Starting phenix.real_space_refine on Mon Jun 23 05:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghg_40045/06_2025/8ghg_40045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghg_40045/06_2025/8ghg_40045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghg_40045/06_2025/8ghg_40045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghg_40045/06_2025/8ghg_40045.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghg_40045/06_2025/8ghg_40045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghg_40045/06_2025/8ghg_40045.cif" } resolution = 3.3 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= 0.016 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 17307 2.51 5 N 4336 2.21 5 O 4844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26659 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 816, 6525 Classifications: {'peptide': 816} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 816, 6525 Classifications: {'peptide': 816} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6664 Chain: "C" Number of atoms: 6802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 853, 6794 Classifications: {'peptide': 853} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 825} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 853, 6794 Classifications: {'peptide': 853} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 825} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6940 Chain: "B" Number of atoms: 6549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 817, 6541 Classifications: {'peptide': 817} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 791} Chain breaks: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 817, 6541 Classifications: {'peptide': 817} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 791} Chain breaks: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6681 Chain: "D" Number of atoms: 6775 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 849, 6767 Classifications: {'peptide': 849} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 821} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 849, 6767 Classifications: {'peptide': 849} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 821} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6912 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN A 826 " occ=0.45 residue: pdb=" N AASN C 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN C 826 " occ=0.41 residue: pdb=" N AASN B 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN B 826 " occ=0.45 residue: pdb=" N AASN D 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN D 826 " occ=0.41 Time building chain proxies: 25.64, per 1000 atoms: 0.96 Number of scatterers: 26659 At special positions: 0 Unit cell: (147.96, 147.96, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 172 16.00 O 4844 8.00 N 4336 7.00 C 17307 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: 7.28 Conformation dependent library (CDL) restraints added in 7.4 seconds 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6350 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 20 sheets defined 51.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 108 through 128 removed outlier: 4.003A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 149 through 170 removed outlier: 4.042A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 180 through 199 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 229 through 260 removed outlier: 3.596A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.727A pdb=" N CYS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 4.050A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.683A pdb=" N GLY A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.947A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.854A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 485 through 500 removed outlier: 3.555A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.962A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.791A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.528A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.718A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.783A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.517A pdb=" N GLY A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 918 through 921 removed outlier: 3.789A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.655A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN C 136 " --> pdb=" O ILE C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 170 removed outlier: 3.968A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 232 through 260 Processing helix chain 'C' and resid 273 through 285 removed outlier: 4.026A pdb=" N TYR C 279 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 297 through 310 removed outlier: 4.459A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.949A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.506A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 485 through 500 removed outlier: 3.506A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.079A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 733 through 739 removed outlier: 3.644A pdb=" N LEU C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.879A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 759 through 768 removed outlier: 4.235A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.589A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 removed outlier: 3.775A pdb=" N LEU C 905 " --> pdb=" O GLU C 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 902 through 905' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 918 through 921 removed outlier: 3.850A pdb=" N ASP C 921 " --> pdb=" O SER C 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 969 through 973 removed outlier: 3.719A pdb=" N ARG C 972 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 4.213A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP C 992 " --> pdb=" O ASP C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 109 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 147 through 170 removed outlier: 4.115A pdb=" N ILE B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.333A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 212 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.676A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 260 removed outlier: 3.542A pdb=" N GLY B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 319 removed outlier: 4.545A pdb=" N PHE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.789A pdb=" N ILE B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU B 324 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 326 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 432 through 451 removed outlier: 4.165A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.513A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 472 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 500 removed outlier: 4.240A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.979A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 4.276A pdb=" N VAL B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.706A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.625A pdb=" N VAL B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 804 through 808 removed outlier: 3.863A pdb=" N GLN B 807 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN B 808 " --> pdb=" O ALA B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 808' Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.954A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.739A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 918 through 921 removed outlier: 3.647A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 922 through 930 removed outlier: 3.759A pdb=" N PHE B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 4.175A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 957 Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'D' and resid 24 through 33 removed outlier: 3.669A pdb=" N ALA D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER D 29 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N MET D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR D 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 122 through 136 Processing helix chain 'D' and resid 150 through 171 removed outlier: 3.598A pdb=" N ALA D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.610A pdb=" N LEU D 212 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 4.246A pdb=" N SER D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 260 removed outlier: 4.383A pdb=" N SER D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 297 through 318 removed outlier: 3.987A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.059A pdb=" N ILE D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.596A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.570A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.139A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 601 through 606 Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.633A pdb=" N LEU D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.563A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 759 through 767 removed outlier: 3.653A pdb=" N LEU D 763 " --> pdb=" O SER D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 884 through 892 removed outlier: 3.695A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.436A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.697A pdb=" N ARG D 972 " --> pdb=" O LEU D 969 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 974 " --> pdb=" O ASN D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 989 removed outlier: 4.202A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 400 removed outlier: 6.446A pdb=" N ILE A 375 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 482 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 458 " --> pdb=" O ASP A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.245A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.690A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 720 " --> pdb=" O MET A 799 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1014 through 1017 Processing sheet with id=AA5, first strand: chain 'C' and resid 398 through 399 removed outlier: 6.550A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 482 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 458 " --> pdb=" O ASP C 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 535 through 538 removed outlier: 3.914A pdb=" N ILE C 598 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 568 through 569 Processing sheet with id=AA8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.547A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 141 removed outlier: 3.612A pdb=" N SER B 140 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.150A pdb=" N ILE B 375 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR B 401 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE B 377 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 535 through 540 removed outlier: 7.048A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.669A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 720 " --> pdb=" O MET B 799 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 975 through 976 Processing sheet with id=AB6, first strand: chain 'B' and resid 1014 through 1017 Processing sheet with id=AB7, first strand: chain 'D' and resid 398 through 402 removed outlier: 8.719A pdb=" N GLU D 399 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 375 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR D 401 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE D 377 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS D 343 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL D 376 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 539 removed outlier: 4.019A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.520A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.523A pdb=" N MET D1053 " --> pdb=" O ARG D 976 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.82 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8413 1.35 - 1.47: 6806 1.47 - 1.59: 11794 1.59 - 1.72: 0 1.72 - 1.84: 256 Bond restraints: 27269 Sorted by residual: bond pdb=" C PRO D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.335 1.375 -0.039 1.30e-02 5.92e+03 9.19e+00 bond pdb=" CG MET B 282 " pdb=" SD MET B 282 " ideal model delta sigma weight residual 1.803 1.842 -0.039 2.50e-02 1.60e+03 2.48e+00 bond pdb=" C VAL A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.11e+00 bond pdb=" CA ASN B 225 " pdb=" CB ASN B 225 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.63e+00 bond pdb=" N MET B 282 " pdb=" CA MET B 282 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.23e-02 6.61e+03 1.58e+00 ... (remaining 27264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 36673 3.09 - 6.18: 278 6.18 - 9.27: 33 9.27 - 12.36: 7 12.36 - 15.45: 3 Bond angle restraints: 36994 Sorted by residual: angle pdb=" CB MET B 30 " pdb=" CG MET B 30 " pdb=" SD MET B 30 " ideal model delta sigma weight residual 112.70 128.15 -15.45 3.00e+00 1.11e-01 2.65e+01 angle pdb=" CG MET B 282 " pdb=" SD MET B 282 " pdb=" CE MET B 282 " ideal model delta sigma weight residual 100.90 112.12 -11.22 2.20e+00 2.07e-01 2.60e+01 angle pdb=" N PHE C 307 " pdb=" CA PHE C 307 " pdb=" CB PHE C 307 " ideal model delta sigma weight residual 110.12 116.17 -6.05 1.47e+00 4.63e-01 1.69e+01 angle pdb=" C LEU B 224 " pdb=" N ASN B 225 " pdb=" CA ASN B 225 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C VAL B 119 " pdb=" N PHE B 120 " pdb=" CA PHE B 120 " ideal model delta sigma weight residual 121.14 114.13 7.01 1.75e+00 3.27e-01 1.60e+01 ... (remaining 36989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 14513 17.66 - 35.32: 1321 35.32 - 52.98: 205 52.98 - 70.65: 27 70.65 - 88.31: 14 Dihedral angle restraints: 16080 sinusoidal: 6288 harmonic: 9792 Sorted by residual: dihedral pdb=" CA LEU B 281 " pdb=" C LEU B 281 " pdb=" N MET B 282 " pdb=" CA MET B 282 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU D 238 " pdb=" C LEU D 238 " pdb=" N LEU D 239 " pdb=" CA LEU D 239 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE C 303 " pdb=" C PHE C 303 " pdb=" N MET C 304 " pdb=" CA MET C 304 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 16077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2908 0.042 - 0.084: 1003 0.084 - 0.125: 295 0.125 - 0.167: 26 0.167 - 0.209: 5 Chirality restraints: 4237 Sorted by residual: chirality pdb=" CB VAL A 371 " pdb=" CA VAL A 371 " pdb=" CG1 VAL A 371 " pdb=" CG2 VAL A 371 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU A 272 " pdb=" CB LEU A 272 " pdb=" CD1 LEU A 272 " pdb=" CD2 LEU A 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA ASN B 225 " pdb=" N ASN B 225 " pdb=" C ASN B 225 " pdb=" CB ASN B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 4234 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 178 " -0.027 2.00e-02 2.50e+03 2.79e-02 1.95e+01 pdb=" CG TRP B 178 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 178 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 178 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 178 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 178 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 178 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 178 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 307 " -0.029 2.00e-02 2.50e+03 2.38e-02 9.90e+00 pdb=" CG PHE C 307 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 307 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 307 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 307 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 307 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO A 192 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.034 5.00e-02 4.00e+02 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 925 2.71 - 3.26: 27975 3.26 - 3.81: 43500 3.81 - 4.35: 52369 4.35 - 4.90: 86040 Nonbonded interactions: 210809 Sorted by model distance: nonbonded pdb=" O PHE A 177 " pdb=" OG SER A 183 " model vdw 2.168 3.040 nonbonded pdb=" O MET B 691 " pdb=" OG SER B 744 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR B 273 " pdb=" OE1 GLU B 276 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR C 965 " pdb=" O GLN C 967 " model vdw 2.251 3.040 nonbonded pdb=" O MET B 282 " pdb=" OG SER B 286 " model vdw 2.257 3.040 ... (remaining 210804 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 33 or resid 111 through 368 or resid 371 throug \ h 825 or resid 827 through 1056)) selection = (chain 'B' and (resid 19 through 33 or resid 111 through 368 or resid 371 throug \ h 825 or resid 827 through 976 or resid 995 through 1056)) selection = (chain 'C' and (resid 19 through 33 or resid 111 through 368 or resid 371 throug \ h 570 or resid 591 through 825 or resid 827 through 958 or resid 964 through 976 \ or resid 995 through 1056)) selection = (chain 'D' and (resid 19 through 33 or resid 111 through 570 or resid 591 throug \ h 825 or resid 827 through 958 or resid 964 through 976 or resid 995 through 105 \ 6)) } 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=0.41 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 76.200 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27269 Z= 0.131 Angle : 0.696 15.454 36994 Z= 0.346 Chirality : 0.044 0.209 4237 Planarity : 0.004 0.060 4650 Dihedral : 13.544 88.307 9730 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.10 % Allowed : 0.37 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3295 helix: -0.45 (0.13), residues: 1534 sheet: 0.95 (0.30), residues: 338 loop : -1.15 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRP B 178 HIS 0.004 0.001 HIS C 586 PHE 0.053 0.001 PHE C 307 TYR 0.023 0.001 TYR B1015 ARG 0.014 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.13706 ( 1082) hydrogen bonds : angle 6.00228 ( 3049) covalent geometry : bond 0.00267 (27269) covalent geometry : angle 0.69634 (36994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 2.793 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.9058 (m-10) cc_final: 0.8848 (m-80) REVERT: A 242 PHE cc_start: 0.9559 (t80) cc_final: 0.9194 (t80) REVERT: A 252 PHE cc_start: 0.9330 (t80) cc_final: 0.8826 (t80) REVERT: A 285 MET cc_start: 0.9138 (mpp) cc_final: 0.8896 (mpp) REVERT: A 307 PHE cc_start: 0.8943 (m-10) cc_final: 0.8537 (m-80) REVERT: A 314 MET cc_start: 0.9140 (tmm) cc_final: 0.8790 (tmm) REVERT: A 881 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 30 MET cc_start: 0.9346 (pmm) cc_final: 0.9107 (pmm) REVERT: C 34 PHE cc_start: 0.6851 (m-80) cc_final: 0.6426 (m-80) REVERT: C 285 MET cc_start: 0.9174 (mpp) cc_final: 0.8772 (mpp) REVERT: C 304 MET cc_start: 0.9499 (mmp) cc_final: 0.8975 (mmm) REVERT: C 312 LEU cc_start: 0.9239 (mm) cc_final: 0.8936 (mm) REVERT: C 314 MET cc_start: 0.8695 (tpt) cc_final: 0.8296 (tpp) REVERT: C 460 MET cc_start: 0.7837 (mmm) cc_final: 0.7574 (mmm) REVERT: C 1009 MET cc_start: 0.8808 (tpp) cc_final: 0.8525 (tpp) REVERT: B 120 PHE cc_start: 0.8643 (p90) cc_final: 0.8179 (p90) REVERT: B 154 MET cc_start: 0.7766 (mmp) cc_final: 0.7533 (mmm) REVERT: B 558 PHE cc_start: 0.7180 (t80) cc_final: 0.6918 (t80) REVERT: B 1009 MET cc_start: 0.7909 (pmm) cc_final: 0.7322 (pmm) REVERT: D 284 THR cc_start: 0.9321 (m) cc_final: 0.9100 (m) REVERT: D 302 LEU cc_start: 0.9801 (mt) cc_final: 0.9572 (mt) REVERT: D 303 PHE cc_start: 0.9333 (m-10) cc_final: 0.9050 (m-80) REVERT: D 306 PHE cc_start: 0.9476 (m-80) cc_final: 0.9116 (m-80) REVERT: D 1009 MET cc_start: 0.8976 (mmp) cc_final: 0.8732 (mmp) outliers start: 3 outliers final: 3 residues processed: 181 average time/residue: 0.3295 time to fit residues: 102.1237 Evaluate side-chains 153 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain B residue 329 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 85 optimal weight: 40.0000 chunk 169 optimal weight: 50.0000 chunk 134 optimal weight: 2.9990 chunk 259 optimal weight: 40.0000 chunk 100 optimal weight: 0.0770 chunk 157 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 200 ASN A 222 GLN A 462 GLN A 749 HIS A 771 HIS A 816 GLN A 893 GLN A 967 GLN C 397 GLN C 402 GLN C 464 HIS C 534 ASN C 736 ASN C 808 ASN B 344 HIS B 464 HIS B 465 ASN B 496 GLN B 509 ASN B 808 ASN B 907 GLN D 225 ASN D 344 HIS D 534 ASN D 693 HIS ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS D 808 ASN D 932 ASN D 971 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.069923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046705 restraints weight = 280755.861| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 7.69 r_work: 0.2878 rms_B_bonded: 7.47 restraints_weight: 2.0000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27269 Z= 0.169 Angle : 0.613 10.807 36994 Z= 0.312 Chirality : 0.042 0.171 4237 Planarity : 0.004 0.058 4650 Dihedral : 4.419 36.467 3568 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 0.41 % Allowed : 5.60 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3295 helix: -0.08 (0.13), residues: 1528 sheet: 0.80 (0.29), residues: 360 loop : -0.98 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 178 HIS 0.004 0.001 HIS B 350 PHE 0.046 0.001 PHE C 307 TYR 0.033 0.001 TYR C 163 ARG 0.005 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1082) hydrogen bonds : angle 5.31571 ( 3049) covalent geometry : bond 0.00373 (27269) covalent geometry : angle 0.61313 (36994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.9531 (t80) cc_final: 0.9296 (t80) REVERT: A 252 PHE cc_start: 0.9479 (t80) cc_final: 0.9158 (t80) REVERT: A 307 PHE cc_start: 0.9090 (m-10) cc_final: 0.8631 (m-80) REVERT: A 314 MET cc_start: 0.9027 (tmm) cc_final: 0.8633 (tmm) REVERT: A 881 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8791 (tm-30) REVERT: C 30 MET cc_start: 0.9370 (pmm) cc_final: 0.9081 (pmm) REVERT: C 34 PHE cc_start: 0.6861 (m-80) cc_final: 0.6417 (m-80) REVERT: C 285 MET cc_start: 0.9336 (mpp) cc_final: 0.8897 (mpp) REVERT: C 304 MET cc_start: 0.9607 (mmp) cc_final: 0.9168 (mmm) REVERT: C 307 PHE cc_start: 0.8501 (m-80) cc_final: 0.7988 (m-80) REVERT: C 312 LEU cc_start: 0.8723 (mm) cc_final: 0.8291 (mt) REVERT: C 314 MET cc_start: 0.8646 (tpt) cc_final: 0.8350 (tpp) REVERT: C 315 PHE cc_start: 0.8126 (m-10) cc_final: 0.7911 (m-10) REVERT: C 565 MET cc_start: 0.8908 (mmp) cc_final: 0.8657 (mmp) REVERT: C 597 PHE cc_start: 0.8770 (m-10) cc_final: 0.8475 (m-10) REVERT: C 1009 MET cc_start: 0.9188 (tpp) cc_final: 0.8852 (tpp) REVERT: B 304 MET cc_start: 0.9688 (ptm) cc_final: 0.9358 (ppp) REVERT: B 808 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.7816 (t0) REVERT: B 830 MET cc_start: 0.8589 (tpp) cc_final: 0.7934 (tpp) REVERT: B 1009 MET cc_start: 0.8400 (pmm) cc_final: 0.7769 (pmm) REVERT: B 1053 MET cc_start: 0.8998 (mmt) cc_final: 0.8797 (mmm) REVERT: D 284 THR cc_start: 0.9164 (m) cc_final: 0.8935 (m) REVERT: D 302 LEU cc_start: 0.9822 (mt) cc_final: 0.9526 (mt) REVERT: D 306 PHE cc_start: 0.9627 (m-80) cc_final: 0.9256 (m-80) REVERT: D 799 MET cc_start: 0.9604 (tpp) cc_final: 0.9380 (tpp) REVERT: D 881 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 1009 MET cc_start: 0.9257 (mmp) cc_final: 0.9033 (mmp) outliers start: 12 outliers final: 11 residues processed: 169 average time/residue: 0.3261 time to fit residues: 94.9424 Evaluate side-chains 162 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 808 ASN Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 30 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 chunk 193 optimal weight: 1.9990 chunk 246 optimal weight: 0.0050 chunk 255 optimal weight: 50.0000 chunk 296 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS A 930 ASN A1008 ASN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.070479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.046986 restraints weight = 298138.744| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 7.97 r_work: 0.2806 rms_B_bonded: 7.74 restraints_weight: 2.0000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27269 Z= 0.118 Angle : 0.580 10.522 36994 Z= 0.292 Chirality : 0.042 0.340 4237 Planarity : 0.004 0.057 4650 Dihedral : 4.309 35.613 3568 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.34 % Allowed : 7.70 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3295 helix: 0.01 (0.13), residues: 1529 sheet: 0.80 (0.29), residues: 365 loop : -0.95 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.047 0.001 PHE C 306 TYR 0.041 0.001 TYR B 279 ARG 0.004 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1082) hydrogen bonds : angle 5.16362 ( 3049) covalent geometry : bond 0.00259 (27269) covalent geometry : angle 0.58022 (36994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.9489 (t80) cc_final: 0.9227 (t80) REVERT: A 252 PHE cc_start: 0.9505 (t80) cc_final: 0.9275 (t80) REVERT: A 285 MET cc_start: 0.9472 (mpp) cc_final: 0.8764 (mmp) REVERT: A 314 MET cc_start: 0.9064 (tmm) cc_final: 0.8658 (tmm) REVERT: A 881 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 1008 ASN cc_start: 0.9344 (OUTLIER) cc_final: 0.9134 (p0) REVERT: C 304 MET cc_start: 0.9654 (mmp) cc_final: 0.9064 (mmm) REVERT: C 307 PHE cc_start: 0.8507 (m-80) cc_final: 0.7969 (m-80) REVERT: C 312 LEU cc_start: 0.8934 (mm) cc_final: 0.8262 (mt) REVERT: C 314 MET cc_start: 0.8717 (tpt) cc_final: 0.8441 (tpp) REVERT: C 565 MET cc_start: 0.8975 (mmp) cc_final: 0.8678 (mmp) REVERT: C 597 PHE cc_start: 0.8831 (m-10) cc_final: 0.8609 (m-10) REVERT: C 1009 MET cc_start: 0.9210 (tpp) cc_final: 0.8928 (tpp) REVERT: B 154 MET cc_start: 0.8245 (mmm) cc_final: 0.8002 (mmm) REVERT: B 304 MET cc_start: 0.9671 (ptm) cc_final: 0.9381 (ppp) REVERT: B 739 MET cc_start: 0.9272 (tpt) cc_final: 0.9031 (tpt) REVERT: B 830 MET cc_start: 0.8725 (tpp) cc_final: 0.8022 (tpp) REVERT: B 1009 MET cc_start: 0.8354 (pmm) cc_final: 0.7677 (pmm) REVERT: D 302 LEU cc_start: 0.9761 (mt) cc_final: 0.9435 (mt) REVERT: D 303 PHE cc_start: 0.9470 (m-10) cc_final: 0.9245 (m-10) REVERT: D 306 PHE cc_start: 0.9587 (m-80) cc_final: 0.9201 (m-80) REVERT: D 565 MET cc_start: 0.8535 (tmm) cc_final: 0.8147 (tmm) REVERT: D 597 PHE cc_start: 0.9432 (m-10) cc_final: 0.9192 (m-10) REVERT: D 881 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8330 (tm-30) outliers start: 10 outliers final: 7 residues processed: 168 average time/residue: 0.3472 time to fit residues: 100.5942 Evaluate side-chains 158 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 1000 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 5 optimal weight: 40.0000 chunk 156 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN A1008 ASN C 379 HIS C 496 GLN C 749 HIS C 771 HIS B 771 HIS ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.068782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045366 restraints weight = 289840.425| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 7.70 r_work: 0.2762 rms_B_bonded: 7.50 restraints_weight: 2.0000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27269 Z= 0.213 Angle : 0.636 12.741 36994 Z= 0.320 Chirality : 0.043 0.339 4237 Planarity : 0.004 0.057 4650 Dihedral : 4.387 37.139 3567 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 0.85 % Allowed : 9.77 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3295 helix: 0.06 (0.13), residues: 1530 sheet: 0.65 (0.28), residues: 366 loop : -0.86 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 178 HIS 0.006 0.001 HIS A 749 PHE 0.038 0.001 PHE C 303 TYR 0.027 0.001 TYR C 163 ARG 0.004 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1082) hydrogen bonds : angle 5.24562 ( 3049) covalent geometry : bond 0.00470 (27269) covalent geometry : angle 0.63624 (36994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 PHE cc_start: 0.9472 (t80) cc_final: 0.9187 (t80) REVERT: A 252 PHE cc_start: 0.9488 (t80) cc_final: 0.9251 (t80) REVERT: A 303 PHE cc_start: 0.9630 (t80) cc_final: 0.9353 (t80) REVERT: A 314 MET cc_start: 0.9068 (tmm) cc_final: 0.8640 (tmm) REVERT: A 881 GLU cc_start: 0.9350 (tm-30) cc_final: 0.9010 (tm-30) REVERT: A 1008 ASN cc_start: 0.9377 (OUTLIER) cc_final: 0.9176 (p0) REVERT: C 34 PHE cc_start: 0.6876 (m-80) cc_final: 0.6533 (m-80) REVERT: C 285 MET cc_start: 0.9422 (mpp) cc_final: 0.8985 (mpp) REVERT: C 304 MET cc_start: 0.9694 (mmp) cc_final: 0.9156 (mmm) REVERT: C 307 PHE cc_start: 0.8526 (m-80) cc_final: 0.8133 (m-80) REVERT: C 312 LEU cc_start: 0.8986 (mm) cc_final: 0.8328 (mt) REVERT: C 314 MET cc_start: 0.8781 (tpt) cc_final: 0.8474 (tpp) REVERT: C 565 MET cc_start: 0.9172 (mmp) cc_final: 0.8909 (mmp) REVERT: C 1009 MET cc_start: 0.9204 (tpp) cc_final: 0.8993 (tpp) REVERT: B 154 MET cc_start: 0.8347 (mmm) cc_final: 0.8079 (mmm) REVERT: B 304 MET cc_start: 0.9671 (ptm) cc_final: 0.9367 (ppp) REVERT: B 830 MET cc_start: 0.8887 (tpp) cc_final: 0.8159 (tpp) REVERT: B 1009 MET cc_start: 0.8630 (pmm) cc_final: 0.7984 (pmm) REVERT: D 302 LEU cc_start: 0.9742 (mt) cc_final: 0.9399 (mt) REVERT: D 306 PHE cc_start: 0.9612 (m-80) cc_final: 0.9223 (m-80) REVERT: D 881 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 1009 MET cc_start: 0.9253 (mmp) cc_final: 0.9000 (mmp) outliers start: 25 outliers final: 14 residues processed: 165 average time/residue: 0.3492 time to fit residues: 99.6246 Evaluate side-chains 157 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1008 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 265 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 330 optimal weight: 0.2980 chunk 210 optimal weight: 7.9990 chunk 306 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A1008 ASN ** C 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 ASN ** D 745 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 = 0.069397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.045890 restraints weight = 315999.713| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 8.01 r_work: 0.2757 rms_B_bonded: 7.82 restraints_weight: 2.0000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27269 Z= 0.142 Angle : 0.596 11.374 36994 Z= 0.300 Chirality : 0.042 0.376 4237 Planarity : 0.004 0.057 4650 Dihedral : 4.317 38.427 3566 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 0.81 % Allowed : 11.20 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3295 helix: 0.13 (0.13), residues: 1530 sheet: 0.67 (0.29), residues: 366 loop : -0.83 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.032 0.001 PHE C 303 TYR 0.028 0.001 TYR B 279 ARG 0.003 0.000 ARG B 765 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 1082) hydrogen bonds : angle 5.16281 ( 3049) covalent geometry : bond 0.00317 (27269) covalent geometry : angle 0.59644 (36994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 PHE cc_start: 0.9644 (OUTLIER) cc_final: 0.9427 (t80) REVERT: A 881 GLU cc_start: 0.9341 (tm-30) cc_final: 0.8984 (tm-30) REVERT: C 285 MET cc_start: 0.9392 (mpp) cc_final: 0.8974 (mpp) REVERT: C 304 MET cc_start: 0.9663 (mmp) cc_final: 0.9132 (mmm) REVERT: C 307 PHE cc_start: 0.8381 (m-80) cc_final: 0.7912 (m-80) REVERT: C 312 LEU cc_start: 0.8974 (mm) cc_final: 0.8555 (mm) REVERT: C 314 MET cc_start: 0.8759 (tpt) cc_final: 0.8390 (tpp) REVERT: C 565 MET cc_start: 0.9148 (mmp) cc_final: 0.8928 (mmp) REVERT: B 154 MET cc_start: 0.8408 (mmm) cc_final: 0.8206 (mmm) REVERT: B 304 MET cc_start: 0.9653 (ptm) cc_final: 0.9333 (ppp) REVERT: B 739 MET cc_start: 0.9360 (tpt) cc_final: 0.9154 (tpt) REVERT: B 808 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.7806 (t0) REVERT: B 830 MET cc_start: 0.8839 (tpp) cc_final: 0.7557 (tpp) REVERT: B 1009 MET cc_start: 0.8524 (pmm) cc_final: 0.7816 (pmm) REVERT: D 30 MET cc_start: 0.8328 (tpp) cc_final: 0.8048 (tpp) REVERT: D 302 LEU cc_start: 0.9726 (mt) cc_final: 0.9451 (mt) REVERT: D 306 PHE cc_start: 0.9576 (m-80) cc_final: 0.9186 (m-80) REVERT: D 565 MET cc_start: 0.8832 (tmm) cc_final: 0.8558 (tmm) REVERT: D 881 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 1009 MET cc_start: 0.9259 (mmp) cc_final: 0.9058 (mmp) outliers start: 24 outliers final: 15 residues processed: 162 average time/residue: 0.3222 time to fit residues: 90.2166 Evaluate side-chains 162 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 808 ASN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 126 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 289 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.069281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045840 restraints weight = 267434.924| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 7.38 r_work: 0.2780 rms_B_bonded: 7.35 restraints_weight: 2.0000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27269 Z= 0.152 Angle : 0.603 12.661 36994 Z= 0.302 Chirality : 0.042 0.375 4237 Planarity : 0.004 0.056 4650 Dihedral : 4.309 39.809 3566 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 0.68 % Allowed : 12.08 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3295 helix: 0.14 (0.13), residues: 1530 sheet: 0.68 (0.29), residues: 364 loop : -0.82 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.033 0.001 PHE C 303 TYR 0.023 0.001 TYR C 163 ARG 0.003 0.000 ARG B 765 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 1082) hydrogen bonds : angle 5.13597 ( 3049) covalent geometry : bond 0.00339 (27269) covalent geometry : angle 0.60294 (36994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 MET cc_start: 0.9495 (mmp) cc_final: 0.9275 (mmm) REVERT: A 881 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8995 (tm-30) REVERT: A 1049 ILE cc_start: 0.1862 (OUTLIER) cc_final: 0.0200 (tp) REVERT: C 285 MET cc_start: 0.9452 (mpp) cc_final: 0.9058 (mpp) REVERT: C 307 PHE cc_start: 0.8399 (m-80) cc_final: 0.7830 (m-80) REVERT: C 314 MET cc_start: 0.8771 (tpt) cc_final: 0.8449 (tpp) REVERT: C 513 MET cc_start: 0.8957 (tpt) cc_final: 0.8652 (tpt) REVERT: C 565 MET cc_start: 0.9154 (mmp) cc_final: 0.8940 (mmp) REVERT: C 934 LEU cc_start: 0.9560 (tp) cc_final: 0.9328 (tt) REVERT: C 1009 MET cc_start: 0.9367 (tpp) cc_final: 0.8964 (tpp) REVERT: B 304 MET cc_start: 0.9648 (ptm) cc_final: 0.9311 (ppp) REVERT: B 830 MET cc_start: 0.8874 (tpp) cc_final: 0.7628 (tpp) REVERT: B 1009 MET cc_start: 0.8500 (pmm) cc_final: 0.7774 (pmm) REVERT: D 30 MET cc_start: 0.8584 (tpp) cc_final: 0.8341 (tpp) REVERT: D 302 LEU cc_start: 0.9700 (mt) cc_final: 0.9416 (mt) REVERT: D 306 PHE cc_start: 0.9571 (m-80) cc_final: 0.9186 (m-80) REVERT: D 565 MET cc_start: 0.8763 (tmm) cc_final: 0.8333 (tmm) REVERT: D 881 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8387 (tm-30) REVERT: D 1009 MET cc_start: 0.9247 (mmp) cc_final: 0.9016 (mmp) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.3281 time to fit residues: 87.9943 Evaluate side-chains 160 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 256 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 221 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 ASN B B 893 GLN ** D 745 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 = 0.3571 r_free = 0.3571 target = 0.068444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045026 restraints weight = 271597.968| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 7.31 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27269 Z= 0.209 Angle : 0.641 13.192 36994 Z= 0.323 Chirality : 0.043 0.391 4237 Planarity : 0.004 0.057 4650 Dihedral : 4.427 42.615 3566 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer: Outliers : 0.68 % Allowed : 12.83 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3295 helix: 0.10 (0.13), residues: 1525 sheet: 0.59 (0.29), residues: 364 loop : -0.83 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 178 HIS 0.006 0.001 HIS A 749 PHE 0.033 0.001 PHE C 303 TYR 0.025 0.001 TYR B 279 ARG 0.003 0.000 ARG D 976 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1082) hydrogen bonds : angle 5.22118 ( 3049) covalent geometry : bond 0.00460 (27269) covalent geometry : angle 0.64141 (36994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 MET cc_start: 0.9250 (mmp) cc_final: 0.8979 (mmm) REVERT: A 565 MET cc_start: 0.8471 (ppp) cc_final: 0.8013 (ppp) REVERT: A 881 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 1009 MET cc_start: 0.8824 (tpt) cc_final: 0.8613 (tpt) REVERT: A 1049 ILE cc_start: 0.1022 (OUTLIER) cc_final: 0.0007 (tp) REVERT: C 307 PHE cc_start: 0.8104 (m-80) cc_final: 0.7790 (m-80) REVERT: C 314 MET cc_start: 0.8813 (tpt) cc_final: 0.8373 (tmm) REVERT: C 565 MET cc_start: 0.9062 (mmp) cc_final: 0.8836 (mmp) REVERT: C 1009 MET cc_start: 0.9212 (tpp) cc_final: 0.8836 (tpp) REVERT: B 304 MET cc_start: 0.9570 (ptm) cc_final: 0.9200 (ppp) REVERT: B 830 MET cc_start: 0.8771 (tpp) cc_final: 0.7548 (tpp) REVERT: B 881 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 1009 MET cc_start: 0.8538 (pmm) cc_final: 0.7786 (pmm) REVERT: D 30 MET cc_start: 0.8496 (tpp) cc_final: 0.8231 (tpp) REVERT: D 306 PHE cc_start: 0.9540 (m-80) cc_final: 0.9099 (m-80) REVERT: D 565 MET cc_start: 0.8402 (tmm) cc_final: 0.8025 (tmm) REVERT: D 881 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 1009 MET cc_start: 0.9232 (mmp) cc_final: 0.9007 (mmp) outliers start: 20 outliers final: 16 residues processed: 153 average time/residue: 0.3173 time to fit residues: 84.5385 Evaluate side-chains 156 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 301 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 GLN B 440 ASN B 451 HIS ** D 745 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 = 0.3594 r_free = 0.3594 target = 0.069438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046015 restraints weight = 306270.147| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 7.83 r_work: 0.2770 rms_B_bonded: 7.69 restraints_weight: 2.0000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27269 Z= 0.131 Angle : 0.608 13.257 36994 Z= 0.303 Chirality : 0.042 0.344 4237 Planarity : 0.004 0.056 4650 Dihedral : 4.349 43.789 3566 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.61 % Allowed : 13.03 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3295 helix: 0.15 (0.13), residues: 1523 sheet: 0.63 (0.29), residues: 364 loop : -0.80 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 178 HIS 0.004 0.001 HIS A 749 PHE 0.032 0.001 PHE C 303 TYR 0.022 0.001 TYR C 163 ARG 0.004 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1082) hydrogen bonds : angle 5.09985 ( 3049) covalent geometry : bond 0.00292 (27269) covalent geometry : angle 0.60778 (36994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 MET cc_start: 0.9505 (mmp) cc_final: 0.9266 (mmm) REVERT: A 881 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9008 (tm-30) REVERT: A 1009 MET cc_start: 0.8856 (tpt) cc_final: 0.8618 (tpt) REVERT: A 1049 ILE cc_start: 0.1748 (OUTLIER) cc_final: 0.0078 (tp) REVERT: C 302 LEU cc_start: 0.9553 (mt) cc_final: 0.9344 (pp) REVERT: C 303 PHE cc_start: 0.9469 (t80) cc_final: 0.9133 (t80) REVERT: C 307 PHE cc_start: 0.8302 (m-80) cc_final: 0.7669 (m-80) REVERT: C 312 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8514 (mm) REVERT: C 314 MET cc_start: 0.8814 (tpt) cc_final: 0.8366 (tmm) REVERT: C 513 MET cc_start: 0.8911 (tpt) cc_final: 0.8497 (tpt) REVERT: C 565 MET cc_start: 0.9201 (mmp) cc_final: 0.8999 (mmp) REVERT: C 1009 MET cc_start: 0.9325 (tpp) cc_final: 0.9047 (tpp) REVERT: B 304 MET cc_start: 0.9649 (ptm) cc_final: 0.9317 (ppp) REVERT: B 436 GLU cc_start: 0.9288 (mp0) cc_final: 0.8772 (mp0) REVERT: B 830 MET cc_start: 0.8812 (tpp) cc_final: 0.7602 (tpp) REVERT: B 881 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8885 (tm-30) REVERT: B 1009 MET cc_start: 0.8559 (pmm) cc_final: 0.7719 (pmm) REVERT: D 30 MET cc_start: 0.8709 (tpp) cc_final: 0.8499 (tpp) REVERT: D 285 MET cc_start: 0.9407 (pmm) cc_final: 0.9159 (pmm) REVERT: D 302 LEU cc_start: 0.9694 (mt) cc_final: 0.9441 (mt) REVERT: D 304 MET cc_start: 0.9615 (tpp) cc_final: 0.9338 (tpp) REVERT: D 306 PHE cc_start: 0.9526 (m-80) cc_final: 0.9132 (m-80) REVERT: D 565 MET cc_start: 0.8765 (tmm) cc_final: 0.8318 (tmm) REVERT: D 881 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 1009 MET cc_start: 0.9283 (mmp) cc_final: 0.9081 (mmp) outliers start: 18 outliers final: 14 residues processed: 158 average time/residue: 0.3288 time to fit residues: 90.4078 Evaluate side-chains 159 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 513 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 330 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 214 optimal weight: 0.0370 chunk 99 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 274 optimal weight: 0.0970 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.070139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046586 restraints weight = 314489.932| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 8.19 r_work: 0.2903 rms_B_bonded: 7.74 restraints_weight: 2.0000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27269 Z= 0.107 Angle : 0.599 13.949 36994 Z= 0.297 Chirality : 0.042 0.362 4237 Planarity : 0.004 0.057 4650 Dihedral : 4.240 44.705 3566 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.61 % Allowed : 13.06 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3295 helix: 0.21 (0.13), residues: 1517 sheet: 0.69 (0.29), residues: 352 loop : -0.73 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 178 HIS 0.004 0.001 HIS A 749 PHE 0.028 0.001 PHE C 303 TYR 0.030 0.001 TYR B 279 ARG 0.003 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 1082) hydrogen bonds : angle 5.03361 ( 3049) covalent geometry : bond 0.00237 (27269) covalent geometry : angle 0.59878 (36994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 4.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.9331 (t80) cc_final: 0.9125 (t80) REVERT: A 285 MET cc_start: 0.9315 (mmp) cc_final: 0.9066 (mmm) REVERT: A 881 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8792 (tm-30) REVERT: A 1009 MET cc_start: 0.8720 (tpt) cc_final: 0.8434 (tpt) REVERT: A 1049 ILE cc_start: 0.1399 (OUTLIER) cc_final: -0.0281 (pt) REVERT: C 252 PHE cc_start: 0.9565 (t80) cc_final: 0.9315 (t80) REVERT: C 302 LEU cc_start: 0.9597 (mt) cc_final: 0.9376 (pp) REVERT: C 303 PHE cc_start: 0.9432 (t80) cc_final: 0.9061 (t80) REVERT: C 307 PHE cc_start: 0.8131 (m-80) cc_final: 0.7565 (m-80) REVERT: C 312 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8058 (mm) REVERT: C 314 MET cc_start: 0.8706 (tpt) cc_final: 0.8207 (tmm) REVERT: C 513 MET cc_start: 0.8739 (tpt) cc_final: 0.8290 (tpt) REVERT: C 1009 MET cc_start: 0.9298 (tpp) cc_final: 0.8973 (tpp) REVERT: B 252 PHE cc_start: 0.9340 (t80) cc_final: 0.9124 (t80) REVERT: B 304 MET cc_start: 0.9637 (ptm) cc_final: 0.9314 (ppp) REVERT: B 436 GLU cc_start: 0.9059 (mp0) cc_final: 0.8587 (mp0) REVERT: B 830 MET cc_start: 0.8450 (tpp) cc_final: 0.7213 (tpp) REVERT: B 1009 MET cc_start: 0.8362 (pmm) cc_final: 0.7527 (pmm) REVERT: D 30 MET cc_start: 0.8646 (tpp) cc_final: 0.8390 (tpp) REVERT: D 302 LEU cc_start: 0.9711 (mt) cc_final: 0.9462 (mt) REVERT: D 304 MET cc_start: 0.9589 (tpp) cc_final: 0.9306 (tpp) REVERT: D 306 PHE cc_start: 0.9471 (m-80) cc_final: 0.9084 (m-80) REVERT: D 460 MET cc_start: 0.9210 (mmm) cc_final: 0.8957 (mmm) REVERT: D 565 MET cc_start: 0.8778 (tmm) cc_final: 0.8337 (tmm) REVERT: D 881 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8019 (tm-30) outliers start: 18 outliers final: 14 residues processed: 171 average time/residue: 0.4047 time to fit residues: 120.0528 Evaluate side-chains 166 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 218 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 113 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 808 ASN ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.070659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047166 restraints weight = 301669.019| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 8.03 r_work: 0.2813 rms_B_bonded: 7.68 restraints_weight: 2.0000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27269 Z= 0.105 Angle : 0.613 14.349 36994 Z= 0.301 Chirality : 0.042 0.367 4237 Planarity : 0.004 0.055 4650 Dihedral : 4.165 45.520 3566 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.75 % Allowed : 13.13 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.15), residues: 3295 helix: 0.21 (0.13), residues: 1515 sheet: 0.74 (0.29), residues: 364 loop : -0.74 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 22 HIS 0.004 0.000 HIS A 749 PHE 0.025 0.001 PHE C 303 TYR 0.023 0.001 TYR B 279 ARG 0.003 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 1082) hydrogen bonds : angle 4.99581 ( 3049) covalent geometry : bond 0.00229 (27269) covalent geometry : angle 0.61253 (36994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: A 285 MET cc_start: 0.9499 (mmp) cc_final: 0.9254 (mmm) REVERT: A 881 GLU cc_start: 0.9304 (tm-30) cc_final: 0.8968 (tm-30) REVERT: A 1049 ILE cc_start: 0.1575 (OUTLIER) cc_final: 0.0052 (tp) REVERT: C 252 PHE cc_start: 0.9545 (t80) cc_final: 0.9326 (t80) REVERT: C 281 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8781 (mm) REVERT: C 285 MET cc_start: 0.9255 (mmm) cc_final: 0.8855 (mpp) REVERT: C 302 LEU cc_start: 0.9577 (mt) cc_final: 0.9335 (pp) REVERT: C 303 PHE cc_start: 0.9388 (t80) cc_final: 0.9009 (t80) REVERT: C 307 PHE cc_start: 0.8306 (m-80) cc_final: 0.7661 (m-80) REVERT: C 312 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8605 (mm) REVERT: C 314 MET cc_start: 0.8781 (tpt) cc_final: 0.8263 (tmm) REVERT: C 1009 MET cc_start: 0.9322 (tpp) cc_final: 0.8954 (tpp) REVERT: B 304 MET cc_start: 0.9634 (ptm) cc_final: 0.9313 (ppp) REVERT: B 436 GLU cc_start: 0.9251 (mp0) cc_final: 0.8814 (mp0) REVERT: B 808 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7687 (t0) REVERT: B 830 MET cc_start: 0.8820 (tpp) cc_final: 0.7648 (tpp) REVERT: B 1009 MET cc_start: 0.8393 (pmm) cc_final: 0.7609 (pmm) REVERT: D 30 MET cc_start: 0.8716 (tpp) cc_final: 0.8453 (tpp) REVERT: D 304 MET cc_start: 0.9536 (tpp) cc_final: 0.9257 (tpp) REVERT: D 306 PHE cc_start: 0.9442 (m-80) cc_final: 0.9014 (m-80) REVERT: D 536 MET cc_start: 0.9048 (tmm) cc_final: 0.8784 (tmm) REVERT: D 565 MET cc_start: 0.8776 (tmm) cc_final: 0.8352 (tmm) REVERT: D 597 PHE cc_start: 0.9323 (m-10) cc_final: 0.9057 (m-10) REVERT: D 881 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8406 (tm-30) outliers start: 22 outliers final: 15 residues processed: 173 average time/residue: 0.3360 time to fit residues: 101.1199 Evaluate side-chains 170 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 808 ASN Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 132 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 264 optimal weight: 0.3980 chunk 206 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 266 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.069885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.046590 restraints weight = 262798.259| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 7.37 r_work: 0.2891 rms_B_bonded: 7.08 restraints_weight: 2.0000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27269 Z= 0.136 Angle : 0.622 16.095 36994 Z= 0.305 Chirality : 0.042 0.379 4237 Planarity : 0.004 0.055 4650 Dihedral : 4.170 46.336 3566 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.61 % Allowed : 13.47 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3295 helix: 0.24 (0.14), residues: 1516 sheet: 0.71 (0.29), residues: 364 loop : -0.69 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 178 HIS 0.004 0.001 HIS A 749 PHE 0.036 0.001 PHE A 188 TYR 0.025 0.001 TYR B 279 ARG 0.006 0.000 ARG A 974 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 1082) hydrogen bonds : angle 5.03825 ( 3049) covalent geometry : bond 0.00305 (27269) covalent geometry : angle 0.62240 (36994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16552.59 seconds wall clock time: 289 minutes 46.92 seconds (17386.92 seconds total)