Starting phenix.real_space_refine on Thu Jul 31 03:28:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p1h_20235/07_2025/6p1h_20235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p1h_20235/07_2025/6p1h_20235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p1h_20235/07_2025/6p1h_20235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p1h_20235/07_2025/6p1h_20235.map" model { file = "/net/cci-nas-00/data/ceres_data/6p1h_20235/07_2025/6p1h_20235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p1h_20235/07_2025/6p1h_20235.cif" } resolution = 3.2 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= 0.011 sd= 1.053 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Fe 4 7.16 5 P 30 5.49 5 S 67 5.16 5 C 8171 2.51 5 N 2180 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13006 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7691 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 920} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3755 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 27, 'TRANS': 441} Chain breaks: 2 Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 921 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 233 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 40 Unusual residues: {' CA': 4, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7452 SG CYS A1069 62.579 62.764 63.623 1.00 91.25 S ATOM 7489 SG CYS A1074 64.626 65.090 58.264 1.00 84.90 S ATOM 7355 SG CYS A1056 58.493 66.521 60.923 1.00 96.71 S ATOM 7381 SG CYS A1059 60.216 60.875 58.005 1.00 95.96 S Time building chain proxies: 8.27, per 1000 atoms: 0.64 Number of scatterers: 13006 At special positions: 0 Unit cell: (143.623, 129.945, 100.023, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 5 19.99 S 67 16.00 P 30 15.00 O 2549 8.00 N 2180 7.00 C 8171 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: 3.47 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1069 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1074 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A1059 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1056 " Number of angles added : 12 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 17 sheets defined 35.3% alpha, 15.2% beta 12 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.512A pdb=" N ASN A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 172 through 187 Processing helix chain 'A' and resid 222 through 234 removed outlier: 4.129A pdb=" N LYS A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 497 through 504 removed outlier: 4.281A pdb=" N ASP A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.859A pdb=" N LEU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 552' Processing helix chain 'A' and resid 556 through 572 Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 661 through 682 removed outlier: 4.086A pdb=" N ILE A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 680 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.540A pdb=" N ASP A 691 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.740A pdb=" N GLN A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.147A pdb=" N TYR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.775A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 791 removed outlier: 3.591A pdb=" N GLU A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 859 removed outlier: 3.601A pdb=" N SER A 847 " --> pdb=" O CYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 879 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 901 through 915 Processing helix chain 'A' and resid 941 through 949 removed outlier: 3.531A pdb=" N GLU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 removed outlier: 3.793A pdb=" N TYR A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 975 Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 975 through 984 removed outlier: 3.721A pdb=" N ALA A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1037 Processing helix chain 'A' and resid 1041 through 1061 removed outlier: 4.405A pdb=" N GLU A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN A1057 " --> pdb=" O TRP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1095 removed outlier: 3.516A pdb=" N GLU A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 54 through 73 removed outlier: 4.526A pdb=" N GLU B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.700A pdb=" N ILE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 321 through 327 removed outlier: 4.283A pdb=" N SER B 326 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.583A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.861A pdb=" N LEU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 46 removed outlier: 4.909A pdb=" N LYS C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.505A pdb=" N VAL A 137 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 151 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL A 293 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 150 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE A 295 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN A 152 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163 removed outlier: 3.786A pdb=" N SER A 193 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL A 574 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN A 200 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.642A pdb=" N SER A 319 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN A 344 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP A 321 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 342 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 323 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.563A pdb=" N VAL A 397 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 320 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 436 through 441 Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 removed outlier: 6.906A pdb=" N ARG A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR A 816 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN A 832 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 818 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 830 " --> pdb=" O GLY A 818 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE A 820 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR A 822 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LYS A 826 " --> pdb=" O THR A 822 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.707A pdb=" N LYS A 803 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP A 608 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 801 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 628 removed outlier: 4.045A pdb=" N TYR A 652 " --> pdb=" O CYS A 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 757 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 889 through 892 Processing sheet with id=AB3, first strand: chain 'B' and resid 102 through 111 removed outlier: 4.670A pdb=" N ILE B 146 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 155 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 153 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 176 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 190 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY B 174 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 173 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 106 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 102 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.274A pdb=" N ARG B 256 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.525A pdb=" N TYR B 347 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 440 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 445 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 56 removed outlier: 4.851A pdb=" N VAL C 55 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.676A pdb=" N ASP C 82 " --> pdb=" O CYS C 59 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 5412 1.40 - 1.62: 7765 1.62 - 1.84: 99 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 13288 Sorted by residual: bond pdb=" C3' DCP A1102 " pdb=" C4' DCP A1102 " ideal model delta sigma weight residual 1.527 1.335 0.192 1.10e-02 8.26e+03 3.05e+02 bond pdb=" C4' DCP A1102 " pdb=" O4' DCP A1102 " ideal model delta sigma weight residual 1.444 1.603 -0.159 1.00e-02 1.00e+04 2.52e+02 bond pdb=" C4 DCP A1102 " pdb=" N4 DCP A1102 " ideal model delta sigma weight residual 1.334 1.466 -0.132 1.20e-02 6.94e+03 1.21e+02 bond pdb=" C1' DCP A1102 " pdb=" O4' DCP A1102 " ideal model delta sigma weight residual 1.418 1.291 0.127 1.20e-02 6.94e+03 1.12e+02 bond pdb=" C5 DCP A1102 " pdb=" C6 DCP A1102 " ideal model delta sigma weight residual 1.345 1.495 -0.150 1.80e-02 3.09e+03 6.99e+01 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 18024 3.92 - 7.84: 91 7.84 - 11.76: 5 11.76 - 15.69: 1 15.69 - 19.61: 2 Bond angle restraints: 18123 Sorted by residual: angle pdb=" PB DCP A1102 " pdb=" O3B DCP A1102 " pdb=" PG DCP A1102 " ideal model delta sigma weight residual 139.87 120.26 19.61 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PA DCP A1102 " pdb=" O3A DCP A1102 " pdb=" PB DCP A1102 " ideal model delta sigma weight residual 136.83 119.63 17.20 1.00e+00 1.00e+00 2.96e+02 angle pdb=" C2' DCP A1102 " pdb=" C1' DCP A1102 " pdb=" N1 DCP A1102 " ideal model delta sigma weight residual 113.92 106.37 7.55 1.28e+00 6.12e-01 3.49e+01 angle pdb=" O2G DCP A1102 " pdb=" PG DCP A1102 " pdb=" O3B DCP A1102 " ideal model delta sigma weight residual 104.48 110.31 -5.83 1.14e+00 7.76e-01 2.64e+01 angle pdb=" O3A DCP A1102 " pdb=" PB DCP A1102 " pdb=" O3B DCP A1102 " ideal model delta sigma weight residual 101.57 109.28 -7.71 1.54e+00 4.24e-01 2.52e+01 ... (remaining 18118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6972 17.94 - 35.89: 774 35.89 - 53.83: 182 53.83 - 71.77: 40 71.77 - 89.71: 11 Dihedral angle restraints: 7979 sinusoidal: 3447 harmonic: 4532 Sorted by residual: dihedral pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N LEU B 88 " pdb=" CA LEU B 88 " ideal model delta harmonic sigma weight residual 180.00 -122.71 -57.29 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA PRO B 22 " pdb=" C PRO B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA GLN B 85 " pdb=" C GLN B 85 " pdb=" N LEU B 86 " pdb=" CA LEU B 86 " ideal model delta harmonic sigma weight residual -180.00 -139.58 -40.42 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 7976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1497 0.054 - 0.108: 457 0.108 - 0.161: 68 0.161 - 0.215: 5 0.215 - 0.269: 2 Chirality restraints: 2029 Sorted by residual: chirality pdb=" C3' DCP A1102 " pdb=" C2' DCP A1102 " pdb=" C4' DCP A1102 " pdb=" O3' DCP A1102 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE C 109 " pdb=" CA ILE C 109 " pdb=" CG1 ILE C 109 " pdb=" CG2 ILE C 109 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2026 not shown) Planarity restraints: 2223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 405 " -0.015 2.00e-02 2.50e+03 1.28e-02 4.08e+00 pdb=" CG TRP B 405 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 405 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 405 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 405 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 405 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 405 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 405 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 405 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 663 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 664 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 806 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 807 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " 0.026 5.00e-02 4.00e+02 ... (remaining 2220 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 157 2.53 - 3.12: 10667 3.12 - 3.72: 19561 3.72 - 4.31: 29252 4.31 - 4.90: 48283 Nonbonded interactions: 107920 Sorted by model distance: nonbonded pdb=" OD2 ASP A 321 " pdb="CA CA A1106 " model vdw 1.939 2.510 nonbonded pdb=" OE1 GLN A 832 " pdb=" OG SER A 837 " model vdw 2.023 3.040 nonbonded pdb=" OD2 ASP B 297 " pdb=" OH TYR B 347 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 307 " model vdw 2.176 3.040 nonbonded pdb=" O ASP A 337 " pdb=" OH TYR A 410 " model vdw 2.181 3.040 ... (remaining 107915 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 12.550 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 41.140 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.010 0.192 13292 Z= 0.485 Angle : 1.004 30.036 18135 Z= 0.535 Chirality : 0.051 0.269 2029 Planarity : 0.005 0.046 2223 Dihedral : 15.972 89.712 5057 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.17 % Favored : 90.18 % Rotamer: Outliers : 0.07 % Allowed : 8.69 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % 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: -3.47 (0.18), residues: 1527 helix: -1.69 (0.19), residues: 504 sheet: -2.96 (0.29), residues: 217 loop : -2.53 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 405 HIS 0.005 0.001 HIS C 27 PHE 0.021 0.002 PHE A 806 TYR 0.020 0.002 TYR A 805 ARG 0.006 0.001 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.17610 ( 464) hydrogen bonds : angle 7.86960 ( 1283) metal coordination : bond 0.12120 ( 4) metal coordination : angle 18.23200 ( 12) covalent geometry : bond 0.00945 (13288) covalent geometry : angle 0.88774 (18123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8392 (mmmt) REVERT: A 1089 GLU cc_start: 0.8294 (tp30) cc_final: 0.7963 (tp30) REVERT: A 1092 GLU cc_start: 0.8551 (tp30) cc_final: 0.8289 (tp30) REVERT: B 5 LEU cc_start: 0.7141 (mm) cc_final: 0.6228 (mm) REVERT: B 211 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7695 (tpp80) REVERT: C 8 PHE cc_start: 0.7380 (t80) cc_final: 0.7110 (t80) REVERT: C 41 PHE cc_start: 0.8960 (t80) cc_final: 0.8717 (t80) REVERT: C 62 ASP cc_start: 0.8614 (p0) cc_final: 0.8397 (p0) REVERT: C 89 ASN cc_start: 0.6604 (t0) cc_final: 0.5119 (t0) REVERT: C 91 MET cc_start: 0.7870 (mpp) cc_final: 0.7001 (tmm) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2820 time to fit residues: 73.3184 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.6980 chunk 116 optimal weight: 0.0370 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 171 ASN A 175 GLN A 181 HIS A 283 ASN A 284 ASN A 358 ASN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 434 GLN A 485 HIS A 949 ASN A1073 ASN A1088 GLN A1093 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 124 ASN B 272 ASN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 312 GLN B 332 ASN B 337 ASN C 28 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075668 restraints weight = 23765.336| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.63 r_work: 0.2934 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13292 Z= 0.139 Angle : 0.688 11.024 18135 Z= 0.352 Chirality : 0.045 0.273 2029 Planarity : 0.005 0.043 2223 Dihedral : 14.234 89.816 1995 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.94 % Favored : 92.73 % Rotamer: Outliers : 1.15 % Allowed : 10.92 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.20), residues: 1527 helix: -0.34 (0.22), residues: 515 sheet: -2.71 (0.30), residues: 220 loop : -1.95 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1053 HIS 0.004 0.001 HIS A 181 PHE 0.015 0.001 PHE C 88 TYR 0.018 0.002 TYR C 43 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 464) hydrogen bonds : angle 5.39363 ( 1283) metal coordination : bond 0.00929 ( 4) metal coordination : angle 4.43331 ( 12) covalent geometry : bond 0.00308 (13288) covalent geometry : angle 0.67852 (18123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8569 (t0) cc_final: 0.8350 (t0) REVERT: A 336 TYR cc_start: 0.9050 (m-80) cc_final: 0.8849 (m-80) REVERT: A 491 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8307 (mmmt) REVERT: A 506 ASP cc_start: 0.8041 (t0) cc_final: 0.7732 (p0) REVERT: A 698 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8830 (tt) REVERT: A 912 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7925 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8552 (tp30) cc_final: 0.8318 (tp30) REVERT: A 1092 GLU cc_start: 0.8705 (tp30) cc_final: 0.8395 (tp30) REVERT: C 8 PHE cc_start: 0.7456 (t80) cc_final: 0.7222 (t80) REVERT: C 24 ASP cc_start: 0.9047 (m-30) cc_final: 0.8661 (p0) REVERT: C 29 LEU cc_start: 0.9456 (mp) cc_final: 0.9132 (tp) REVERT: C 41 PHE cc_start: 0.8966 (t80) cc_final: 0.8681 (t80) REVERT: C 62 ASP cc_start: 0.8828 (p0) cc_final: 0.8242 (p0) outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 0.2429 time to fit residues: 66.7055 Evaluate side-chains 151 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain C residue 59 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 chunk 141 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS B 15 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073878 restraints weight = 23869.539| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.71 r_work: 0.2912 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13292 Z= 0.179 Angle : 0.678 11.717 18135 Z= 0.346 Chirality : 0.046 0.254 2029 Planarity : 0.005 0.041 2223 Dihedral : 14.044 89.593 1995 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 2.01 % Allowed : 13.00 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1527 helix: 0.03 (0.23), residues: 519 sheet: -2.33 (0.29), residues: 241 loop : -1.70 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 PHE 0.012 0.001 PHE B 345 TYR 0.030 0.002 TYR C 43 ARG 0.004 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 464) hydrogen bonds : angle 5.08150 ( 1283) metal coordination : bond 0.00586 ( 4) metal coordination : angle 4.05237 ( 12) covalent geometry : bond 0.00418 (13288) covalent geometry : angle 0.67003 (18123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8738 (t0) cc_final: 0.8430 (t0) REVERT: A 336 TYR cc_start: 0.9132 (m-80) cc_final: 0.8914 (m-80) REVERT: A 491 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8302 (mmmt) REVERT: A 506 ASP cc_start: 0.8004 (t0) cc_final: 0.7655 (p0) REVERT: A 912 ARG cc_start: 0.8525 (ttp80) cc_final: 0.7889 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8581 (tp30) cc_final: 0.8361 (tp30) REVERT: C 24 ASP cc_start: 0.9043 (m-30) cc_final: 0.8631 (p0) REVERT: C 29 LEU cc_start: 0.9379 (mp) cc_final: 0.9087 (tp) REVERT: C 41 PHE cc_start: 0.8966 (t80) cc_final: 0.8663 (t80) REVERT: C 52 TYR cc_start: 0.5694 (p90) cc_final: 0.4616 (p90) REVERT: C 53 ASN cc_start: 0.7843 (m110) cc_final: 0.7318 (m-40) REVERT: C 62 ASP cc_start: 0.8929 (p0) cc_final: 0.8648 (p0) outliers start: 28 outliers final: 21 residues processed: 167 average time/residue: 0.2914 time to fit residues: 74.2501 Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074431 restraints weight = 23602.655| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.62 r_work: 0.2918 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13292 Z= 0.180 Angle : 0.659 10.939 18135 Z= 0.336 Chirality : 0.045 0.238 2029 Planarity : 0.004 0.040 2223 Dihedral : 13.924 89.761 1995 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.33 % Favored : 92.47 % Rotamer: Outliers : 2.51 % Allowed : 13.51 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.21), residues: 1527 helix: 0.21 (0.23), residues: 520 sheet: -2.17 (0.29), residues: 240 loop : -1.55 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 PHE 0.014 0.001 PHE C 84 TYR 0.014 0.001 TYR A 410 ARG 0.003 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 464) hydrogen bonds : angle 4.93528 ( 1283) metal coordination : bond 0.00560 ( 4) metal coordination : angle 4.10624 ( 12) covalent geometry : bond 0.00422 (13288) covalent geometry : angle 0.65086 (18123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8891 (t0) cc_final: 0.8521 (t0) REVERT: A 336 TYR cc_start: 0.9196 (m-80) cc_final: 0.8953 (m-80) REVERT: A 491 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8340 (mmmt) REVERT: A 506 ASP cc_start: 0.8204 (t0) cc_final: 0.7784 (p0) REVERT: A 698 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 912 ARG cc_start: 0.8637 (ttp80) cc_final: 0.7952 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8659 (tp30) cc_final: 0.8269 (tp30) REVERT: A 1092 GLU cc_start: 0.8609 (tp30) cc_final: 0.8370 (tp30) REVERT: B 241 MET cc_start: 0.8565 (mmt) cc_final: 0.8228 (mmm) REVERT: B 469 MET cc_start: 0.9078 (mtm) cc_final: 0.8854 (ttm) REVERT: C 29 LEU cc_start: 0.9370 (mp) cc_final: 0.9064 (tp) REVERT: C 62 ASP cc_start: 0.8939 (p0) cc_final: 0.8612 (p0) REVERT: C 89 ASN cc_start: 0.7283 (t0) cc_final: 0.6780 (t0) REVERT: C 91 MET cc_start: 0.8276 (pmm) cc_final: 0.7593 (pmm) outliers start: 35 outliers final: 26 residues processed: 174 average time/residue: 0.2697 time to fit residues: 73.7064 Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 131 optimal weight: 0.0470 chunk 115 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 0.0170 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074819 restraints weight = 23555.144| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.70 r_work: 0.2926 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13292 Z= 0.158 Angle : 0.647 10.566 18135 Z= 0.329 Chirality : 0.045 0.233 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.779 89.909 1995 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.07 % Favored : 92.73 % Rotamer: Outliers : 2.51 % Allowed : 14.66 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1527 helix: 0.31 (0.23), residues: 520 sheet: -2.05 (0.30), residues: 240 loop : -1.43 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 417 HIS 0.005 0.001 HIS C 28 PHE 0.018 0.001 PHE B 8 TYR 0.013 0.001 TYR C 43 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 464) hydrogen bonds : angle 4.84505 ( 1283) metal coordination : bond 0.00479 ( 4) metal coordination : angle 3.97777 ( 12) covalent geometry : bond 0.00366 (13288) covalent geometry : angle 0.63860 (18123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8781 (t0) cc_final: 0.8441 (t0) REVERT: A 336 TYR cc_start: 0.9139 (m-80) cc_final: 0.8891 (m-80) REVERT: A 491 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8269 (mmmt) REVERT: A 506 ASP cc_start: 0.7976 (t0) cc_final: 0.7651 (p0) REVERT: A 912 ARG cc_start: 0.8522 (ttp80) cc_final: 0.7832 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8589 (tp30) cc_final: 0.8190 (tp30) REVERT: A 1092 GLU cc_start: 0.8592 (tp30) cc_final: 0.8310 (tp30) REVERT: B 178 MET cc_start: 0.7754 (mtm) cc_final: 0.7541 (mtm) REVERT: B 431 LYS cc_start: 0.9073 (pttp) cc_final: 0.8814 (pttm) REVERT: B 476 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7886 (mm-30) REVERT: C 29 LEU cc_start: 0.9348 (mp) cc_final: 0.9023 (tp) REVERT: C 62 ASP cc_start: 0.8909 (p0) cc_final: 0.8538 (p0) REVERT: C 89 ASN cc_start: 0.7155 (t0) cc_final: 0.6104 (t0) REVERT: C 91 MET cc_start: 0.8208 (pmm) cc_final: 0.7614 (pmm) outliers start: 35 outliers final: 28 residues processed: 176 average time/residue: 0.2173 time to fit residues: 58.8749 Evaluate side-chains 172 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 141 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN C 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.076900 restraints weight = 23886.558| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.76 r_work: 0.2964 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13292 Z= 0.124 Angle : 0.621 10.231 18135 Z= 0.316 Chirality : 0.044 0.233 2029 Planarity : 0.004 0.043 2223 Dihedral : 13.556 89.583 1995 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 2.73 % Allowed : 15.23 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1527 helix: 0.45 (0.23), residues: 527 sheet: -1.78 (0.31), residues: 247 loop : -1.33 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 417 HIS 0.006 0.001 HIS C 28 PHE 0.013 0.001 PHE B 8 TYR 0.010 0.001 TYR A 805 ARG 0.003 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 464) hydrogen bonds : angle 4.69938 ( 1283) metal coordination : bond 0.00403 ( 4) metal coordination : angle 3.82980 ( 12) covalent geometry : bond 0.00280 (13288) covalent geometry : angle 0.61366 (18123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8773 (t0) cc_final: 0.8438 (t0) REVERT: A 336 TYR cc_start: 0.9142 (m-80) cc_final: 0.8912 (m-80) REVERT: A 491 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8212 (mmmt) REVERT: A 912 ARG cc_start: 0.8524 (ttp80) cc_final: 0.7845 (mtm-85) REVERT: A 1047 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 1089 GLU cc_start: 0.8591 (tp30) cc_final: 0.8347 (tp30) REVERT: A 1092 GLU cc_start: 0.8744 (tp30) cc_final: 0.8426 (tp30) REVERT: B 253 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8075 (pp) REVERT: B 431 LYS cc_start: 0.9052 (pttp) cc_final: 0.8785 (pttm) REVERT: B 476 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7807 (mm-30) REVERT: C 29 LEU cc_start: 0.9365 (mp) cc_final: 0.9028 (tp) REVERT: C 62 ASP cc_start: 0.8896 (p0) cc_final: 0.8489 (p0) REVERT: C 88 PHE cc_start: 0.8486 (m-80) cc_final: 0.8227 (m-80) REVERT: C 89 ASN cc_start: 0.6967 (t0) cc_final: 0.5702 (t0) REVERT: C 91 MET cc_start: 0.8197 (pmm) cc_final: 0.7673 (pmm) outliers start: 38 outliers final: 24 residues processed: 191 average time/residue: 0.2092 time to fit residues: 61.4691 Evaluate side-chains 178 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS A 620 HIS A 754 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 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 = 0.3552 r_free = 0.3552 target = 0.102709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074029 restraints weight = 23867.089| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.71 r_work: 0.2915 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13292 Z= 0.203 Angle : 0.667 9.853 18135 Z= 0.341 Chirality : 0.046 0.246 2029 Planarity : 0.004 0.045 2223 Dihedral : 13.694 89.110 1995 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.67 % Rotamer: Outliers : 2.73 % Allowed : 15.52 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1527 helix: 0.45 (0.23), residues: 520 sheet: -2.10 (0.29), residues: 261 loop : -1.24 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 417 HIS 0.006 0.001 HIS A 495 PHE 0.018 0.002 PHE B 388 TYR 0.017 0.002 TYR C 43 ARG 0.002 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 464) hydrogen bonds : angle 4.78534 ( 1283) metal coordination : bond 0.00596 ( 4) metal coordination : angle 3.75633 ( 12) covalent geometry : bond 0.00481 (13288) covalent geometry : angle 0.66037 (18123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8802 (t0) cc_final: 0.8463 (t0) REVERT: A 336 TYR cc_start: 0.9145 (m-80) cc_final: 0.8870 (m-80) REVERT: A 491 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8320 (mmmt) REVERT: A 506 ASP cc_start: 0.8034 (t0) cc_final: 0.7677 (p0) REVERT: A 540 MET cc_start: 0.9116 (tpt) cc_final: 0.8648 (tpt) REVERT: A 1089 GLU cc_start: 0.8632 (tp30) cc_final: 0.8218 (tp30) REVERT: A 1092 GLU cc_start: 0.8670 (tp30) cc_final: 0.8356 (tp30) REVERT: B 253 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8102 (pp) REVERT: B 476 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7769 (mm-30) REVERT: C 29 LEU cc_start: 0.9344 (mp) cc_final: 0.9007 (tp) REVERT: C 62 ASP cc_start: 0.8927 (p0) cc_final: 0.8486 (p0) REVERT: C 63 GLN cc_start: 0.8054 (mp10) cc_final: 0.7836 (mp10) REVERT: C 88 PHE cc_start: 0.8601 (m-80) cc_final: 0.8286 (m-80) REVERT: C 89 ASN cc_start: 0.6979 (t0) cc_final: 0.5639 (t0) REVERT: C 91 MET cc_start: 0.8185 (pmm) cc_final: 0.7688 (pmm) outliers start: 38 outliers final: 32 residues processed: 173 average time/residue: 0.2272 time to fit residues: 60.7914 Evaluate side-chains 177 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 83 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077497 restraints weight = 23537.291| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.73 r_work: 0.2979 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13292 Z= 0.123 Angle : 0.631 9.675 18135 Z= 0.320 Chirality : 0.044 0.255 2029 Planarity : 0.004 0.047 2223 Dihedral : 13.501 89.603 1995 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 2.37 % Allowed : 16.38 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1527 helix: 0.58 (0.23), residues: 527 sheet: -1.88 (0.31), residues: 242 loop : -1.17 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1053 HIS 0.007 0.001 HIS A 495 PHE 0.049 0.001 PHE C 8 TYR 0.014 0.001 TYR A 496 ARG 0.004 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 464) hydrogen bonds : angle 4.68201 ( 1283) metal coordination : bond 0.00343 ( 4) metal coordination : angle 3.86389 ( 12) covalent geometry : bond 0.00276 (13288) covalent geometry : angle 0.62314 (18123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8758 (t0) cc_final: 0.8437 (t0) REVERT: A 336 TYR cc_start: 0.9149 (m-80) cc_final: 0.8904 (m-80) REVERT: A 434 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8400 (mm-40) REVERT: A 491 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8193 (mmmt) REVERT: A 506 ASP cc_start: 0.7966 (t0) cc_final: 0.7567 (p0) REVERT: A 618 MET cc_start: 0.9191 (mtp) cc_final: 0.8880 (mtm) REVERT: A 850 MET cc_start: 0.9078 (mmm) cc_final: 0.8767 (mmt) REVERT: A 912 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7603 (mtm-85) REVERT: A 1047 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 1089 GLU cc_start: 0.8604 (tp30) cc_final: 0.8364 (tp30) REVERT: A 1092 GLU cc_start: 0.8774 (tp30) cc_final: 0.8444 (tp30) REVERT: B 253 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 431 LYS cc_start: 0.9035 (pttp) cc_final: 0.8756 (pttm) REVERT: B 476 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 29 LEU cc_start: 0.9320 (mp) cc_final: 0.8992 (tp) REVERT: C 62 ASP cc_start: 0.8961 (p0) cc_final: 0.8545 (p0) REVERT: C 63 GLN cc_start: 0.8082 (mp10) cc_final: 0.7748 (pm20) REVERT: C 88 PHE cc_start: 0.8586 (m-80) cc_final: 0.8199 (m-80) REVERT: C 89 ASN cc_start: 0.7007 (t0) cc_final: 0.6183 (t0) REVERT: C 91 MET cc_start: 0.8116 (pmm) cc_final: 0.6971 (ppp) outliers start: 33 outliers final: 22 residues processed: 178 average time/residue: 0.2644 time to fit residues: 72.9786 Evaluate side-chains 179 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 434 GLN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 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 = 0.3596 r_free = 0.3596 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.077185 restraints weight = 23626.326| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.69 r_work: 0.2962 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13292 Z= 0.140 Angle : 0.634 9.748 18135 Z= 0.322 Chirality : 0.044 0.274 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.510 89.026 1995 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 1.80 % Allowed : 17.17 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.99 (0.22), residues: 1527 helix: 0.69 (0.24), residues: 520 sheet: -1.90 (0.30), residues: 248 loop : -1.12 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 417 HIS 0.006 0.001 HIS A 495 PHE 0.024 0.001 PHE B 388 TYR 0.020 0.001 TYR C 113 ARG 0.004 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 464) hydrogen bonds : angle 4.65708 ( 1283) metal coordination : bond 0.00456 ( 4) metal coordination : angle 3.76075 ( 12) covalent geometry : bond 0.00324 (13288) covalent geometry : angle 0.62637 (18123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8774 (t0) cc_final: 0.8465 (t0) REVERT: A 336 TYR cc_start: 0.9153 (m-80) cc_final: 0.8897 (m-80) REVERT: A 491 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8219 (mmmt) REVERT: A 618 MET cc_start: 0.9171 (mtp) cc_final: 0.8850 (mtm) REVERT: A 850 MET cc_start: 0.9136 (mmm) cc_final: 0.8864 (mmt) REVERT: A 912 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7607 (mtm-85) REVERT: A 1047 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 1089 GLU cc_start: 0.8596 (tp30) cc_final: 0.8361 (tp30) REVERT: A 1092 GLU cc_start: 0.8765 (tp30) cc_final: 0.8434 (tp30) REVERT: B 253 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 299 MET cc_start: 0.8759 (mmm) cc_final: 0.8269 (mmm) REVERT: B 431 LYS cc_start: 0.9049 (pttp) cc_final: 0.8776 (pttm) REVERT: B 476 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7700 (mm-30) REVERT: C 29 LEU cc_start: 0.9283 (mp) cc_final: 0.8958 (tp) REVERT: C 62 ASP cc_start: 0.8969 (p0) cc_final: 0.8568 (p0) REVERT: C 63 GLN cc_start: 0.8101 (mp10) cc_final: 0.7746 (pm20) REVERT: C 88 PHE cc_start: 0.8739 (m-80) cc_final: 0.8205 (m-80) REVERT: C 89 ASN cc_start: 0.7055 (t0) cc_final: 0.6432 (t0) REVERT: C 91 MET cc_start: 0.8068 (pmm) cc_final: 0.6926 (ppp) outliers start: 25 outliers final: 22 residues processed: 172 average time/residue: 0.2879 time to fit residues: 74.2892 Evaluate side-chains 175 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 0.0070 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075435 restraints weight = 23688.187| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.71 r_work: 0.2936 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 13292 Z= 0.169 Angle : 0.652 10.045 18135 Z= 0.329 Chirality : 0.045 0.310 2029 Planarity : 0.004 0.038 2223 Dihedral : 13.579 88.918 1995 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.88 % Favored : 93.06 % Rotamer: Outliers : 1.80 % Allowed : 17.74 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1527 helix: 0.70 (0.24), residues: 520 sheet: -1.96 (0.30), residues: 258 loop : -1.12 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 417 HIS 0.009 0.001 HIS A 495 PHE 0.037 0.001 PHE C 8 TYR 0.016 0.001 TYR C 113 ARG 0.004 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 464) hydrogen bonds : angle 4.68822 ( 1283) metal coordination : bond 0.00510 ( 4) metal coordination : angle 3.74605 ( 12) covalent geometry : bond 0.00400 (13288) covalent geometry : angle 0.64469 (18123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8769 (t0) cc_final: 0.8471 (t0) REVERT: A 336 TYR cc_start: 0.9161 (m-80) cc_final: 0.8878 (m-80) REVERT: A 491 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8269 (mmmt) REVERT: A 506 ASP cc_start: 0.7968 (t0) cc_final: 0.7552 (p0) REVERT: A 540 MET cc_start: 0.9099 (tpt) cc_final: 0.8720 (tpt) REVERT: A 850 MET cc_start: 0.9169 (mmm) cc_final: 0.8880 (mmt) REVERT: A 912 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7590 (mtm-85) REVERT: A 1089 GLU cc_start: 0.8612 (tp30) cc_final: 0.8371 (tp30) REVERT: A 1092 GLU cc_start: 0.8667 (tp30) cc_final: 0.8354 (tp30) REVERT: B 241 MET cc_start: 0.8611 (mmt) cc_final: 0.8170 (mmm) REVERT: B 253 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8149 (pp) REVERT: B 299 MET cc_start: 0.8771 (mmm) cc_final: 0.8326 (mmm) REVERT: B 476 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 29 LEU cc_start: 0.9270 (mp) cc_final: 0.8960 (tp) REVERT: C 62 ASP cc_start: 0.8984 (p0) cc_final: 0.8597 (p0) REVERT: C 63 GLN cc_start: 0.8168 (mp10) cc_final: 0.7795 (pm20) REVERT: C 88 PHE cc_start: 0.8781 (m-80) cc_final: 0.8186 (m-80) REVERT: C 89 ASN cc_start: 0.7281 (t0) cc_final: 0.6649 (t0) REVERT: C 91 MET cc_start: 0.8027 (pmm) cc_final: 0.6988 (ppp) REVERT: C 110 LYS cc_start: 0.7755 (tmtt) cc_final: 0.7524 (tmtt) outliers start: 25 outliers final: 23 residues processed: 166 average time/residue: 0.2289 time to fit residues: 59.8574 Evaluate side-chains 174 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 4 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 134 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077036 restraints weight = 23688.393| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.73 r_work: 0.2968 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13292 Z= 0.131 Angle : 0.630 10.170 18135 Z= 0.318 Chirality : 0.044 0.302 2029 Planarity : 0.004 0.039 2223 Dihedral : 13.497 89.300 1995 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 1.94 % Allowed : 17.67 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.95 (0.22), residues: 1527 helix: 0.75 (0.24), residues: 519 sheet: -1.92 (0.30), residues: 256 loop : -1.09 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 417 HIS 0.009 0.001 HIS A 495 PHE 0.025 0.001 PHE B 388 TYR 0.018 0.001 TYR A 496 ARG 0.004 0.000 ARG B 211 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 464) hydrogen bonds : angle 4.62591 ( 1283) metal coordination : bond 0.00420 ( 4) metal coordination : angle 3.82907 ( 12) covalent geometry : bond 0.00304 (13288) covalent geometry : angle 0.62269 (18123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6466.54 seconds wall clock time: 116 minutes 35.10 seconds (6995.10 seconds total)