_final: 0.6914 (tpt) REVERT: A 604 GLU cc_start: 0.7490 (mp0) cc_final: 0.7059 (mp0) REVERT: A 830 MET cc_start: 0.8346 (mtp) cc_final: 0.8014 (mtp) REVERT: A 918 SER cc_start: 0.8606 (p) cc_final: 0.8162 (t) REVERT: A 1002 LYS cc_start: 0.8101 (mppt) cc_final: 0.7828 (mmmt) REVERT: A 1008 ASN cc_start: 0.6791 (m-40) cc_final: 0.6237 (m110) REVERT: A 1009 MET cc_start: 0.5480 (mmp) cc_final: 0.4291 (mtt) REVERT: A 1036 ASN cc_start: 0.5801 (t0) cc_final: 0.5514 (t0) REVERT: B 21 MET cc_start: 0.6196 (tpt) cc_final: 0.5604 (mtt) REVERT: B 136 ASN cc_start: 0.6677 (t0) cc_final: 0.6247 (m-40) REVERT: B 163 TYR cc_start: 0.7662 (t80) cc_final: 0.7266 (t80) REVERT: B 178 TRP cc_start: 0.5598 (t-100) cc_final: 0.5330 (t-100) REVERT: B 188 PHE cc_start: 0.7723 (m-80) cc_final: 0.7275 (m-80) REVERT: B 204 LEU cc_start: 0.7814 (mm) cc_final: 0.7594 (mm) REVERT: B 231 ASN cc_start: 0.7833 (m110) cc_final: 0.6947 (p0) REVERT: B 521 GLU cc_start: 0.7822 (pm20) cc_final: 0.7424 (tp30) REVERT: B 685 LYS cc_start: 0.7414 (ttpp) cc_final: 0.6883 (mttp) REVERT: B 712 MET cc_start: 0.8175 (ttp) cc_final: 0.7973 (ttp) REVERT: B 739 MET cc_start: 0.8521 (tpp) cc_final: 0.8309 (ttm) REVERT: B 830 MET cc_start: 0.8314 (tpp) cc_final: 0.7754 (tpp) REVERT: B 930 ASN cc_start: 0.8046 (t0) cc_final: 0.7827 (t0) REVERT: C 94 MET cc_start: 0.3726 (ptt) cc_final: 0.2804 (pmm) REVERT: C 168 PHE cc_start: 0.5856 (t80) cc_final: 0.5392 (t80) REVERT: C 203 TRP cc_start: 0.6767 (t60) cc_final: 0.6281 (t60) REVERT: C 279 TYR cc_start: 0.8850 (t80) cc_final: 0.8618 (t80) REVERT: C 286 SER cc_start: 0.8940 (p) cc_final: 0.8659 (m) REVERT: C 404 SER cc_start: 0.8165 (t) cc_final: 0.7568 (p) REVERT: C 436 GLU cc_start: 0.6867 (tp30) cc_final: 0.6636 (tt0) REVERT: C 605 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7486 (p) REVERT: C 989 ASP cc_start: 0.7100 (p0) cc_final: 0.6875 (p0) REVERT: D 142 GLN cc_start: 0.2507 (tp40) cc_final: 0.2090 (mm110) REVERT: D 153 ASP cc_start: 0.8057 (p0) cc_final: 0.7355 (t0) REVERT: D 391 PHE cc_start: 0.7364 (m-80) cc_final: 0.6824 (m-10) REVERT: D 529 LEU cc_start: 0.8408 (mt) cc_final: 0.7832 (tt) REVERT: D 892 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: D 1009 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5138 (mmp) outliers start: 63 outliers final: 49 residues processed: 419 average time/residue: 0.1648 time to fit residues: 117.3097 Evaluate side-chains 403 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 350 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 TYR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 396 THR 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 917 VAL Chi-restraints excluded: chain A residue 983 LEU 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 302 LEU 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 727 VAL Chi-restraints excluded: chain B residue 779 LEU 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 184 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL 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 720 VAL 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 1014 ILE 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: 5.9990 chunk 78 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 341 optimal weight: 0.0170 chunk 13 optimal weight: 0.7980 chunk 345 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.130138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105558 restraints weight = 66230.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106326 restraints weight = 49281.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107104 restraints weight = 41543.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107406 restraints weight = 34786.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107509 restraints weight = 32574.565| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28480 Z= 0.109 Angle : 0.578 14.508 38652 Z= 0.283 Chirality : 0.041 0.217 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.759 23.850 3728 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.92 % Allowed : 21.41 % Favored : 76.66 % 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 aren not related in a simple way. whole: -0.06 (0.14), residues: 3444 helix: 0.62 (0.13), residues: 1764 sheet: 0.10 (0.28), residues: 398 loop : -0.90 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 213 TYR 0.033 0.001 TYR B 163 PHE 0.045 0.001 PHE B 391 TRP 0.021 0.001 TRP B 100 HIS 0.004 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00242 (28480) covalent geometry : angle 0.57836 (38652) hydrogen bonds : bond 0.03574 ( 1280) hydrogen bonds : angle 4.56430 ( 3627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4499.86 seconds wall clock time: 79 minutes 18.93 seconds (4758.93 seconds total)