Starting phenix.real_space_refine on Fri Feb 6 18:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwo_49888/02_2026/9nwo_49888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwo_49888/02_2026/9nwo_49888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nwo_49888/02_2026/9nwo_49888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwo_49888/02_2026/9nwo_49888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nwo_49888/02_2026/9nwo_49888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwo_49888/02_2026/9nwo_49888.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 156 5.16 5 C 16848 2.51 5 N 4528 2.21 5 O 4968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26500 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 808} Chain: "B" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "C" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "D" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Time building chain proxies: 5.95, per 1000 atoms: 0.22 Number of scatterers: 26500 At special positions: 0 Unit cell: (125.4, 175.56, 190, 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 156 16.00 O 4968 8.00 N 4528 7.00 C 16848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 355 " distance=2.02 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 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: 1.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 31 sheets defined 48.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.661A pdb=" N ASP A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.500A pdb=" N ALA A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.780A pdb=" N GLY A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.093A pdb=" N ILE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.958A pdb=" N ASP A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.524A pdb=" N PHE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.658A pdb=" N ASN A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.844A pdb=" N SER A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.542A pdb=" N GLN A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.582A pdb=" N ARG A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.569A pdb=" N ASP A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 3.510A pdb=" N ASN A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.879A pdb=" N LEU A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.846A pdb=" N GLU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 4.016A pdb=" N TYR A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 566 through 590 removed outlier: 3.972A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.070A pdb=" N VAL A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 659 removed outlier: 4.051A pdb=" N LEU A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 702 through 713 removed outlier: 4.315A pdb=" N SER A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 removed outlier: 3.613A pdb=" N LYS A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.615A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 795 removed outlier: 4.414A pdb=" N VAL A 783 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 803 Processing helix chain 'A' and resid 827 through 860 removed outlier: 5.562A pdb=" N GLY A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 851 " --> pdb=" O PHE A 847 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 858 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.606A pdb=" N ASP B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.531A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.184A pdb=" N GLY B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.551A pdb=" N GLY B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.969A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.557A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.807A pdb=" N PHE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 removed outlier: 4.506A pdb=" N ARG B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 249 removed outlier: 3.967A pdb=" N SER B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.717A pdb=" N GLU B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.880A pdb=" N MET B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 344 removed outlier: 3.931A pdb=" N LEU B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 374 removed outlier: 4.229A pdb=" N GLU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 4.213A pdb=" N LEU B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 559 through 563 Processing helix chain 'B' and resid 566 through 591 removed outlier: 3.654A pdb=" N LEU B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 589 " --> pdb=" O TYR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.566A pdb=" N VAL B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 659 removed outlier: 3.653A pdb=" N ALA B 636 " --> pdb=" O MET B 632 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.839A pdb=" N SER B 663 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 702 through 714 Processing helix chain 'B' and resid 715 through 718 Processing helix chain 'B' and resid 724 through 734 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.661A pdb=" N TYR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 782 removed outlier: 3.764A pdb=" N ARG B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.976A pdb=" N ARG B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 805 Processing helix chain 'B' and resid 831 through 858 removed outlier: 3.965A pdb=" N ILE B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 848 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.799A pdb=" N ASP C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 98 through 113 removed outlier: 4.326A pdb=" N SER C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.930A pdb=" N GLY C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.613A pdb=" N GLY C 180 " --> pdb=" O ASP C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 181 through 192 removed outlier: 3.624A pdb=" N GLN C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 266 through 277 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.455A pdb=" N CYS C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 321 through 344 removed outlier: 3.722A pdb=" N LEU C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 375 removed outlier: 3.557A pdb=" N ARG C 367 " --> pdb=" O TRP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 483 removed outlier: 4.159A pdb=" N TYR C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 514 Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.647A pdb=" N ASN C 532 " --> pdb=" O ASP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 563 removed outlier: 3.548A pdb=" N ALA C 563 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 590 removed outlier: 3.681A pdb=" N LEU C 582 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 585 " --> pdb=" O GLY C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 615 Processing helix chain 'C' and resid 627 through 659 removed outlier: 3.776A pdb=" N MET C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA C 636 " --> pdb=" O MET C 632 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 703 through 713 removed outlier: 3.677A pdb=" N GLN C 707 " --> pdb=" O SER C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 735 Processing helix chain 'C' and resid 743 through 753 Processing helix chain 'C' and resid 780 through 795 Processing helix chain 'C' and resid 795 through 803 removed outlier: 4.010A pdb=" N LYS C 801 " --> pdb=" O MET C 797 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 803 " --> pdb=" O ILE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 856 removed outlier: 3.886A pdb=" N PHE C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS C 836 " --> pdb=" O ALA C 832 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 838 " --> pdb=" O VAL C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 removed outlier: 3.889A pdb=" N ASP D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.688A pdb=" N ALA D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 235 through 249 Processing helix chain 'D' and resid 266 through 277 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 321 through 344 removed outlier: 3.795A pdb=" N LEU D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 375 removed outlier: 3.603A pdb=" N ARG D 367 " --> pdb=" O TRP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 removed outlier: 4.228A pdb=" N TYR D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.707A pdb=" N GLU D 511 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 552 through 554 No H-bonds generated for 'chain 'D' and resid 552 through 554' Processing helix chain 'D' and resid 558 through 562 removed outlier: 3.978A pdb=" N CYS D 561 " --> pdb=" O MET D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 591 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 659 removed outlier: 3.930A pdb=" N LEU D 639 " --> pdb=" O GLY D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 703 through 713 removed outlier: 3.523A pdb=" N GLN D 707 " --> pdb=" O SER D 703 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 711 " --> pdb=" O GLN D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 718 Processing helix chain 'D' and resid 724 through 735 removed outlier: 3.659A pdb=" N LYS D 731 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 753 removed outlier: 3.923A pdb=" N ASN D 752 " --> pdb=" O TYR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 794 removed outlier: 3.646A pdb=" N PHE D 784 " --> pdb=" O TYR D 780 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 785 " --> pdb=" O ARG D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 803 Processing helix chain 'D' and resid 827 through 860 removed outlier: 5.378A pdb=" N GLY D 833 " --> pdb=" O LYS D 829 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 834 " --> pdb=" O SER D 830 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE D 835 " --> pdb=" O PHE D 831 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS D 836 " --> pdb=" O ALA D 832 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 838 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 850 " --> pdb=" O CYS D 846 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 6.607A pdb=" N ILE A 29 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N THR A 68 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 31 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL A 70 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE A 33 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N HIS A 28 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL A 94 " --> pdb=" O HIS A 28 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 30 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N SER A 96 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 32 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 93 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199 removed outlier: 3.624A pdb=" N TYR A 172 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 230 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE A 398 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS A 418 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 400 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 380 removed outlier: 3.591A pdb=" N GLY A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.024A pdb=" N LYS A 466 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN A 459 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 541 through 542 removed outlier: 4.154A pdb=" N MET A 541 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 679 through 680 removed outlier: 6.743A pdb=" N GLY A 680 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASP A 742 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 739 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 545 " --> pdb=" O ASN A 763 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 70 removed outlier: 6.585A pdb=" N LEU B 93 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 119 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER B 95 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS B 116 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.768A pdb=" N LYS B 167 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE B 231 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 169 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL B 233 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 171 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 230 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 281 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 403 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 417 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY B 402 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LYS B 415 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 420 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.588A pdb=" N GLY B 383 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 485 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.336A pdb=" N LYS B 466 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN B 459 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 679 through 680 removed outlier: 6.939A pdb=" N GLY B 680 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 11.732A pdb=" N MET B 541 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N ASP B 767 " --> pdb=" O MET B 541 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR B 543 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 765 " --> pdb=" O TYR B 543 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 545 " --> pdb=" O ASN B 763 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 70 removed outlier: 3.826A pdb=" N ALA C 31 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 93 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE C 119 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER C 95 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS C 116 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 194 through 199 removed outlier: 8.365A pdb=" N ILE C 231 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 169 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL C 233 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 171 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE C 260 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLN C 286 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY C 402 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS C 415 " --> pdb=" O GLY C 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AC1, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AC2, first strand: chain 'C' and resid 485 through 490 removed outlier: 3.555A pdb=" N THR C 447 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 519 " --> pdb=" O ARG C 444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 455 through 460 removed outlier: 7.170A pdb=" N LYS C 466 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN C 459 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 541 through 542 removed outlier: 4.063A pdb=" N MET C 541 " --> pdb=" O TYR C 770 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 679 through 680 removed outlier: 7.131A pdb=" N GLY C 680 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ASP C 742 " --> pdb=" O GLY C 680 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.228A pdb=" N GLY D 30 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER D 96 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE D 32 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 93 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N HIS D 116 " --> pdb=" O LEU D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 194 through 200 removed outlier: 3.500A pdb=" N PHE D 168 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS D 167 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE D 231 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE D 169 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL D 233 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 171 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 230 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU D 281 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 398 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N CYS D 418 " --> pdb=" O PHE D 398 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE D 400 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AC9, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD1, first strand: chain 'D' and resid 485 through 490 Processing sheet with id=AD2, first strand: chain 'D' and resid 455 through 460 removed outlier: 6.697A pdb=" N VAL D 456 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR D 467 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU D 458 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AD4, first strand: chain 'D' and resid 679 through 681 removed outlier: 7.034A pdb=" N GLY D 680 " --> pdb=" O VAL D 740 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 739 " --> pdb=" O LEU D 548 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3402 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: 4.25 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8718 1.34 - 1.46: 5786 1.46 - 1.58: 12300 1.58 - 1.70: 0 1.70 - 1.82: 256 Bond restraints: 27060 Sorted by residual: bond pdb=" N ILE C 27 " pdb=" CA ILE C 27 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N ILE D 27 " pdb=" CA ILE D 27 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ILE B 27 " pdb=" CA ILE B 27 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N ILE A 27 " pdb=" CA ILE A 27 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" C PRO C 148 " pdb=" N PRO C 149 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.21e-02 6.83e+03 1.34e+00 ... (remaining 27055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 35207 1.31 - 2.62: 1302 2.62 - 3.93: 161 3.93 - 5.24: 16 5.24 - 6.55: 6 Bond angle restraints: 36692 Sorted by residual: angle pdb=" C LEU C 569 " pdb=" N TRP C 570 " pdb=" CA TRP C 570 " ideal model delta sigma weight residual 121.58 115.33 6.25 1.95e+00 2.63e-01 1.03e+01 angle pdb=" N ARG C 660 " pdb=" CA ARG C 660 " pdb=" C ARG C 660 " ideal model delta sigma weight residual 113.72 118.50 -4.78 1.52e+00 4.33e-01 9.87e+00 angle pdb=" CA TRP C 570 " pdb=" CB TRP C 570 " pdb=" CG TRP C 570 " ideal model delta sigma weight residual 113.60 119.21 -5.61 1.90e+00 2.77e-01 8.72e+00 angle pdb=" N TRP C 570 " pdb=" CA TRP C 570 " pdb=" CB TRP C 570 " ideal model delta sigma weight residual 110.41 115.19 -4.78 1.68e+00 3.54e-01 8.11e+00 angle pdb=" CA ARG D 660 " pdb=" CB ARG D 660 " pdb=" CG ARG D 660 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.94e+00 ... (remaining 36687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 15116 17.50 - 35.00: 800 35.00 - 52.51: 153 52.51 - 70.01: 38 70.01 - 87.51: 29 Dihedral angle restraints: 16136 sinusoidal: 6480 harmonic: 9656 Sorted by residual: dihedral pdb=" CA GLU A 451 " pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta harmonic sigma weight residual 180.00 -130.34 -49.66 0 5.00e+00 4.00e-02 9.86e+01 dihedral pdb=" CA LEU A 409 " pdb=" C LEU A 409 " pdb=" N GLY A 410 " pdb=" CA GLY A 410 " ideal model delta harmonic sigma weight residual 180.00 -151.26 -28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ILE B 356 " pdb=" C ILE B 356 " pdb=" N ARG B 357 " pdb=" CA ARG B 357 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 16133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2677 0.033 - 0.066: 988 0.066 - 0.099: 244 0.099 - 0.132: 156 0.132 - 0.165: 27 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CA ILE A 231 " pdb=" N ILE A 231 " pdb=" C ILE A 231 " pdb=" CB ILE A 231 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA TRP C 570 " pdb=" N TRP C 570 " pdb=" C TRP C 570 " pdb=" CB TRP C 570 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE B 27 " pdb=" N ILE B 27 " pdb=" C ILE B 27 " pdb=" CB ILE B 27 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 4089 not shown) Planarity restraints: 4720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 481 " -0.009 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR B 481 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR B 481 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 481 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 481 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 481 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 481 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR B 481 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 642 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.60e+00 pdb=" C LEU B 642 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU B 642 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 643 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 706 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C SER C 706 " -0.052 2.00e-02 2.50e+03 pdb=" O SER C 706 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN C 707 " 0.017 2.00e-02 2.50e+03 ... (remaining 4717 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 21326 3.13 - 3.72: 38099 3.72 - 4.31: 54213 4.31 - 4.90: 89918 Nonbonded interactions: 203673 Sorted by model distance: nonbonded pdb=" OG1 THR D 627 " pdb=" OG1 THR D 630 " model vdw 1.952 3.040 nonbonded pdb=" O GLU A 451 " pdb=" N PHE A 453 " model vdw 2.186 3.120 nonbonded pdb=" NH1 ARG D 660 " pdb=" O LYS D 822 " model vdw 2.211 3.120 nonbonded pdb=" O GLY B 406 " pdb=" N GLY B 410 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP A 827 " pdb=" N ILE A 828 " model vdw 2.261 3.120 ... (remaining 203668 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 22.530 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 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 : 0.002 0.032 27076 Z= 0.133 Angle : 0.581 6.551 36724 Z= 0.354 Chirality : 0.042 0.165 4092 Planarity : 0.007 0.099 4720 Dihedral : 12.241 87.512 9896 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.96 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 3336 helix: -1.37 (0.11), residues: 1486 sheet: -0.02 (0.26), residues: 378 loop : -1.09 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 275 TYR 0.041 0.004 TYR B 481 PHE 0.015 0.002 PHE A 33 TRP 0.036 0.003 TRP C 570 HIS 0.012 0.002 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00245 (27060) covalent geometry : angle 0.58015 (36692) SS BOND : bond 0.00271 ( 16) SS BOND : angle 1.10914 ( 32) hydrogen bonds : bond 0.16078 ( 1204) hydrogen bonds : angle 6.78219 ( 3402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.7678 (tm-30) cc_final: 0.6979 (mt0) REVERT: A 492 PRO cc_start: 0.6869 (Cg_endo) cc_final: 0.6608 (Cg_exo) REVERT: B 234 MET cc_start: 0.8258 (ptp) cc_final: 0.7997 (ptp) REVERT: B 438 MET cc_start: 0.4861 (mtp) cc_final: 0.4624 (mtp) REVERT: B 634 MET cc_start: 0.7604 (mmm) cc_final: 0.7247 (mmt) REVERT: B 708 MET cc_start: 0.6637 (mtp) cc_final: 0.5996 (ttp) REVERT: C 112 MET cc_start: 0.0836 (mmm) cc_final: 0.0094 (mtp) REVERT: C 193 MET cc_start: -0.1044 (mtt) cc_final: -0.1318 (mmm) REVERT: C 215 MET cc_start: -0.0216 (mtt) cc_final: -0.1520 (mmm) REVERT: C 597 MET cc_start: 0.3836 (mpp) cc_final: 0.3491 (mmt) REVERT: C 612 VAL cc_start: 0.8863 (t) cc_final: 0.8621 (m) REVERT: D 215 MET cc_start: -0.4885 (mtt) cc_final: -0.5090 (tpp) REVERT: D 320 MET cc_start: 0.0604 (mtp) cc_final: 0.0403 (mmm) REVERT: D 350 MET cc_start: 0.0630 (mtm) cc_final: 0.0094 (ttm) REVERT: D 603 THR cc_start: 0.6794 (m) cc_final: 0.6461 (t) REVERT: D 665 ILE cc_start: 0.6150 (mt) cc_final: 0.5784 (pt) REVERT: D 671 LEU cc_start: 0.6933 (tp) cc_final: 0.6644 (mt) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1599 time to fit residues: 103.4759 Evaluate side-chains 233 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 3.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 666 GLN A 802 HIS B 113 HIS B 359 ASN B 364 GLN B 485 ASN C 588 ASN D 619 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.238036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.211435 restraints weight = 39933.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.206752 restraints weight = 60029.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.201328 restraints weight = 60517.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.200774 restraints weight = 62399.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.198915 restraints weight = 49137.921| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27076 Z= 0.151 Angle : 0.613 10.338 36724 Z= 0.331 Chirality : 0.044 0.187 4092 Planarity : 0.004 0.064 4720 Dihedral : 5.302 62.136 3644 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 1.10 % Allowed : 5.17 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3336 helix: 0.25 (0.13), residues: 1499 sheet: 0.12 (0.25), residues: 392 loop : -0.83 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 147 TYR 0.029 0.002 TYR B 543 PHE 0.020 0.002 PHE C 470 TRP 0.027 0.002 TRP A 804 HIS 0.010 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00343 (27060) covalent geometry : angle 0.61310 (36692) SS BOND : bond 0.00278 ( 16) SS BOND : angle 0.87700 ( 32) hydrogen bonds : bond 0.05021 ( 1204) hydrogen bonds : angle 5.09755 ( 3402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 MET cc_start: 0.7737 (mmm) cc_final: 0.7493 (tpp) REVERT: A 737 TYR cc_start: 0.7413 (t80) cc_final: 0.7209 (t80) REVERT: B 634 MET cc_start: 0.7598 (mmm) cc_final: 0.7252 (mmt) REVERT: B 708 MET cc_start: 0.6047 (mtp) cc_final: 0.5708 (ttp) REVERT: C 112 MET cc_start: -0.0336 (mmm) cc_final: -0.1092 (ptm) REVERT: C 193 MET cc_start: 0.0168 (mtt) cc_final: -0.0214 (mmm) REVERT: C 215 MET cc_start: -0.0212 (mtt) cc_final: -0.1322 (mmt) REVERT: C 822 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4678 (mmmt) REVERT: D 215 MET cc_start: -0.4160 (mtt) cc_final: -0.4600 (tpp) REVERT: D 320 MET cc_start: 0.0480 (mtp) cc_final: -0.0225 (mmm) REVERT: D 350 MET cc_start: 0.0919 (mtm) cc_final: 0.0055 (ttm) REVERT: D 369 MET cc_start: -0.2875 (tpp) cc_final: -0.3264 (ttt) REVERT: D 665 ILE cc_start: 0.6029 (mt) cc_final: 0.5581 (pt) REVERT: D 797 MET cc_start: 0.5031 (ttm) cc_final: 0.4554 (ttt) outliers start: 32 outliers final: 20 residues processed: 271 average time/residue: 0.1503 time to fit residues: 66.5030 Evaluate side-chains 232 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 802 HIS Chi-restraints excluded: chain C residue 822 LYS Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 329 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 181 optimal weight: 40.0000 chunk 330 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 257 HIS A 775 GLN A 802 HIS A 808 ASN B 324 ASN B 726 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.236985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.210227 restraints weight = 39972.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.205829 restraints weight = 61946.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.201447 restraints weight = 54525.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.199627 restraints weight = 56843.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.196613 restraints weight = 56594.349| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27076 Z= 0.151 Angle : 0.577 11.040 36724 Z= 0.309 Chirality : 0.043 0.188 4092 Planarity : 0.004 0.067 4720 Dihedral : 5.021 60.687 3644 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 1.27 % Allowed : 6.78 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3336 helix: 0.72 (0.13), residues: 1501 sheet: 0.09 (0.25), residues: 392 loop : -0.92 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 304 TYR 0.024 0.002 TYR B 543 PHE 0.019 0.001 PHE B 470 TRP 0.018 0.001 TRP A 804 HIS 0.011 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00357 (27060) covalent geometry : angle 0.57693 (36692) SS BOND : bond 0.00216 ( 16) SS BOND : angle 0.89039 ( 32) hydrogen bonds : bond 0.04645 ( 1204) hydrogen bonds : angle 4.84886 ( 3402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7797 (t0) cc_final: 0.7205 (t0) REVERT: A 194 ASP cc_start: 0.7440 (t70) cc_final: 0.7132 (t0) REVERT: A 609 MET cc_start: 0.7751 (mmm) cc_final: 0.7428 (tpp) REVERT: A 705 TYR cc_start: 0.6866 (m-80) cc_final: 0.6658 (m-80) REVERT: A 755 ASP cc_start: 0.6628 (m-30) cc_final: 0.5519 (t0) REVERT: B 198 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7254 (mm-40) REVERT: B 708 MET cc_start: 0.5860 (mtp) cc_final: 0.5588 (ttp) REVERT: C 215 MET cc_start: 0.0244 (mtt) cc_final: -0.0285 (tpt) REVERT: C 600 MET cc_start: 0.3486 (mmp) cc_final: 0.3249 (mmp) REVERT: D 215 MET cc_start: -0.4280 (mtt) cc_final: -0.4751 (tpp) REVERT: D 320 MET cc_start: 0.0275 (mtp) cc_final: -0.0326 (mmm) REVERT: D 350 MET cc_start: 0.0965 (mtm) cc_final: -0.0033 (ttm) REVERT: D 369 MET cc_start: -0.2737 (tpp) cc_final: -0.3025 (ttt) REVERT: D 438 MET cc_start: 0.5504 (mmp) cc_final: 0.5296 (mmt) REVERT: D 541 MET cc_start: 0.5544 (tpp) cc_final: 0.5339 (tpp) REVERT: D 632 MET cc_start: 0.7039 (mmt) cc_final: 0.6742 (mpp) outliers start: 37 outliers final: 21 residues processed: 252 average time/residue: 0.1592 time to fit residues: 65.9799 Evaluate side-chains 227 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain D residue 587 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 69 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 258 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS C 591 ASN C 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.237023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.210742 restraints weight = 39995.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.204449 restraints weight = 55278.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.198934 restraints weight = 65123.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.198292 restraints weight = 69069.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.196710 restraints weight = 55134.602| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27076 Z= 0.143 Angle : 0.557 11.411 36724 Z= 0.295 Chirality : 0.043 0.280 4092 Planarity : 0.004 0.068 4720 Dihedral : 4.780 58.291 3644 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 1.48 % Allowed : 7.71 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3336 helix: 0.99 (0.13), residues: 1493 sheet: 0.09 (0.26), residues: 389 loop : -0.94 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 275 TYR 0.020 0.001 TYR D 540 PHE 0.021 0.001 PHE B 470 TRP 0.018 0.001 TRP A 804 HIS 0.011 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00338 (27060) covalent geometry : angle 0.55683 (36692) SS BOND : bond 0.00190 ( 16) SS BOND : angle 0.79012 ( 32) hydrogen bonds : bond 0.04320 ( 1204) hydrogen bonds : angle 4.68114 ( 3402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 MET cc_start: 0.7739 (mmm) cc_final: 0.7449 (tpp) REVERT: A 737 TYR cc_start: 0.7467 (t80) cc_final: 0.7226 (t80) REVERT: B 198 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7852 (mm-40) REVERT: B 207 MET cc_start: 0.8284 (ttt) cc_final: 0.7998 (ttp) REVERT: B 345 ARG cc_start: 0.5793 (mtt90) cc_final: 0.5292 (mmp80) REVERT: B 634 MET cc_start: 0.7486 (mmm) cc_final: 0.7196 (mmt) REVERT: C 112 MET cc_start: -0.0235 (mtp) cc_final: -0.0898 (ptt) REVERT: C 215 MET cc_start: 0.0182 (mtt) cc_final: -0.0148 (tpt) REVERT: D 215 MET cc_start: -0.4312 (mtt) cc_final: -0.4787 (tpp) REVERT: D 320 MET cc_start: 0.0262 (mtp) cc_final: -0.0365 (mmm) REVERT: D 350 MET cc_start: 0.1157 (mtm) cc_final: 0.0379 (ttm) REVERT: D 369 MET cc_start: -0.2377 (tpp) cc_final: -0.2856 (ttt) REVERT: D 438 MET cc_start: 0.5457 (mmp) cc_final: 0.5248 (mmt) outliers start: 43 outliers final: 31 residues processed: 241 average time/residue: 0.1438 time to fit residues: 58.3053 Evaluate side-chains 227 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 811 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 281 optimal weight: 0.0010 chunk 121 optimal weight: 8.9990 chunk 218 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 267 optimal weight: 50.0000 chunk 72 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 311 optimal weight: 0.9990 chunk 201 optimal weight: 40.0000 chunk 10 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN A 802 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.238523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.205249 restraints weight = 40649.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.199400 restraints weight = 59955.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.194429 restraints weight = 53920.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.193747 restraints weight = 49497.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.191130 restraints weight = 44201.498| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27076 Z= 0.112 Angle : 0.524 12.804 36724 Z= 0.275 Chirality : 0.042 0.219 4092 Planarity : 0.004 0.070 4720 Dihedral : 4.515 54.715 3644 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 1.41 % Allowed : 8.47 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3336 helix: 1.36 (0.14), residues: 1474 sheet: 0.16 (0.25), residues: 394 loop : -0.91 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 787 TYR 0.017 0.001 TYR B 543 PHE 0.020 0.001 PHE B 470 TRP 0.014 0.001 TRP C 570 HIS 0.014 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00255 (27060) covalent geometry : angle 0.52307 (36692) SS BOND : bond 0.00156 ( 16) SS BOND : angle 1.25302 ( 32) hydrogen bonds : bond 0.03832 ( 1204) hydrogen bonds : angle 4.51249 ( 3402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.6468 (OUTLIER) cc_final: 0.6215 (p) REVERT: A 318 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: A 449 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7922 (tt) REVERT: A 609 MET cc_start: 0.7887 (mmm) cc_final: 0.7630 (tpp) REVERT: B 198 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: B 207 MET cc_start: 0.8167 (ttt) cc_final: 0.7908 (ttp) REVERT: B 345 ARG cc_start: 0.5895 (mtt90) cc_final: 0.5358 (mmp80) REVERT: B 634 MET cc_start: 0.7426 (mmm) cc_final: 0.7188 (mmt) REVERT: C 112 MET cc_start: -0.0100 (mtp) cc_final: -0.0944 (ptm) REVERT: C 215 MET cc_start: 0.0447 (mtt) cc_final: 0.0096 (tpt) REVERT: D 320 MET cc_start: -0.0077 (mtp) cc_final: -0.0462 (mmm) REVERT: D 350 MET cc_start: 0.0975 (mtm) cc_final: 0.0364 (ttm) REVERT: D 369 MET cc_start: -0.2339 (tpp) cc_final: -0.2816 (ttt) REVERT: D 438 MET cc_start: 0.5635 (mmp) cc_final: 0.5431 (mmt) REVERT: D 632 MET cc_start: 0.7187 (mmt) cc_final: 0.6732 (mpp) outliers start: 41 outliers final: 27 residues processed: 245 average time/residue: 0.1473 time to fit residues: 60.2799 Evaluate side-chains 230 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 811 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 45 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 263 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS B 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.235510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.205950 restraints weight = 40448.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200083 restraints weight = 60025.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.195483 restraints weight = 53615.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.193305 restraints weight = 54185.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.191037 restraints weight = 54079.775| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 27076 Z= 0.183 Angle : 0.601 12.016 36724 Z= 0.313 Chirality : 0.044 0.207 4092 Planarity : 0.004 0.073 4720 Dihedral : 4.709 53.292 3644 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 1.89 % Allowed : 8.57 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3336 helix: 1.17 (0.13), residues: 1484 sheet: 0.02 (0.26), residues: 385 loop : -0.98 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 229 TYR 0.019 0.002 TYR B 679 PHE 0.022 0.002 PHE A 171 TRP 0.015 0.001 TRP A 804 HIS 0.016 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00448 (27060) covalent geometry : angle 0.59992 (36692) SS BOND : bond 0.00228 ( 16) SS BOND : angle 1.26767 ( 32) hydrogen bonds : bond 0.04649 ( 1204) hydrogen bonds : angle 4.72671 ( 3402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 455 MET cc_start: 0.6456 (pmm) cc_final: 0.5896 (mpp) REVERT: A 609 MET cc_start: 0.7792 (mmm) cc_final: 0.7544 (tpp) REVERT: B 198 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7563 (mm-40) REVERT: B 345 ARG cc_start: 0.5789 (mtt90) cc_final: 0.5304 (mmp80) REVERT: B 705 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6763 (t80) REVERT: C 112 MET cc_start: -0.0125 (mtp) cc_final: -0.0976 (ptm) REVERT: C 215 MET cc_start: 0.0384 (mtt) cc_final: 0.0050 (tpt) REVERT: C 642 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8015 (tp) REVERT: D 320 MET cc_start: -0.0055 (mtp) cc_final: -0.0264 (mmm) REVERT: D 369 MET cc_start: -0.2331 (tpp) cc_final: -0.2591 (ttt) REVERT: D 438 MET cc_start: 0.5697 (mmp) cc_final: 0.5478 (mmt) REVERT: D 632 MET cc_start: 0.7278 (mmt) cc_final: 0.6842 (mpp) outliers start: 55 outliers final: 41 residues processed: 246 average time/residue: 0.1492 time to fit residues: 61.6131 Evaluate side-chains 241 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 273 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 266 optimal weight: 20.0000 chunk 286 optimal weight: 40.0000 chunk 297 optimal weight: 30.0000 chunk 216 optimal weight: 0.0870 chunk 211 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 146 optimal weight: 0.0270 chunk 236 optimal weight: 0.9980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.238477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205592 restraints weight = 40486.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.199492 restraints weight = 59507.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.194413 restraints weight = 54140.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193520 restraints weight = 50355.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.191315 restraints weight = 44484.030| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27076 Z= 0.098 Angle : 0.518 12.362 36724 Z= 0.267 Chirality : 0.041 0.293 4092 Planarity : 0.004 0.081 4720 Dihedral : 4.286 51.260 3644 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 1.21 % Allowed : 9.50 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3336 helix: 1.56 (0.14), residues: 1466 sheet: 0.26 (0.26), residues: 385 loop : -0.86 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 787 TYR 0.025 0.001 TYR B 679 PHE 0.013 0.001 PHE C 470 TRP 0.017 0.001 TRP C 637 HIS 0.003 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00213 (27060) covalent geometry : angle 0.51691 (36692) SS BOND : bond 0.00191 ( 16) SS BOND : angle 1.21850 ( 32) hydrogen bonds : bond 0.03488 ( 1204) hydrogen bonds : angle 4.41210 ( 3402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.6434 (p) cc_final: 0.6200 (p) REVERT: A 287 THR cc_start: 0.9016 (t) cc_final: 0.8649 (p) REVERT: A 455 MET cc_start: 0.6692 (pmm) cc_final: 0.6169 (mpp) REVERT: A 512 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7352 (mt) REVERT: A 609 MET cc_start: 0.7846 (mmm) cc_final: 0.7610 (tpp) REVERT: B 142 TYR cc_start: 0.7169 (m-80) cc_final: 0.6902 (m-10) REVERT: B 186 ASP cc_start: 0.7445 (m-30) cc_final: 0.7199 (t0) REVERT: B 345 ARG cc_start: 0.5926 (mtt90) cc_final: 0.5436 (mmp80) REVERT: B 634 MET cc_start: 0.7365 (mmm) cc_final: 0.7092 (mmt) REVERT: C 112 MET cc_start: 0.0054 (mtp) cc_final: -0.0900 (ptm) REVERT: C 215 MET cc_start: 0.0459 (mtt) cc_final: 0.0101 (tpt) REVERT: C 612 VAL cc_start: 0.9135 (p) cc_final: 0.8798 (m) REVERT: C 786 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6724 (mt0) REVERT: D 320 MET cc_start: -0.0068 (mtp) cc_final: -0.0321 (mmm) REVERT: D 369 MET cc_start: -0.2500 (tpp) cc_final: -0.2769 (ttt) REVERT: D 438 MET cc_start: 0.5723 (mmp) cc_final: 0.5515 (mmt) REVERT: D 632 MET cc_start: 0.7100 (mmt) cc_final: 0.6773 (mpp) outliers start: 35 outliers final: 27 residues processed: 247 average time/residue: 0.1628 time to fit residues: 67.0307 Evaluate side-chains 230 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 786 GLN Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 176 optimal weight: 40.0000 chunk 283 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 185 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 794 ASN A 802 HIS B 286 GLN B 397 HIS B 721 ASN C 775 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.232524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.202678 restraints weight = 40821.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.197234 restraints weight = 58920.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.192858 restraints weight = 49757.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.190720 restraints weight = 49631.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188238 restraints weight = 55812.133| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 27076 Z= 0.331 Angle : 0.753 13.580 36724 Z= 0.391 Chirality : 0.049 0.263 4092 Planarity : 0.005 0.079 4720 Dihedral : 5.084 48.302 3644 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 1.86 % Allowed : 9.54 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3336 helix: 0.80 (0.13), residues: 1484 sheet: -0.23 (0.25), residues: 387 loop : -1.16 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 216 TYR 0.031 0.002 TYR A 737 PHE 0.029 0.002 PHE B 44 TRP 0.027 0.002 TRP A 804 HIS 0.013 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00819 (27060) covalent geometry : angle 0.75186 (36692) SS BOND : bond 0.00388 ( 16) SS BOND : angle 1.41369 ( 32) hydrogen bonds : bond 0.05855 ( 1204) hydrogen bonds : angle 5.18877 ( 3402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 MET cc_start: 0.7950 (mmm) cc_final: 0.7582 (mmp) REVERT: B 86 MET cc_start: 0.8113 (mtt) cc_final: 0.7893 (mtt) REVERT: B 198 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: B 345 ARG cc_start: 0.6087 (mtt90) cc_final: 0.5499 (mmp80) REVERT: C 112 MET cc_start: -0.0295 (mtp) cc_final: -0.1217 (ptm) REVERT: C 215 MET cc_start: 0.0569 (mtt) cc_final: 0.0212 (tpt) REVERT: C 612 VAL cc_start: 0.9228 (p) cc_final: 0.8957 (m) REVERT: C 786 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: D 320 MET cc_start: 0.0002 (mtp) cc_final: -0.0326 (mmm) REVERT: D 350 MET cc_start: -0.0255 (OUTLIER) cc_final: -0.0639 (tpp) REVERT: D 369 MET cc_start: -0.2332 (tpp) cc_final: -0.2765 (ttt) REVERT: D 438 MET cc_start: 0.5726 (mmp) cc_final: 0.5506 (mmt) REVERT: D 541 MET cc_start: 0.3889 (tpp) cc_final: 0.3373 (tpp) outliers start: 54 outliers final: 38 residues processed: 246 average time/residue: 0.1477 time to fit residues: 60.0830 Evaluate side-chains 231 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 786 GLN Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 243 optimal weight: 0.0470 chunk 98 optimal weight: 0.8980 chunk 187 optimal weight: 50.0000 chunk 233 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS C 190 GLN C 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.237622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.208834 restraints weight = 40388.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.204252 restraints weight = 56683.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.199743 restraints weight = 46262.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.198002 restraints weight = 47737.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.194988 restraints weight = 48488.834| |-----------------------------------------------------------------------------| r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 27076 Z= 0.110 Angle : 0.577 15.654 36724 Z= 0.291 Chirality : 0.042 0.235 4092 Planarity : 0.004 0.082 4720 Dihedral : 4.475 48.943 3644 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 1.38 % Allowed : 10.40 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3336 helix: 1.30 (0.14), residues: 1476 sheet: -0.04 (0.25), residues: 389 loop : -1.02 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 551 TYR 0.026 0.001 TYR A 737 PHE 0.025 0.001 PHE B 739 TRP 0.026 0.001 TRP B 804 HIS 0.020 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00243 (27060) covalent geometry : angle 0.57653 (36692) SS BOND : bond 0.00139 ( 16) SS BOND : angle 0.86464 ( 32) hydrogen bonds : bond 0.03899 ( 1204) hydrogen bonds : angle 4.58883 ( 3402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.6394 (p) cc_final: 0.6182 (p) REVERT: A 455 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6053 (mpp) REVERT: A 609 MET cc_start: 0.7787 (mmm) cc_final: 0.7391 (mmp) REVERT: B 219 GLU cc_start: 0.5718 (mt-10) cc_final: 0.5298 (tp30) REVERT: B 345 ARG cc_start: 0.5815 (mtt90) cc_final: 0.5436 (mmp80) REVERT: C 112 MET cc_start: -0.0074 (mtp) cc_final: -0.1070 (ptm) REVERT: C 215 MET cc_start: 0.0597 (mtt) cc_final: 0.0242 (tpt) REVERT: C 612 VAL cc_start: 0.9132 (p) cc_final: 0.8835 (m) REVERT: C 658 ILE cc_start: 0.8433 (mm) cc_final: 0.8079 (mt) REVERT: C 786 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: D 320 MET cc_start: 0.0001 (mtp) cc_final: -0.0341 (mmm) REVERT: D 350 MET cc_start: -0.0258 (OUTLIER) cc_final: -0.0621 (tpp) REVERT: D 369 MET cc_start: -0.2308 (tpp) cc_final: -0.2873 (ttt) REVERT: D 438 MET cc_start: 0.5557 (mmp) cc_final: 0.5338 (mmt) REVERT: D 632 MET cc_start: 0.7205 (mmt) cc_final: 0.6732 (mpp) outliers start: 40 outliers final: 32 residues processed: 236 average time/residue: 0.1465 time to fit residues: 58.5586 Evaluate side-chains 233 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 786 GLN Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 36 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 256 optimal weight: 30.0000 chunk 189 optimal weight: 50.0000 chunk 219 optimal weight: 0.0870 chunk 188 optimal weight: 1.9990 chunk 252 optimal weight: 0.2980 chunk 141 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 28 optimal weight: 0.0670 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.239075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.206321 restraints weight = 40602.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.200099 restraints weight = 60398.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.194839 restraints weight = 50824.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.194341 restraints weight = 48816.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.192459 restraints weight = 39501.838| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 27076 Z= 0.098 Angle : 0.561 17.028 36724 Z= 0.278 Chirality : 0.042 0.236 4092 Planarity : 0.004 0.078 4720 Dihedral : 4.199 43.286 3644 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 1.24 % Allowed : 10.67 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3336 helix: 1.56 (0.14), residues: 1472 sheet: 0.25 (0.26), residues: 388 loop : -0.91 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 787 TYR 0.025 0.001 TYR B 679 PHE 0.030 0.001 PHE B 655 TRP 0.020 0.001 TRP C 637 HIS 0.013 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00215 (27060) covalent geometry : angle 0.56084 (36692) SS BOND : bond 0.00116 ( 16) SS BOND : angle 0.74794 ( 32) hydrogen bonds : bond 0.03504 ( 1204) hydrogen bonds : angle 4.44915 ( 3402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 THR cc_start: 0.8996 (t) cc_final: 0.8650 (p) REVERT: A 455 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6169 (mpp) REVERT: A 609 MET cc_start: 0.7912 (mmm) cc_final: 0.7415 (mmp) REVERT: B 186 ASP cc_start: 0.7698 (m-30) cc_final: 0.7436 (t0) REVERT: B 345 ARG cc_start: 0.5724 (mtt90) cc_final: 0.5346 (mmp80) REVERT: C 112 MET cc_start: 0.0046 (mtp) cc_final: -0.0911 (ptm) REVERT: C 215 MET cc_start: 0.0612 (mtt) cc_final: 0.0262 (tpt) REVERT: C 612 VAL cc_start: 0.9140 (p) cc_final: 0.8813 (m) REVERT: C 658 ILE cc_start: 0.8411 (mm) cc_final: 0.8078 (mt) REVERT: C 786 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6594 (mt0) REVERT: D 320 MET cc_start: -0.0061 (mtp) cc_final: -0.0399 (mmm) REVERT: D 350 MET cc_start: -0.0520 (OUTLIER) cc_final: -0.0837 (tpp) REVERT: D 369 MET cc_start: -0.2400 (tpp) cc_final: -0.2875 (ttt) REVERT: D 632 MET cc_start: 0.7161 (mmt) cc_final: 0.6722 (mpp) outliers start: 36 outliers final: 30 residues processed: 243 average time/residue: 0.1458 time to fit residues: 59.2337 Evaluate side-chains 233 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 786 GLN Chi-restraints excluded: chain C residue 819 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 156 optimal weight: 5.9990 chunk 235 optimal weight: 0.0070 chunk 315 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS D 619 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.234558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.205062 restraints weight = 40335.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.200308 restraints weight = 58738.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.195642 restraints weight = 49462.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.193290 restraints weight = 51808.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.190583 restraints weight = 54456.687| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27076 Z= 0.214 Angle : 0.649 15.080 36724 Z= 0.331 Chirality : 0.045 0.224 4092 Planarity : 0.004 0.086 4720 Dihedral : 4.624 48.458 3644 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 10.74 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3336 helix: 1.21 (0.14), residues: 1476 sheet: 0.09 (0.26), residues: 381 loop : -1.00 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 631 TYR 0.026 0.002 TYR B 679 PHE 0.031 0.002 PHE B 739 TRP 0.018 0.002 TRP A 804 HIS 0.015 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00529 (27060) covalent geometry : angle 0.64872 (36692) SS BOND : bond 0.00261 ( 16) SS BOND : angle 1.06661 ( 32) hydrogen bonds : bond 0.04774 ( 1204) hydrogen bonds : angle 4.82064 ( 3402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.79 seconds wall clock time: 64 minutes 12.35 seconds (3852.35 seconds total)