Starting phenix.real_space_refine on Tue Jun 24 00:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo5_33982/06_2025/7yo5_33982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo5_33982/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yo5_33982/06_2025/7yo5_33982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo5_33982/06_2025/7yo5_33982.map" model { file = "/net/cci-nas-00/data/ceres_data/7yo5_33982/06_2025/7yo5_33982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo5_33982/06_2025/7yo5_33982.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.03, per 1000 atoms: 0.58 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: 6.59 Conformation dependent library (CDL) restraints added in 3.5 seconds 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 22 sheets defined 54.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 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: 11.14 Time building geometry restraints manager: 7.88 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: 0.07 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.230 Set scattering table: 0.240 Process input model: 61.600 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.520 ------------------------------------------------------------------------------- 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 : 11.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (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 TRP 0.034 0.001 TRP B 263 HIS 0.003 0.001 HIS D 379 PHE 0.037 0.001 PHE A 34 TYR 0.031 0.001 TYR D1039 ARG 0.006 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.15481 ( 1280) hydrogen bonds : angle 6.48623 ( 3627) covalent geometry : bond 0.00319 (28480) covalent geometry : angle 0.64265 (38652) *********************** 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 : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6260 (m-80) cc_final: 0.5898 (m-10) REVERT: A 120 PHE cc_start: 0.6218 (t80) cc_final: 0.5866 (t80) REVERT: A 180 GLU cc_start: 0.6618 (tt0) cc_final: 0.5840 (mm-30) REVERT: A 195 VAL cc_start: 0.7393 (p) cc_final: 0.7094 (t) REVERT: A 210 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7868 (mmt90) REVERT: A 252 PHE cc_start: 0.8083 (t80) cc_final: 0.7711 (t80) REVERT: A 309 LEU cc_start: 0.8803 (mp) cc_final: 0.8398 (mp) REVERT: A 409 HIS cc_start: 0.8380 (m-70) cc_final: 0.7824 (m90) REVERT: A 414 VAL cc_start: 0.8509 (m) cc_final: 0.8262 (t) REVERT: A 415 LYS cc_start: 0.8804 (mptt) cc_final: 0.8180 (mmtt) REVERT: A 536 MET cc_start: 0.7979 (tmm) cc_final: 0.6734 (tmm) REVERT: A 1009 MET cc_start: 0.5226 (mmp) cc_final: 0.4114 (mtt) REVERT: B 104 MET cc_start: 0.6420 (tpt) cc_final: 0.5581 (mtt) REVERT: B 154 MET cc_start: 0.6409 (tpp) cc_final: 0.5885 (tpt) REVERT: B 180 GLU cc_start: 0.7028 (tm-30) cc_final: 0.5403 (mm-30) REVERT: B 184 VAL cc_start: 0.7535 (t) cc_final: 0.7168 (t) REVERT: B 188 PHE cc_start: 0.7541 (m-80) cc_final: 0.6945 (m-80) REVERT: B 257 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 353 LEU cc_start: 0.8118 (tp) cc_final: 0.7876 (tt) REVERT: B 384 ASN cc_start: 0.3931 (t0) cc_final: 0.3196 (p0) REVERT: B 386 GLU cc_start: 0.6589 (mp0) cc_final: 0.5629 (tp30) REVERT: B 391 PHE cc_start: 0.5371 (m-10) cc_final: 0.5147 (m-80) REVERT: B 427 ASN cc_start: 0.7122 (t0) cc_final: 0.6666 (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: 0.6580 (m-30) REVERT: B 884 ASN cc_start: 0.8779 (t0) cc_final: 0.8484 (t0) REVERT: B 948 GLU cc_start: 0.7962 (pt0) cc_final: 0.7759 (tt0) REVERT: B 1017 LEU cc_start: 0.7085 (mt) cc_final: 0.6864 (mt) REVERT: B 1053 MET cc_start: 0.6836 (ptm) cc_final: 0.6604 (ptm) REVERT: C 94 MET cc_start: 0.3812 (ptt) cc_final: 0.3383 (mmp) REVERT: C 142 GLN cc_start: 0.6264 (tt0) cc_final: 0.5884 (tm-30) REVERT: C 154 MET cc_start: 0.5763 (tpp) cc_final: 0.5492 (tpp) REVERT: C 159 PHE cc_start: 0.7857 (t80) cc_final: 0.7588 (t80) REVERT: C 388 GLU cc_start: 0.6850 (tt0) cc_final: 0.6630 (tt0) REVERT: C 399 GLU cc_start: 0.6506 (pt0) cc_final: 0.5627 (tp30) REVERT: C 404 SER cc_start: 0.7433 (t) cc_final: 0.6623 (p) REVERT: C 442 MET cc_start: 0.8438 (mmt) cc_final: 0.8230 (tpp) REVERT: C 466 LYS cc_start: 0.8106 (tttm) cc_final: 0.7804 (tptt) REVERT: C 516 PHE cc_start: 0.5007 (t80) cc_final: 0.4776 (t80) REVERT: C 739 MET cc_start: 0.8117 (mmm) cc_final: 0.7457 (mtm) REVERT: C 760 ILE cc_start: 0.8110 (tt) cc_final: 0.7862 (mt) REVERT: C 785 SER cc_start: 0.8964 (m) cc_final: 0.8594 (p) REVERT: C 816 GLN cc_start: 0.7730 (mm110) cc_final: 0.7271 (mp10) REVERT: C 952 LEU cc_start: 0.7933 (mm) cc_final: 0.7506 (mp) REVERT: D 142 GLN cc_start: 0.2567 (tp40) cc_final: 0.2266 (mm110) REVERT: D 153 ASP cc_start: 0.8231 (p0) cc_final: 0.7653 (t0) REVERT: D 252 PHE cc_start: 0.7545 (t80) cc_final: 0.7167 (m-80) REVERT: D 318 TYR cc_start: 0.6696 (m-10) cc_final: 0.6461 (m-80) REVERT: D 374 GLU cc_start: 0.6244 (tp30) cc_final: 0.5808 (tt0) REVERT: D 391 PHE cc_start: 0.7470 (m-80) cc_final: 0.6951 (m-10) REVERT: D 514 ARG cc_start: 0.6078 (mmm160) cc_final: 0.5746 (mmm160) REVERT: D 782 THR cc_start: 0.9151 (m) cc_final: 0.8923 (p) REVERT: D 1005 LYS cc_start: 0.7618 (pttp) cc_final: 0.7280 (mttp) REVERT: D 1044 VAL cc_start: 0.6399 (t) cc_final: 0.6175 (m) outliers start: 9 outliers final: 4 residues processed: 785 average time/residue: 0.4055 time to fit residues: 496.5442 Evaluate side-chains 422 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 3.182 ------------------------------------------------------------------------------- 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 293 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 272 optimal weight: 0.0040 chunk 105 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 316 optimal weight: 6.9990 overall best weight: 3.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 HIS A 372 ASN A 449 ASN A 462 GLN A 753 HIS ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN B 887 ASN ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 379 HIS C 402 GLN 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 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.101640 restraints weight = 66089.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102928 restraints weight = 49098.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103660 restraints weight = 38432.304| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28480 Z= 0.228 Angle : 0.702 18.662 38652 Z= 0.359 Chirality : 0.047 0.297 4440 Planarity : 0.005 0.057 4832 Dihedral : 4.620 46.947 3735 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.77 % Allowed : 12.58 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3444 helix: 0.07 (0.12), residues: 1786 sheet: 0.35 (0.31), residues: 302 loop : -1.22 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 477 HIS 0.007 0.002 HIS B 693 PHE 0.033 0.003 PHE B 187 TYR 0.036 0.002 TYR D1015 ARG 0.007 0.001 ARG D 393 Details of bonding type rmsd hydrogen bonds : bond 0.05019 ( 1280) hydrogen bonds : angle 5.31373 ( 3627) covalent geometry : bond 0.00508 (28480) covalent geometry : angle 0.70164 (38652) *********************** 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 548 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 463 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6171 (m-80) cc_final: 0.5868 (m-10) REVERT: A 120 PHE cc_start: 0.6299 (t80) cc_final: 0.5961 (t80) REVERT: A 180 GLU cc_start: 0.6620 (tt0) cc_final: 0.5772 (mm-30) REVERT: A 244 SER cc_start: 0.8376 (p) cc_final: 0.8167 (p) REVERT: A 252 PHE cc_start: 0.7723 (t80) cc_final: 0.7491 (t80) REVERT: A 309 LEU cc_start: 0.9105 (mp) cc_final: 0.8708 (mp) REVERT: A 324 GLU cc_start: 0.6187 (pm20) cc_final: 0.5972 (mt-10) REVERT: A 409 HIS cc_start: 0.8028 (m-70) cc_final: 0.7711 (m90) REVERT: A 415 LYS cc_start: 0.8916 (mptt) cc_final: 0.8573 (mmmt) REVERT: A 425 LEU cc_start: 0.9022 (mm) cc_final: 0.8752 (mt) REVERT: A 1009 MET cc_start: 0.5523 (mmp) cc_final: 0.4444 (mtt) REVERT: A 1036 ASN cc_start: 0.5866 (t0) cc_final: 0.5507 (t0) REVERT: B 104 MET cc_start: 0.6398 (tpt) cc_final: 0.5837 (mtt) REVERT: B 130 TYR cc_start: 0.7957 (t80) cc_final: 0.7170 (t80) REVERT: B 154 MET cc_start: 0.5487 (tpp) cc_final: 0.5121 (tpt) REVERT: B 180 GLU cc_start: 0.6976 (tm-30) cc_final: 0.5194 (mm-30) REVERT: B 184 VAL cc_start: 0.7588 (t) cc_final: 0.7010 (t) REVERT: B 187 PHE cc_start: 0.5641 (p90) cc_final: 0.4815 (p90) REVERT: B 188 PHE cc_start: 0.8052 (m-80) cc_final: 0.7384 (m-80) REVERT: B 197 VAL cc_start: 0.7352 (p) cc_final: 0.7094 (p) REVERT: B 224 LEU cc_start: 0.4948 (mm) cc_final: 0.4661 (mt) REVERT: B 392 LYS cc_start: 0.7611 (pttm) cc_final: 0.7141 (mmtm) REVERT: B 521 GLU cc_start: 0.7833 (pm20) cc_final: 0.7507 (tp30) REVERT: B 536 MET cc_start: 0.8527 (tmm) cc_final: 0.8110 (ttt) REVERT: B 556 LEU cc_start: 0.7334 (tp) cc_final: 0.6940 (tt) REVERT: B 685 LYS cc_start: 0.7623 (ttpp) cc_final: 0.7102 (mttp) REVERT: B 739 MET cc_start: 0.8536 (tpp) cc_final: 0.8192 (ttm) REVERT: B 1005 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7709 (pttm) REVERT: C 94 MET cc_start: 0.3828 (ptt) cc_final: 0.3231 (mmp) REVERT: C 154 MET cc_start: 0.5789 (tpp) cc_final: 0.5586 (tpp) REVERT: C 203 TRP cc_start: 0.6677 (t60) cc_final: 0.6377 (t60) REVERT: C 279 TYR cc_start: 0.8834 (t80) cc_final: 0.8434 (t80) REVERT: C 332 TYR cc_start: 0.6001 (m-80) cc_final: 0.5695 (m-80) REVERT: C 353 LEU cc_start: 0.7283 (tp) cc_final: 0.6833 (tp) REVERT: C 399 GLU cc_start: 0.6821 (pt0) cc_final: 0.6331 (tp30) REVERT: C 404 SER cc_start: 0.8002 (t) cc_final: 0.7148 (p) REVERT: C 429 TYR cc_start: 0.7478 (m-80) cc_final: 0.7138 (m-80) REVERT: C 739 MET cc_start: 0.8153 (mmm) cc_final: 0.7727 (mtm) REVERT: D 29 SER cc_start: 0.7295 (m) cc_final: 0.7086 (p) REVERT: D 104 MET cc_start: 0.5304 (mmt) cc_final: 0.4970 (mmm) REVERT: D 142 GLN cc_start: 0.2623 (tp40) cc_final: 0.2170 (mm110) REVERT: D 153 ASP cc_start: 0.8029 (p0) cc_final: 0.7522 (t0) REVERT: D 199 LEU cc_start: 0.5656 (mm) cc_final: 0.5101 (tp) REVERT: D 264 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6706 (mm-30) REVERT: D 366 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7513 (tttt) REVERT: D 374 GLU cc_start: 0.6117 (tp30) cc_final: 0.5413 (tt0) REVERT: D 391 PHE cc_start: 0.7655 (m-80) cc_final: 0.7009 (m-10) REVERT: D 892 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: D 924 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: D 984 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6781 (p0) REVERT: D 1005 LYS cc_start: 0.7447 (pttp) cc_final: 0.7187 (mttp) outliers start: 85 outliers final: 61 residues processed: 519 average time/residue: 0.3672 time to fit residues: 312.9827 Evaluate side-chains 437 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 ILE 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 323 ILE Chi-restraints excluded: chain A residue 374 GLU 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 777 SER 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 987 PHE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 557 CYS Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 732 ILE 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 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 559 VAL Chi-restraints excluded: chain D residue 695 CYS 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 777 SER Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 924 MET 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 230 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 342 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 344 HIS A 771 HIS ** 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** ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103298 restraints weight = 66097.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104064 restraints weight = 48644.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104805 restraints weight = 40611.465| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28480 Z= 0.136 Angle : 0.575 18.388 38652 Z= 0.291 Chirality : 0.042 0.195 4440 Planarity : 0.004 0.056 4832 Dihedral : 4.292 41.489 3734 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 15.29 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3444 helix: 0.27 (0.12), residues: 1764 sheet: 0.11 (0.29), residues: 356 loop : -1.07 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 263 HIS 0.007 0.001 HIS B 365 PHE 0.028 0.002 PHE D1000 TYR 0.018 0.001 TYR A 996 ARG 0.004 0.000 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 1280) hydrogen bonds : angle 5.01055 ( 3627) covalent geometry : bond 0.00305 (28480) covalent geometry : angle 0.57544 (38652) *********************** 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 497 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 406 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7835 (mmm) cc_final: 0.7091 (ptt) REVERT: A 38 PHE cc_start: 0.5967 (m-80) cc_final: 0.5743 (m-10) REVERT: A 180 GLU cc_start: 0.6627 (tt0) cc_final: 0.5738 (mm-30) REVERT: A 244 SER cc_start: 0.8395 (p) cc_final: 0.8194 (p) REVERT: A 409 HIS cc_start: 0.7946 (m-70) cc_final: 0.7609 (m90) REVERT: A 415 LYS cc_start: 0.8910 (mptt) cc_final: 0.8442 (mmmt) REVERT: A 425 LEU cc_start: 0.9070 (mm) cc_final: 0.8744 (mt) REVERT: A 471 ASN cc_start: 0.6203 (m-40) cc_final: 0.5665 (m110) REVERT: A 536 MET cc_start: 0.7933 (ttp) cc_final: 0.7272 (ttm) REVERT: A 604 GLU cc_start: 0.7611 (mp0) cc_final: 0.7122 (mp0) REVERT: A 897 ASP cc_start: 0.6654 (m-30) cc_final: 0.6405 (m-30) REVERT: A 1009 MET cc_start: 0.5582 (mmp) cc_final: 0.4366 (mtt) REVERT: A 1036 ASN cc_start: 0.5722 (t0) cc_final: 0.5402 (t0) REVERT: B 94 MET cc_start: 0.0033 (tpp) cc_final: -0.0352 (tpp) REVERT: B 104 MET cc_start: 0.6316 (tpt) cc_final: 0.5943 (mtt) REVERT: B 130 TYR cc_start: 0.7881 (t80) cc_final: 0.6993 (t80) REVERT: B 154 MET cc_start: 0.5390 (tpp) cc_final: 0.5184 (tpt) REVERT: B 180 GLU cc_start: 0.6815 (tm-30) cc_final: 0.5193 (mm-30) REVERT: B 392 LYS cc_start: 0.7611 (pttm) cc_final: 0.7204 (mmtm) REVERT: B 521 GLU cc_start: 0.7836 (pm20) cc_final: 0.7537 (tp30) REVERT: B 685 LYS cc_start: 0.7505 (ttpp) cc_final: 0.7068 (mttp) REVERT: B 739 MET cc_start: 0.8555 (tpp) cc_final: 0.8254 (ttm) REVERT: C 94 MET cc_start: 0.3752 (ptt) cc_final: 0.3141 (mmp) REVERT: C 151 GLN cc_start: 0.6438 (OUTLIER) cc_final: 0.6227 (pm20) REVERT: C 154 MET cc_start: 0.5810 (tpp) cc_final: 0.5579 (tpp) REVERT: C 203 TRP cc_start: 0.6640 (t60) cc_final: 0.6238 (t60) REVERT: C 279 TYR cc_start: 0.8866 (t80) cc_final: 0.8563 (t80) REVERT: C 332 TYR cc_start: 0.5962 (m-80) cc_final: 0.5677 (m-80) REVERT: C 399 GLU cc_start: 0.6544 (pt0) cc_final: 0.6140 (tp30) REVERT: C 404 SER cc_start: 0.8140 (t) cc_final: 0.7312 (p) REVERT: C 429 TYR cc_start: 0.7300 (m-80) cc_final: 0.6957 (m-80) REVERT: C 605 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7380 (p) REVERT: C 739 MET cc_start: 0.8092 (mmm) cc_final: 0.7802 (mtm) REVERT: C 1053 MET cc_start: 0.7268 (ptp) cc_final: 0.6913 (ptt) REVERT: D 142 GLN cc_start: 0.2515 (tp40) cc_final: 0.2113 (mm110) REVERT: D 153 ASP cc_start: 0.8207 (p0) cc_final: 0.7659 (t0) REVERT: D 374 GLU cc_start: 0.6142 (tp30) cc_final: 0.5676 (tp30) REVERT: D 391 PHE cc_start: 0.7399 (m-80) cc_final: 0.6894 (m-10) REVERT: D 892 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: D 984 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7090 (p0) REVERT: D 1009 MET cc_start: 0.5548 (OUTLIER) cc_final: 0.4747 (mmp) outliers start: 91 outliers final: 56 residues processed: 469 average time/residue: 0.3555 time to fit residues: 277.6057 Evaluate side-chains 410 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 2.967 ------------------------------------------------------------------------------- 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 196 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 777 SER 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 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 376 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 720 VAL 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 917 VAL Chi-restraints excluded: chain C residue 151 GLN 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 552 THR Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain 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 984 ASP Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1009 MET 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 116 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 345 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 339 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 459 GLN ** 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** B 793 ASN ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101888 restraints weight = 66976.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101502 restraints weight = 50066.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102606 restraints weight = 42187.792| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28480 Z= 0.170 Angle : 0.604 17.627 38652 Z= 0.304 Chirality : 0.043 0.231 4440 Planarity : 0.004 0.058 4832 Dihedral : 4.294 41.711 3732 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.72 % Allowed : 16.36 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3444 helix: 0.24 (0.12), residues: 1772 sheet: -0.08 (0.28), residues: 384 loop : -1.11 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 263 HIS 0.006 0.001 HIS A 350 PHE 0.044 0.002 PHE B 391 TYR 0.019 0.002 TYR D1015 ARG 0.006 0.001 ARG B 201 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 1280) hydrogen bonds : angle 4.99754 ( 3627) covalent geometry : bond 0.00392 (28480) covalent geometry : angle 0.60409 (38652) *********************** 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 491 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 377 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7940 (mmm) cc_final: 0.7031 (ptt) REVERT: A 38 PHE cc_start: 0.6102 (m-80) cc_final: 0.5816 (m-10) REVERT: A 120 PHE cc_start: 0.6003 (t80) cc_final: 0.5306 (t80) REVERT: A 179 LEU cc_start: 0.7076 (mp) cc_final: 0.6821 (mt) REVERT: A 180 GLU cc_start: 0.6516 (tt0) cc_final: 0.5665 (mm-30) REVERT: A 244 SER cc_start: 0.8370 (p) cc_final: 0.8166 (p) REVERT: A 304 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8457 (mmm) REVERT: A 409 HIS cc_start: 0.7966 (m-70) cc_final: 0.7633 (m90) REVERT: A 415 LYS cc_start: 0.8890 (mptt) cc_final: 0.8426 (mmmt) REVERT: A 425 LEU cc_start: 0.9072 (mm) cc_final: 0.8775 (mt) REVERT: A 513 MET cc_start: 0.7540 (tpt) cc_final: 0.6961 (tpt) REVERT: A 897 ASP cc_start: 0.6719 (m-30) cc_final: 0.6409 (m-30) REVERT: A 918 SER cc_start: 0.8500 (p) cc_final: 0.8073 (t) REVERT: A 1036 ASN cc_start: 0.5658 (t0) cc_final: 0.5363 (t0) REVERT: A 1053 MET cc_start: 0.6131 (mmm) cc_final: 0.5648 (mmp) REVERT: B 94 MET cc_start: 0.0376 (tpp) cc_final: -0.0126 (tpp) REVERT: B 104 MET cc_start: 0.6282 (tpt) cc_final: 0.5876 (mtm) REVERT: B 130 TYR cc_start: 0.7922 (t80) cc_final: 0.6967 (t80) REVERT: B 163 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7362 (t80) REVERT: B 180 GLU cc_start: 0.6851 (tm-30) cc_final: 0.5420 (mm-30) REVERT: B 285 MET cc_start: 0.8000 (mmt) cc_final: 0.7504 (mmt) REVERT: B 391 PHE cc_start: 0.5865 (m-80) cc_final: 0.5410 (m-80) REVERT: B 392 LYS cc_start: 0.7517 (pttm) cc_final: 0.7184 (mmtm) REVERT: B 521 GLU cc_start: 0.7877 (pm20) cc_final: 0.7542 (tp30) REVERT: B 529 LEU cc_start: 0.8711 (mt) cc_final: 0.8508 (mt) REVERT: B 685 LYS cc_start: 0.7562 (ttpp) cc_final: 0.7056 (mttp) REVERT: B 739 MET cc_start: 0.8562 (tpp) cc_final: 0.8245 (ttm) REVERT: B 830 MET cc_start: 0.8379 (tpp) cc_final: 0.7999 (tpp) REVERT: B 930 ASN cc_start: 0.8188 (t0) cc_final: 0.7877 (t0) REVERT: B 1005 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7540 (pttt) REVERT: C 94 MET cc_start: 0.3717 (ptt) cc_final: 0.3020 (mmp) REVERT: C 151 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: C 203 TRP cc_start: 0.6804 (t60) cc_final: 0.6362 (t60) REVERT: C 279 TYR cc_start: 0.8899 (t80) cc_final: 0.8591 (t80) REVERT: C 399 GLU cc_start: 0.6576 (pt0) cc_final: 0.6283 (tp30) REVERT: C 404 SER cc_start: 0.8160 (t) cc_final: 0.7366 (p) REVERT: C 429 TYR cc_start: 0.7340 (m-80) cc_final: 0.7030 (m-80) REVERT: C 605 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7404 (p) REVERT: C 739 MET cc_start: 0.8038 (mmm) cc_final: 0.7821 (mtm) REVERT: C 989 ASP cc_start: 0.7097 (p0) cc_final: 0.6847 (p0) REVERT: D 142 GLN cc_start: 0.2552 (tp40) cc_final: 0.2048 (mm110) REVERT: D 153 ASP cc_start: 0.8240 (p0) cc_final: 0.7531 (t0) REVERT: D 374 GLU cc_start: 0.6142 (tp30) cc_final: 0.5488 (tt0) REVERT: D 391 PHE cc_start: 0.7430 (m-80) cc_final: 0.6892 (m-10) REVERT: D 892 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7003 (m-30) REVERT: D 984 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7172 (p0) REVERT: D 1009 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.4921 (mmp) REVERT: D 1053 MET cc_start: 0.7350 (mmm) cc_final: 0.7146 (mmm) outliers start: 114 outliers final: 78 residues processed: 457 average time/residue: 0.3476 time to fit residues: 267.4705 Evaluate side-chains 433 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 347 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 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 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 777 SER 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 A residue 1014 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 163 TYR 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 326 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 578 ARG Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 760 ILE 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 1005 LYS Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1055 PHE Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 565 MET 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 759 SER 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 C residue 1014 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 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 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 57 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 336 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** 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 ** 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 = 0.3809 r_free = 0.3809 target = 0.126608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102002 restraints weight = 66233.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101630 restraints weight = 49217.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102827 restraints weight = 40772.087| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4142 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= 0.152 Angle : 0.587 15.855 38652 Z= 0.296 Chirality : 0.043 0.244 4440 Planarity : 0.004 0.059 4832 Dihedral : 4.263 42.157 3732 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 17.80 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3444 helix: 0.29 (0.12), residues: 1760 sheet: 0.14 (0.29), residues: 360 loop : -1.11 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 263 HIS 0.006 0.001 HIS A 350 PHE 0.032 0.002 PHE D 120 TYR 0.017 0.001 TYR C 294 ARG 0.004 0.000 ARG A 786 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 1280) hydrogen bonds : angle 4.92340 ( 3627) covalent geometry : bond 0.00347 (28480) covalent geometry : angle 0.58667 (38652) *********************** 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 506 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 390 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7889 (mmm) cc_final: 0.6832 (ptt) REVERT: A 38 PHE cc_start: 0.6178 (m-80) cc_final: 0.5795 (m-10) REVERT: A 176 TRP cc_start: 0.6303 (m100) cc_final: 0.4951 (m-90) REVERT: A 180 GLU cc_start: 0.6476 (tt0) cc_final: 0.5704 (mm-30) REVERT: A 244 SER cc_start: 0.8381 (p) cc_final: 0.8176 (p) REVERT: A 321 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: A 353 LEU cc_start: 0.5790 (tp) cc_final: 0.5449 (tp) REVERT: A 385 LEU cc_start: 0.7981 (mt) cc_final: 0.7771 (mt) REVERT: A 409 HIS cc_start: 0.7862 (m-70) cc_final: 0.7600 (m90) REVERT: A 415 LYS cc_start: 0.8851 (mptt) cc_final: 0.8356 (mmmt) REVERT: A 425 LEU cc_start: 0.9104 (mm) cc_final: 0.8784 (mt) REVERT: A 513 MET cc_start: 0.7508 (tpt) cc_final: 0.6903 (tpt) REVERT: A 830 MET cc_start: 0.8391 (mtp) cc_final: 0.8142 (mtp) REVERT: A 918 SER cc_start: 0.8643 (p) cc_final: 0.8202 (t) REVERT: A 1008 ASN cc_start: 0.6997 (m-40) cc_final: 0.6356 (m110) REVERT: A 1009 MET cc_start: 0.5847 (mmp) cc_final: 0.4422 (mtt) REVERT: A 1036 ASN cc_start: 0.5675 (t0) cc_final: 0.5404 (t0) REVERT: B 94 MET cc_start: 0.0597 (tpp) cc_final: 0.0102 (tpp) REVERT: B 104 MET cc_start: 0.6534 (tpt) cc_final: 0.6237 (mtt) REVERT: B 130 TYR cc_start: 0.7945 (t80) cc_final: 0.7036 (t80) REVERT: B 136 ASN cc_start: 0.6620 (t0) cc_final: 0.6377 (t0) REVERT: B 391 PHE cc_start: 0.5788 (m-80) cc_final: 0.5248 (m-80) REVERT: B 392 LYS cc_start: 0.7529 (pttm) cc_final: 0.7158 (mmtm) REVERT: B 521 GLU cc_start: 0.7830 (pm20) cc_final: 0.7501 (tp30) REVERT: B 529 LEU cc_start: 0.8752 (mt) cc_final: 0.8518 (mt) REVERT: B 685 LYS cc_start: 0.7577 (ttpp) cc_final: 0.7042 (mttp) REVERT: B 739 MET cc_start: 0.8571 (tpp) cc_final: 0.8269 (ttm) REVERT: C 94 MET cc_start: 0.3855 (ptt) cc_final: 0.3033 (mmp) REVERT: C 151 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: C 203 TRP cc_start: 0.6804 (t60) cc_final: 0.6352 (t60) REVERT: C 279 TYR cc_start: 0.8859 (t80) cc_final: 0.8561 (t80) REVERT: C 404 SER cc_start: 0.8139 (t) cc_final: 0.7337 (p) REVERT: C 605 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7395 (p) REVERT: C 739 MET cc_start: 0.8136 (mmm) cc_final: 0.7726 (mtm) REVERT: C 989 ASP cc_start: 0.7137 (p0) cc_final: 0.6854 (p0) REVERT: C 1029 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8301 (m) REVERT: D 142 GLN cc_start: 0.2505 (tp40) cc_final: 0.2048 (mm110) REVERT: D 153 ASP cc_start: 0.8185 (p0) cc_final: 0.7519 (t0) REVERT: D 374 GLU cc_start: 0.6194 (tp30) cc_final: 0.5336 (tt0) REVERT: D 391 PHE cc_start: 0.7420 (m-80) cc_final: 0.6909 (m-10) REVERT: D 892 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: D 1009 MET cc_start: 0.5430 (mmp) cc_final: 0.4978 (mmp) outliers start: 116 outliers final: 86 residues processed: 470 average time/residue: 0.3445 time to fit residues: 270.4937 Evaluate side-chains 450 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 359 time to evaluate : 3.059 ------------------------------------------------------------------------------- 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 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 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 151 GLN Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 513 MET 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 738 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 ILE 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 1051 CYS 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 365 HIS Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 185 VAL 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 939 THR Chi-restraints excluded: chain D residue 941 VAL 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 242 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 288 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 341 optimal weight: 0.1980 chunk 1 optimal weight: 8.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ** 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 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 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104647 restraints weight = 66236.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104221 restraints weight = 48551.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105180 restraints weight = 41694.547| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28480 Z= 0.107 Angle : 0.550 13.597 38652 Z= 0.274 Chirality : 0.041 0.193 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.940 27.876 3730 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.77 % Allowed : 19.98 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3444 helix: 0.49 (0.13), residues: 1754 sheet: 0.01 (0.28), residues: 392 loop : -0.99 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.004 0.001 HIS A 350 PHE 0.042 0.001 PHE D 144 TYR 0.019 0.001 TYR A 996 ARG 0.011 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 1280) hydrogen bonds : angle 4.74141 ( 3627) covalent geometry : bond 0.00232 (28480) covalent geometry : angle 0.54981 (38652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 404 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7834 (mmm) cc_final: 0.6894 (ptt) REVERT: A 38 PHE cc_start: 0.6209 (m-80) cc_final: 0.5834 (m-10) REVERT: A 120 PHE cc_start: 0.5744 (t80) cc_final: 0.5102 (t80) REVERT: A 176 TRP cc_start: 0.6234 (m100) cc_final: 0.4810 (m-90) REVERT: A 180 GLU cc_start: 0.6414 (tt0) cc_final: 0.5642 (mm-30) REVERT: A 309 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8698 (mp) REVERT: A 321 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: A 332 TYR cc_start: 0.5635 (OUTLIER) cc_final: 0.4940 (t80) REVERT: A 409 HIS cc_start: 0.7849 (m-70) cc_final: 0.7555 (m90) REVERT: A 415 LYS cc_start: 0.8811 (mptt) cc_final: 0.8324 (mmmt) REVERT: A 513 MET cc_start: 0.7585 (tpt) cc_final: 0.7001 (tpt) REVERT: A 536 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: A 762 TYR cc_start: 0.8311 (t80) cc_final: 0.8030 (t80) REVERT: A 830 MET cc_start: 0.8417 (mtp) cc_final: 0.8179 (mtp) REVERT: A 897 ASP cc_start: 0.6823 (m-30) cc_final: 0.6333 (m-30) REVERT: A 918 SER cc_start: 0.8521 (p) cc_final: 0.8106 (t) REVERT: A 1008 ASN cc_start: 0.6960 (m-40) cc_final: 0.6236 (m110) REVERT: A 1009 MET cc_start: 0.5648 (mmp) cc_final: 0.4435 (mtt) REVERT: A 1036 ASN cc_start: 0.5851 (t0) cc_final: 0.5571 (t0) REVERT: B 94 MET cc_start: 0.0664 (tpp) cc_final: 0.0452 (tpp) REVERT: B 104 MET cc_start: 0.6666 (tpt) cc_final: 0.6305 (mtm) REVERT: B 130 TYR cc_start: 0.7912 (t80) cc_final: 0.7062 (t80) REVERT: B 136 ASN cc_start: 0.6724 (t0) cc_final: 0.6272 (m-40) REVERT: B 163 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7306 (t80) REVERT: B 391 PHE cc_start: 0.5608 (m-80) cc_final: 0.5262 (m-80) REVERT: B 392 LYS cc_start: 0.7565 (pttm) cc_final: 0.7148 (mmtm) REVERT: B 521 GLU cc_start: 0.7800 (pm20) cc_final: 0.7540 (tp30) REVERT: B 529 LEU cc_start: 0.8748 (mt) cc_final: 0.8506 (mt) REVERT: B 685 LYS cc_start: 0.7475 (ttpp) cc_final: 0.6942 (mttp) REVERT: B 739 MET cc_start: 0.8563 (tpp) cc_final: 0.8267 (ttm) REVERT: C 94 MET cc_start: 0.3791 (ptt) cc_final: 0.2883 (mmp) REVERT: C 168 PHE cc_start: 0.5916 (t80) cc_final: 0.5475 (t80) REVERT: C 203 TRP cc_start: 0.6665 (t60) cc_final: 0.6218 (t60) REVERT: C 279 TYR cc_start: 0.8865 (t80) cc_final: 0.8569 (t80) REVERT: C 404 SER cc_start: 0.8162 (t) cc_final: 0.7615 (p) REVERT: C 605 VAL cc_start: 0.7605 (t) cc_final: 0.7368 (p) REVERT: C 989 ASP cc_start: 0.7151 (p0) cc_final: 0.6867 (p0) REVERT: D 142 GLN cc_start: 0.2546 (tp40) cc_final: 0.2114 (mm110) REVERT: D 153 ASP cc_start: 0.8187 (p0) cc_final: 0.7482 (t0) REVERT: D 199 LEU cc_start: 0.6766 (mt) cc_final: 0.6196 (tp) REVERT: D 374 GLU cc_start: 0.6206 (tp30) cc_final: 0.5787 (tp30) REVERT: D 391 PHE cc_start: 0.7393 (m-80) cc_final: 0.6918 (m-10) REVERT: D 402 GLN cc_start: 0.6534 (mm110) cc_final: 0.5633 (mt0) REVERT: D 892 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: D 1009 MET cc_start: 0.5195 (OUTLIER) cc_final: 0.4501 (mmp) REVERT: D 1053 MET cc_start: 0.7557 (mmt) cc_final: 0.7108 (mmm) outliers start: 85 outliers final: 60 residues processed: 462 average time/residue: 0.3496 time to fit residues: 271.6642 Evaluate side-chains 425 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TRP 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 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 332 TYR Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 536 MET 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 A residue 1014 ILE Chi-restraints excluded: chain B residue 163 TYR 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 376 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 556 LEU 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 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 760 ILE 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 959 LEU Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain C residue 184 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 365 HIS Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 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 273 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 258 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 342 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ** 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 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C1054 GLN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.127284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102278 restraints weight = 66353.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102556 restraints weight = 48023.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103427 restraints weight = 39248.773| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28480 Z= 0.135 Angle : 0.576 13.647 38652 Z= 0.288 Chirality : 0.042 0.234 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.975 20.816 3728 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.03 % Allowed : 20.27 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3444 helix: 0.46 (0.12), residues: 1762 sheet: 0.03 (0.28), residues: 388 loop : -0.99 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 477 HIS 0.008 0.001 HIS A 350 PHE 0.029 0.002 PHE A1000 TYR 0.029 0.001 TYR A 996 ARG 0.008 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 1280) hydrogen bonds : angle 4.74503 ( 3627) covalent geometry : bond 0.00307 (28480) covalent geometry : angle 0.57647 (38652) *********************** 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 468 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 375 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7745 (mmm) cc_final: 0.6784 (ptt) REVERT: A 38 PHE cc_start: 0.6162 (m-80) cc_final: 0.5738 (m-10) REVERT: A 120 PHE cc_start: 0.5876 (t80) cc_final: 0.5137 (t80) REVERT: A 180 GLU cc_start: 0.6558 (tt0) cc_final: 0.5718 (mm-30) REVERT: A 321 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: A 409 HIS cc_start: 0.7831 (m-70) cc_final: 0.7607 (m90) REVERT: A 415 LYS cc_start: 0.8797 (mptt) cc_final: 0.8350 (mmmt) REVERT: A 513 MET cc_start: 0.7572 (tpt) cc_final: 0.6993 (tpt) REVERT: A 536 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7568 (ttm) REVERT: A 762 TYR cc_start: 0.8350 (t80) cc_final: 0.8105 (t80) REVERT: A 918 SER cc_start: 0.8600 (p) cc_final: 0.8195 (t) REVERT: A 1008 ASN cc_start: 0.6940 (m-40) cc_final: 0.6219 (m110) REVERT: A 1009 MET cc_start: 0.5669 (mmp) cc_final: 0.4308 (mtt) REVERT: A 1036 ASN cc_start: 0.5772 (t0) cc_final: 0.5496 (t0) REVERT: B 130 TYR cc_start: 0.7897 (t80) cc_final: 0.7072 (t80) REVERT: B 136 ASN cc_start: 0.6730 (t0) cc_final: 0.6280 (m-40) REVERT: B 213 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7179 (ttm-80) REVERT: B 391 PHE cc_start: 0.5688 (m-80) cc_final: 0.5261 (m-80) REVERT: B 392 LYS cc_start: 0.7595 (pttm) cc_final: 0.7157 (mmtm) REVERT: B 521 GLU cc_start: 0.7772 (pm20) cc_final: 0.7492 (tp30) REVERT: B 529 LEU cc_start: 0.8780 (mt) cc_final: 0.8554 (mt) REVERT: B 685 LYS cc_start: 0.7483 (ttpp) cc_final: 0.6925 (mttp) REVERT: B 739 MET cc_start: 0.8562 (tpp) cc_final: 0.8243 (ttm) REVERT: C 30 MET cc_start: 0.5985 (tpp) cc_final: 0.4989 (ptt) REVERT: C 94 MET cc_start: 0.3797 (ptt) cc_final: 0.2821 (mmp) REVERT: C 151 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6461 (pm20) REVERT: C 168 PHE cc_start: 0.5946 (t80) cc_final: 0.5481 (t80) REVERT: C 203 TRP cc_start: 0.6702 (t60) cc_final: 0.6284 (t60) REVERT: C 279 TYR cc_start: 0.8888 (t80) cc_final: 0.8622 (t80) REVERT: C 404 SER cc_start: 0.8137 (t) cc_final: 0.7555 (p) REVERT: C 605 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7490 (p) REVERT: C 989 ASP cc_start: 0.6766 (p0) cc_final: 0.6559 (p0) REVERT: C 1000 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5983 (p90) REVERT: C 1039 TYR cc_start: 0.6805 (t80) cc_final: 0.6061 (t80) REVERT: D 142 GLN cc_start: 0.2542 (tp40) cc_final: 0.2070 (mm-40) REVERT: D 153 ASP cc_start: 0.8176 (p0) cc_final: 0.7411 (t0) REVERT: D 199 LEU cc_start: 0.6790 (mt) cc_final: 0.6250 (tp) REVERT: D 374 GLU cc_start: 0.6209 (tp30) cc_final: 0.5278 (tt0) REVERT: D 391 PHE cc_start: 0.7394 (m-80) cc_final: 0.6889 (m-10) REVERT: D 402 GLN cc_start: 0.6606 (mm110) cc_final: 0.5737 (mt0) REVERT: D 892 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: D 1009 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4353 (mmp) REVERT: D 1053 MET cc_start: 0.7621 (mmt) cc_final: 0.7125 (mmm) outliers start: 93 outliers final: 71 residues processed: 437 average time/residue: 0.3649 time to fit residues: 266.2483 Evaluate side-chains 433 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 2.933 ------------------------------------------------------------------------------- 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 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 396 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 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 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 959 LEU Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 184 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 365 HIS 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 563 LEU 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 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 98 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 258 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 440 ASN B 157 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.128815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104469 restraints weight = 66697.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104263 restraints weight = 49678.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105331 restraints weight = 41020.161| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4559 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 : 0.565 13.093 38652 Z= 0.282 Chirality : 0.041 0.249 4440 Planarity : 0.004 0.057 4832 Dihedral : 3.868 21.051 3728 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.03 % Allowed : 20.70 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3444 helix: 0.55 (0.13), residues: 1758 sheet: 0.03 (0.28), residues: 392 loop : -0.95 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 178 HIS 0.003 0.000 HIS A 350 PHE 0.027 0.001 PHE A1000 TYR 0.023 0.001 TYR C 130 ARG 0.008 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 1280) hydrogen bonds : angle 4.66466 ( 3627) covalent geometry : bond 0.00244 (28480) covalent geometry : angle 0.56475 (38652) *********************** 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 467 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 374 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7528 (mmm) cc_final: 0.6622 (ptt) REVERT: A 38 PHE cc_start: 0.6172 (m-80) cc_final: 0.5782 (m-10) REVERT: A 120 PHE cc_start: 0.5727 (t80) cc_final: 0.5081 (t80) REVERT: A 180 GLU cc_start: 0.6490 (tt0) cc_final: 0.5582 (mm-30) REVERT: A 321 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: A 332 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 409 HIS cc_start: 0.7807 (m-70) cc_final: 0.7551 (m90) REVERT: A 415 LYS cc_start: 0.8797 (mptt) cc_final: 0.8355 (mmmt) REVERT: A 513 MET cc_start: 0.7561 (tpt) cc_final: 0.6990 (tpt) REVERT: A 536 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7587 (ttm) REVERT: A 688 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.7914 (t) REVERT: A 918 SER cc_start: 0.8596 (p) cc_final: 0.8159 (t) REVERT: A 1002 LYS cc_start: 0.8239 (mppt) cc_final: 0.7868 (mmmt) REVERT: A 1008 ASN cc_start: 0.6803 (m-40) cc_final: 0.6112 (m110) REVERT: A 1009 MET cc_start: 0.5609 (mmp) cc_final: 0.4400 (mtt) REVERT: A 1036 ASN cc_start: 0.5846 (t0) cc_final: 0.5547 (t0) REVERT: B 136 ASN cc_start: 0.6701 (t0) cc_final: 0.6254 (m-40) REVERT: B 151 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: B 391 PHE cc_start: 0.5578 (m-80) cc_final: 0.5163 (m-80) REVERT: B 392 LYS cc_start: 0.7611 (pttm) cc_final: 0.7181 (mmtm) REVERT: B 513 MET cc_start: 0.6628 (tpp) cc_final: 0.6048 (tpt) REVERT: B 521 GLU cc_start: 0.7783 (pm20) cc_final: 0.7448 (tp30) REVERT: B 529 LEU cc_start: 0.8768 (mt) cc_final: 0.8496 (mt) REVERT: B 685 LYS cc_start: 0.7489 (ttpp) cc_final: 0.6924 (mttp) REVERT: B 739 MET cc_start: 0.8577 (tpp) cc_final: 0.8238 (ttm) REVERT: B 1005 LYS cc_start: 0.7298 (mmtt) cc_final: 0.7080 (pttm) REVERT: C 30 MET cc_start: 0.5910 (tpp) cc_final: 0.4946 (ptt) REVERT: C 94 MET cc_start: 0.3804 (ptt) cc_final: 0.2779 (mmp) REVERT: C 151 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6405 (pm20) REVERT: C 168 PHE cc_start: 0.5828 (t80) cc_final: 0.5398 (t80) REVERT: C 203 TRP cc_start: 0.6672 (t60) cc_final: 0.6238 (t60) REVERT: C 279 TYR cc_start: 0.8825 (t80) cc_final: 0.8554 (t80) REVERT: C 404 SER cc_start: 0.8186 (t) cc_final: 0.7617 (p) REVERT: C 605 VAL cc_start: 0.7715 (t) cc_final: 0.7465 (p) REVERT: C 989 ASP cc_start: 0.6772 (p0) cc_final: 0.6564 (p0) REVERT: C 1029 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8280 (m) REVERT: D 142 GLN cc_start: 0.2526 (tp40) cc_final: 0.1989 (mm110) REVERT: D 153 ASP cc_start: 0.8186 (p0) cc_final: 0.7429 (t0) REVERT: D 199 LEU cc_start: 0.6773 (mt) cc_final: 0.6250 (tp) REVERT: D 374 GLU cc_start: 0.6130 (tp30) cc_final: 0.5844 (tp30) REVERT: D 391 PHE cc_start: 0.7406 (m-80) cc_final: 0.6925 (m-10) REVERT: D 402 GLN cc_start: 0.6558 (mm110) cc_final: 0.5704 (mt0) REVERT: D 892 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: D 1009 MET cc_start: 0.5025 (OUTLIER) cc_final: 0.4154 (mmp) REVERT: D 1053 MET cc_start: 0.7605 (mmt) cc_final: 0.7112 (mmm) outliers start: 93 outliers final: 67 residues processed: 440 average time/residue: 0.4010 time to fit residues: 295.7035 Evaluate side-chains 430 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 354 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU 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 536 MET 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 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 237 ASN 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 593 THR 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 798 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 HIS 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 732 ILE 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 C residue 1029 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 294 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 195 optimal weight: 6.9990 chunk 145 optimal weight: 0.1980 chunk 236 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 overall best weight: 1.8562 ------------------------------------------------------------------------------- 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 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103245 restraints weight = 66613.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103359 restraints weight = 50031.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104286 restraints weight = 41380.335| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28480 Z= 0.131 Angle : 0.579 13.549 38652 Z= 0.290 Chirality : 0.042 0.247 4440 Planarity : 0.004 0.057 4832 Dihedral : 3.921 21.206 3728 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.93 % Allowed : 21.15 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3444 helix: 0.46 (0.12), residues: 1796 sheet: 0.07 (0.28), residues: 380 loop : -0.96 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.004 0.001 HIS A 350 PHE 0.029 0.002 PHE C 395 TYR 0.032 0.001 TYR A 762 ARG 0.008 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1280) hydrogen bonds : angle 4.71116 ( 3627) covalent geometry : bond 0.00302 (28480) covalent geometry : angle 0.57911 (38652) *********************** 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 462 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 372 time to evaluate : 3.236 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.7441 (mmm) cc_final: 0.6643 (ptt) REVERT: A 38 PHE cc_start: 0.6138 (m-80) cc_final: 0.5650 (m-10) REVERT: A 120 PHE cc_start: 0.5801 (t80) cc_final: 0.5086 (t80) REVERT: A 180 GLU cc_start: 0.6523 (tt0) cc_final: 0.5660 (mm-30) REVERT: A 321 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: A 332 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.5030 (t80) REVERT: A 409 HIS cc_start: 0.7821 (m-70) cc_final: 0.7594 (m90) REVERT: A 415 LYS cc_start: 0.8788 (mptt) cc_final: 0.8354 (mmmt) REVERT: A 513 MET cc_start: 0.7509 (tpt) cc_final: 0.6826 (tpt) REVERT: A 536 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7588 (ttm) REVERT: A 688 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.7994 (t) REVERT: A 918 SER cc_start: 0.8625 (p) cc_final: 0.8222 (t) REVERT: A 1002 LYS cc_start: 0.8238 (mppt) cc_final: 0.7873 (mmmt) REVERT: A 1008 ASN cc_start: 0.6852 (m-40) cc_final: 0.6159 (m110) REVERT: A 1009 MET cc_start: 0.5544 (mmp) cc_final: 0.4367 (mtt) REVERT: A 1036 ASN cc_start: 0.5735 (t0) cc_final: 0.5449 (t0) REVERT: B 136 ASN cc_start: 0.6811 (t0) cc_final: 0.6362 (m-40) REVERT: B 231 ASN cc_start: 0.7671 (m-40) cc_final: 0.6851 (p0) REVERT: B 391 PHE cc_start: 0.5617 (m-80) cc_final: 0.5185 (m-80) REVERT: B 392 LYS cc_start: 0.7592 (pttm) cc_final: 0.7159 (mmtm) REVERT: B 513 MET cc_start: 0.6603 (tpp) cc_final: 0.6215 (tpt) REVERT: B 521 GLU cc_start: 0.7853 (pm20) cc_final: 0.7443 (tp30) REVERT: B 529 LEU cc_start: 0.8788 (mt) cc_final: 0.8531 (mt) REVERT: B 685 LYS cc_start: 0.7490 (ttpp) cc_final: 0.6928 (mttp) REVERT: B 739 MET cc_start: 0.8590 (tpp) cc_final: 0.8305 (ttm) REVERT: C 30 MET cc_start: 0.5927 (tpp) cc_final: 0.4986 (ptt) REVERT: C 94 MET cc_start: 0.3660 (ptt) cc_final: 0.2793 (pmm) REVERT: C 151 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: C 168 PHE cc_start: 0.5732 (t80) cc_final: 0.5292 (t80) REVERT: C 203 TRP cc_start: 0.6697 (t60) cc_final: 0.6261 (t60) REVERT: C 279 TYR cc_start: 0.8868 (t80) cc_final: 0.8588 (t80) REVERT: C 404 SER cc_start: 0.8157 (t) cc_final: 0.7576 (p) REVERT: C 605 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7483 (p) REVERT: C 989 ASP cc_start: 0.6912 (p0) cc_final: 0.6692 (p0) REVERT: C 1029 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8289 (m) REVERT: D 142 GLN cc_start: 0.2514 (tp40) cc_final: 0.1952 (mm110) REVERT: D 153 ASP cc_start: 0.8135 (p0) cc_final: 0.7340 (t0) REVERT: D 228 LYS cc_start: 0.6799 (mttt) cc_final: 0.6484 (mttm) REVERT: D 374 GLU cc_start: 0.6167 (tp30) cc_final: 0.5409 (tt0) REVERT: D 391 PHE cc_start: 0.7374 (m-80) cc_final: 0.6888 (m-10) REVERT: D 402 GLN cc_start: 0.6601 (mm110) cc_final: 0.5757 (mt0) REVERT: D 892 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: D 1009 MET cc_start: 0.5086 (OUTLIER) cc_final: 0.4189 (mmp) REVERT: D 1053 MET cc_start: 0.7593 (mmt) cc_final: 0.7123 (mmm) outliers start: 90 outliers final: 73 residues processed: 436 average time/residue: 0.3533 time to fit residues: 259.7546 Evaluate side-chains 436 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 321 GLU 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 396 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 901 THR 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 95 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 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 593 THR 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 798 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain C residue 151 GLN 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 281 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 HIS 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 759 SER Chi-restraints excluded: chain C residue 761 GLU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain C residue 1029 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 244 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 0.0000 chunk 179 optimal weight: 10.0000 chunk 309 optimal weight: 0.0170 chunk 28 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 overall best weight: 0.6024 ------------------------------------------------------------------------------- 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 ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105283 restraints weight = 66671.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104736 restraints weight = 47870.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106142 restraints weight = 42782.714| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28480 Z= 0.109 Angle : 0.568 13.425 38652 Z= 0.283 Chirality : 0.041 0.228 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.832 25.362 3728 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 21.61 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3444 helix: 0.59 (0.13), residues: 1770 sheet: 0.12 (0.28), residues: 386 loop : -0.95 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 178 HIS 0.003 0.000 HIS B 254 PHE 0.029 0.001 PHE C 395 TYR 0.022 0.001 TYR D 198 ARG 0.007 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1280) hydrogen bonds : angle 4.59837 ( 3627) covalent geometry : bond 0.00241 (28480) covalent geometry : angle 0.56790 (38652) ********************** 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 449 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 372 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7327 (mmm) cc_final: 0.6545 (ptt) REVERT: A 38 PHE cc_start: 0.6122 (m-80) cc_final: 0.5653 (m-10) REVERT: A 120 PHE cc_start: 0.5790 (t80) cc_final: 0.5060 (t80) REVERT: A 176 TRP cc_start: 0.6303 (m100) cc_final: 0.5555 (m100) REVERT: A 180 GLU cc_start: 0.6473 (tt0) cc_final: 0.5605 (mm-30) REVERT: A 332 TYR cc_start: 0.5513 (OUTLIER) cc_final: 0.4924 (t80) REVERT: A 409 HIS cc_start: 0.7740 (m-70) cc_final: 0.7531 (m90) REVERT: A 415 LYS cc_start: 0.8764 (mptt) cc_final: 0.8366 (mmmt) REVERT: A 513 MET cc_start: 0.7440 (tpt) cc_final: 0.6811 (tpt) REVERT: A 536 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7405 (ttm) REVERT: A 607 ARG cc_start: 0.6631 (mmt90) cc_final: 0.5762 (mtp180) REVERT: A 688 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.7975 (t) REVERT: A 918 SER cc_start: 0.8598 (p) cc_final: 0.8165 (t) REVERT: A 1002 LYS cc_start: 0.8151 (mppt) cc_final: 0.7835 (mmmt) REVERT: A 1008 ASN cc_start: 0.6962 (m-40) cc_final: 0.6309 (m110) REVERT: A 1009 MET cc_start: 0.5509 (mmp) cc_final: 0.4278 (mtt) REVERT: A 1036 ASN cc_start: 0.5893 (t0) cc_final: 0.5591 (t0) REVERT: B 136 ASN cc_start: 0.6792 (t0) cc_final: 0.6346 (m-40) REVERT: B 178 TRP cc_start: 0.5595 (t-100) cc_final: 0.5345 (t-100) REVERT: B 231 ASN cc_start: 0.7728 (m-40) cc_final: 0.6796 (p0) REVERT: B 391 PHE cc_start: 0.5526 (m-80) cc_final: 0.5220 (m-80) REVERT: B 513 MET cc_start: 0.6450 (tpp) cc_final: 0.5987 (tpt) REVERT: B 521 GLU cc_start: 0.7823 (pm20) cc_final: 0.7430 (tp30) REVERT: B 529 LEU cc_start: 0.8716 (mt) cc_final: 0.8450 (mt) REVERT: B 685 LYS cc_start: 0.7438 (ttpp) cc_final: 0.6911 (mttp) REVERT: B 739 MET cc_start: 0.8559 (tpp) cc_final: 0.8182 (ttm) REVERT: C 30 MET cc_start: 0.5914 (tpp) cc_final: 0.5075 (ptt) REVERT: C 94 MET cc_start: 0.3531 (ptt) cc_final: 0.2678 (pmm) REVERT: C 130 TYR cc_start: 0.7160 (t80) cc_final: 0.6933 (t80) REVERT: C 151 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: C 168 PHE cc_start: 0.5775 (t80) cc_final: 0.5381 (t80) REVERT: C 203 TRP cc_start: 0.6628 (t60) cc_final: 0.6192 (t60) REVERT: C 279 TYR cc_start: 0.8851 (t80) cc_final: 0.8578 (t80) REVERT: C 404 SER cc_start: 0.8157 (t) cc_final: 0.7581 (p) REVERT: C 436 GLU cc_start: 0.6917 (tp30) cc_final: 0.6698 (tt0) REVERT: C 605 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7457 (p) REVERT: C 989 ASP cc_start: 0.6884 (p0) cc_final: 0.6663 (p0) REVERT: D 124 ILE cc_start: 0.8485 (mm) cc_final: 0.8214 (pt) REVERT: D 142 GLN cc_start: 0.2878 (tp40) cc_final: 0.2260 (mm110) REVERT: D 153 ASP cc_start: 0.8156 (p0) cc_final: 0.7370 (t0) REVERT: D 199 LEU cc_start: 0.6855 (mt) cc_final: 0.6310 (tp) REVERT: D 228 LYS cc_start: 0.6790 (mttt) cc_final: 0.6449 (mttm) REVERT: D 374 GLU cc_start: 0.6119 (tp30) cc_final: 0.5838 (tp30) REVERT: D 391 PHE cc_start: 0.7364 (m-80) cc_final: 0.6864 (m-10) REVERT: D 402 GLN cc_start: 0.6621 (mm110) cc_final: 0.5744 (mt0) REVERT: D 529 LEU cc_start: 0.8411 (mt) cc_final: 0.7846 (tt) REVERT: D 892 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: D 1009 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4638 (mmp) outliers start: 77 outliers final: 59 residues processed: 429 average time/residue: 0.3370 time to fit residues: 241.7301 Evaluate side-chains 425 residues out of total 3068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 359 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 TRP Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 901 THR 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 237 ASN 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 593 THR Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 798 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain C residue 151 GLN 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 365 HIS 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 43 TRP Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain D residue 720 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 892 ASP Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain D residue 1039 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 32 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 347 optimal weight: 0.7980 chunk 310 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 0.0070 overall best weight: 1.0802 ------------------------------------------------------------------------------- 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 379 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 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 = 0.3848 r_free = 0.3848 target = 0.129206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104390 restraints weight = 66903.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105189 restraints weight = 47075.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105464 restraints weight = 39678.842| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28480 Z= 0.114 Angle : 0.577 13.159 38652 Z= 0.286 Chirality : 0.041 0.224 4440 Planarity : 0.004 0.056 4832 Dihedral : 3.800 22.482 3728 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 21.90 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3444 helix: 0.61 (0.13), residues: 1768 sheet: 0.14 (0.28), residues: 386 loop : -0.94 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 100 HIS 0.003 0.001 HIS A 350 PHE 0.029 0.001 PHE C 395 TYR 0.021 0.001 TYR D 336 ARG 0.007 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1280) hydrogen bonds : angle 4.57912 ( 3627) covalent geometry : bond 0.00257 (28480) covalent geometry : angle 0.57675 (38652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8806.62 seconds wall clock time: 156 minutes 34.17 seconds (9394.17 seconds total)