Starting phenix.real_space_refine on Mon May 4 10:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yr7_73362/05_2026/9yr7_73362.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yr7_73362/05_2026/9yr7_73362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yr7_73362/05_2026/9yr7_73362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yr7_73362/05_2026/9yr7_73362.map" model { file = "/net/cci-nas-00/data/ceres_data/9yr7_73362/05_2026/9yr7_73362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yr7_73362/05_2026/9yr7_73362.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 112 5.16 5 C 12561 2.51 5 N 3371 2.21 5 O 3758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19808 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7587 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 33, 'TRANS': 906} Chain: "B" Number of atoms: 7487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7487 Classifications: {'peptide': 926} Link IDs: {'PTRANS': 32, 'TRANS': 893} Chain breaks: 1 Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "E" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'ADP': 1, 'PO4': 1, 'XB2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'ADP': 1, 'PO4': 1, 'XB2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19808 At special positions: 0 Unit cell: (95.45, 175.96, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 6 15.00 O 3758 8.00 N 3371 7.00 C 12561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS B 905 " 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: 1.71 Conformation dependent library (CDL) restraints added in 832.7 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4604 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 15 sheets defined 61.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.674A pdb=" N VAL A 8 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 19 through 28 removed outlier: 3.743A pdb=" N GLN A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.763A pdb=" N LEU A 93 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.688A pdb=" N GLY A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.815A pdb=" N ILE A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.789A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.098A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 4.086A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.576A pdb=" N TYR A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.597A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.636A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 495 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.656A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.518A pdb=" N VAL A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 621 Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.645A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 697 through 708 Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 737 through 749 Processing helix chain 'A' and resid 768 through 825 removed outlier: 4.411A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 837 Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 843 through 943 Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.638A pdb=" N GLY B 10 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.766A pdb=" N GLY B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 54 through 58' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 198 removed outlier: 3.908A pdb=" N ILE B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 removed outlier: 4.214A pdb=" N ILE B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.669A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.117A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.994A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.292A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.511A pdb=" N ASP B 309 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.915A pdb=" N MET B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 360 removed outlier: 3.578A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 416 through 448 Processing helix chain 'B' and resid 472 through 495 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.649A pdb=" N ILE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 540 removed outlier: 3.621A pdb=" N LEU B 534 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 556 Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 646 through 664 removed outlier: 3.694A pdb=" N SER B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 723 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 737 through 749 Processing helix chain 'B' and resid 768 through 824 Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 842 through 943 removed outlier: 4.245A pdb=" N GLU B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 66 through 76 removed outlier: 4.095A pdb=" N GLY C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.294A pdb=" N ASN C 98 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 removed outlier: 3.542A pdb=" N PHE C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'D' and resid 43 through 57 removed outlier: 3.677A pdb=" N PHE D 49 " --> pdb=" O GLN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 77 removed outlier: 3.518A pdb=" N GLY D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 removed outlier: 3.503A pdb=" N VAL D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 100 removed outlier: 4.486A pdb=" N ASN D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'E' and resid 23 through 37 Processing helix chain 'E' and resid 46 through 58 removed outlier: 4.139A pdb=" N MET E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 74 removed outlier: 4.023A pdb=" N LYS E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA E 74 " --> pdb=" O MET E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 68 through 74' Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 96 through 108 removed outlier: 3.809A pdb=" N ILE E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.504A pdb=" N GLU E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 140 removed outlier: 4.304A pdb=" N ILE E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 Processing helix chain 'F' and resid 27 through 37 removed outlier: 3.577A pdb=" N ILE F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.513A pdb=" N PHE F 54 " --> pdb=" O ARG F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.573A pdb=" N LEU F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 153 through 162 removed outlier: 3.569A pdb=" N THR F 161 " --> pdb=" O CYS F 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.512A pdb=" N VAL A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.771A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER A 173 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 455 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366 removed outlier: 6.937A pdb=" N LYS A 363 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.513A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.679A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 70 removed outlier: 5.430A pdb=" N LYS B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 63 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 62 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE B 51 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.875A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU B 460 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 174 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 250 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG B 249 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 261 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS B 251 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AB2, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.527A pdb=" N GLY B 584 " --> pdb=" O HIS B 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.691A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 142 1100 hydrogen bonds defined for protein. 3189 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: 3.77 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5040 1.33 - 1.45: 3717 1.45 - 1.58: 11211 1.58 - 1.70: 8 1.70 - 1.82: 198 Bond restraints: 20174 Sorted by residual: bond pdb=" C VAL E 99 " pdb=" N ILE E 100 " ideal model delta sigma weight residual 1.334 1.248 0.086 1.26e-02 6.30e+03 4.70e+01 bond pdb=" C SER A 851 " pdb=" N MET A 852 " ideal model delta sigma weight residual 1.334 1.417 -0.083 1.23e-02 6.61e+03 4.58e+01 bond pdb=" C THR B 177 " pdb=" N GLY B 178 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.13e-02 7.83e+03 4.19e+01 bond pdb=" C ARG B 237 " pdb=" N ASN B 238 " ideal model delta sigma weight residual 1.331 1.411 -0.080 1.29e-02 6.01e+03 3.80e+01 bond pdb=" C GLU A 73 " pdb=" N ASP A 74 " ideal model delta sigma weight residual 1.332 1.417 -0.085 1.52e-02 4.33e+03 3.15e+01 ... (remaining 20169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 26443 2.38 - 4.75: 605 4.75 - 7.13: 64 7.13 - 9.51: 18 9.51 - 11.88: 3 Bond angle restraints: 27133 Sorted by residual: angle pdb=" CA GLU A 73 " pdb=" C GLU A 73 " pdb=" N ASP A 74 " ideal model delta sigma weight residual 119.07 112.92 6.15 1.23e+00 6.61e-01 2.50e+01 angle pdb=" CA SER A 851 " pdb=" C SER A 851 " pdb=" N MET A 852 " ideal model delta sigma weight residual 117.63 111.69 5.94 1.25e+00 6.40e-01 2.26e+01 angle pdb=" O GLU A 73 " pdb=" C GLU A 73 " pdb=" N ASP A 74 " ideal model delta sigma weight residual 122.09 127.20 -5.11 1.09e+00 8.42e-01 2.19e+01 angle pdb=" O SER A 851 " pdb=" C SER A 851 " pdb=" N MET A 852 " ideal model delta sigma weight residual 122.22 127.45 -5.23 1.17e+00 7.31e-01 2.00e+01 angle pdb=" N GLY E 113 " pdb=" CA GLY E 113 " pdb=" C GLY E 113 " ideal model delta sigma weight residual 114.69 109.58 5.11 1.19e+00 7.06e-01 1.84e+01 ... (remaining 27128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 10778 18.01 - 36.02: 1159 36.02 - 54.03: 281 54.03 - 72.04: 90 72.04 - 90.05: 26 Dihedral angle restraints: 12334 sinusoidal: 5209 harmonic: 7125 Sorted by residual: dihedral pdb=" CB CYS A 905 " pdb=" SG CYS A 905 " pdb=" SG CYS B 905 " pdb=" CB CYS B 905 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" C5' ADP A1402 " pdb=" O5' ADP A1402 " pdb=" PA ADP A1402 " pdb=" O2A ADP A1402 " ideal model delta sinusoidal sigma weight residual -60.00 0.55 -60.55 1 2.00e+01 2.50e-03 1.22e+01 dihedral pdb=" CA ASP A 32 " pdb=" CB ASP A 32 " pdb=" CG ASP A 32 " pdb=" OD1 ASP A 32 " ideal model delta sinusoidal sigma weight residual -30.00 -87.84 57.84 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 12331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2261 0.052 - 0.103: 494 0.103 - 0.155: 140 0.155 - 0.206: 24 0.206 - 0.258: 6 Chirality restraints: 2925 Sorted by residual: chirality pdb=" CA ILE A 674 " pdb=" N ILE A 674 " pdb=" C ILE A 674 " pdb=" CB ILE A 674 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 795 " pdb=" N VAL B 795 " pdb=" C VAL B 795 " pdb=" CB VAL B 795 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE A 713 " pdb=" N ILE A 713 " pdb=" C ILE A 713 " pdb=" CB ILE A 713 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2922 not shown) Planarity restraints: 3526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 XB2 B1401 " 0.013 2.00e-02 2.50e+03 7.55e-02 1.57e+02 pdb=" C04 XB2 B1401 " 0.058 2.00e-02 2.50e+03 pdb=" C07 XB2 B1401 " -0.022 2.00e-02 2.50e+03 pdb=" C08 XB2 B1401 " -0.063 2.00e-02 2.50e+03 pdb=" C09 XB2 B1401 " -0.070 2.00e-02 2.50e+03 pdb=" C11 XB2 B1401 " 0.185 2.00e-02 2.50e+03 pdb=" N03 XB2 B1401 " 0.012 2.00e-02 2.50e+03 pdb=" N10 XB2 B1401 " -0.111 2.00e-02 2.50e+03 pdb=" N19 XB2 B1401 " -0.028 2.00e-02 2.50e+03 pdb=" O01 XB2 B1401 " 0.043 2.00e-02 2.50e+03 pdb=" O20 XB2 B1401 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 XB2 A1401 " -0.009 2.00e-02 2.50e+03 5.05e-02 7.00e+01 pdb=" C04 XB2 A1401 " -0.039 2.00e-02 2.50e+03 pdb=" C07 XB2 A1401 " 0.014 2.00e-02 2.50e+03 pdb=" C08 XB2 A1401 " 0.041 2.00e-02 2.50e+03 pdb=" C09 XB2 A1401 " 0.045 2.00e-02 2.50e+03 pdb=" C11 XB2 A1401 " -0.124 2.00e-02 2.50e+03 pdb=" N03 XB2 A1401 " -0.010 2.00e-02 2.50e+03 pdb=" N10 XB2 A1401 " 0.076 2.00e-02 2.50e+03 pdb=" N19 XB2 A1401 " 0.019 2.00e-02 2.50e+03 pdb=" O01 XB2 A1401 " -0.027 2.00e-02 2.50e+03 pdb=" O20 XB2 A1401 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 721 " -0.383 9.50e-02 1.11e+02 1.72e-01 1.81e+01 pdb=" NE ARG A 721 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 721 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 721 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 721 " -0.012 2.00e-02 2.50e+03 ... (remaining 3523 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 16 2.31 - 2.95: 9161 2.95 - 3.60: 31401 3.60 - 4.25: 47181 4.25 - 4.90: 79459 Nonbonded interactions: 167218 Sorted by model distance: nonbonded pdb=" OE2 GLU B 861 " pdb=" N ALA B 862 " model vdw 1.657 3.120 nonbonded pdb=" CD GLU B 861 " pdb=" N ALA B 862 " model vdw 1.808 3.350 nonbonded pdb=" OE2 GLU B 861 " pdb=" CB ALA B 862 " model vdw 2.014 3.460 nonbonded pdb=" O ARG B 858 " pdb=" OE2 GLU B 861 " model vdw 2.036 3.040 nonbonded pdb=" OE2 GLU B 861 " pdb=" CA ALA B 862 " model vdw 2.087 3.470 ... (remaining 167213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 626 or resid 641 through 1403)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.000 Find NCS groups from input model: 0.390 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.006 0.109 20175 Z= 0.365 Angle : 0.787 11.884 27135 Z= 0.490 Chirality : 0.050 0.258 2925 Planarity : 0.005 0.172 3526 Dihedral : 16.589 90.055 7727 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 1.04 % Allowed : 19.48 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2440 helix: 1.25 (0.14), residues: 1385 sheet: -1.23 (0.46), residues: 124 loop : -1.02 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 780 TYR 0.021 0.001 TYR B 624 PHE 0.017 0.001 PHE B 359 TRP 0.035 0.001 TRP B 829 HIS 0.005 0.001 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00573 (20174) covalent geometry : angle 0.78675 (27133) SS BOND : bond 0.00189 ( 1) SS BOND : angle 1.87926 ( 2) hydrogen bonds : bond 0.14529 ( 1100) hydrogen bonds : angle 5.88994 ( 3189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7403 (ptm-80) REVERT: B 883 GLU cc_start: 0.8091 (tp30) cc_final: 0.7873 (tp30) REVERT: C 117 ASN cc_start: 0.8635 (t0) cc_final: 0.8410 (t0) REVERT: D 111 MET cc_start: 0.7294 (tmm) cc_final: 0.6961 (tmm) REVERT: D 112 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7158 (tp40) REVERT: F 57 MET cc_start: 0.7180 (pmm) cc_final: 0.6099 (pp-130) outliers start: 22 outliers final: 13 residues processed: 291 average time/residue: 0.5424 time to fit residues: 180.2082 Evaluate side-chains 254 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 861 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 81 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.0030 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN A 610 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN B 401 HIS ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.154651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095788 restraints weight = 31121.364| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.67 r_work: 0.2948 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20175 Z= 0.203 Angle : 0.617 9.482 27135 Z= 0.311 Chirality : 0.042 0.162 2925 Planarity : 0.004 0.045 3526 Dihedral : 5.286 63.097 2701 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.39 % Allowed : 18.45 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2440 helix: 1.58 (0.14), residues: 1385 sheet: -1.10 (0.45), residues: 123 loop : -0.90 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 706 TYR 0.018 0.001 TYR A 310 PHE 0.017 0.001 PHE B 359 TRP 0.020 0.001 TRP B 829 HIS 0.010 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00471 (20174) covalent geometry : angle 0.61716 (27133) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.86400 ( 2) hydrogen bonds : bond 0.04336 ( 1100) hydrogen bonds : angle 4.63617 ( 3189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7824 (pttp) REVERT: B 177 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8629 (p) REVERT: B 403 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7300 (ptm-80) REVERT: B 719 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8309 (ttt90) REVERT: B 825 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7871 (mmmm) REVERT: B 883 GLU cc_start: 0.8403 (tp30) cc_final: 0.8016 (tm-30) REVERT: C 68 GLN cc_start: 0.8908 (tt0) cc_final: 0.8696 (tt0) REVERT: C 117 ASN cc_start: 0.8709 (t0) cc_final: 0.8506 (t0) REVERT: D 111 MET cc_start: 0.6992 (tmm) cc_final: 0.6631 (tmm) REVERT: D 112 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7477 (tp40) REVERT: E 26 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: F 28 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8205 (tm-30) REVERT: F 112 LYS cc_start: 0.8667 (tptp) cc_final: 0.8216 (pptt) REVERT: F 115 ILE cc_start: 0.4072 (OUTLIER) cc_final: 0.3310 (pt) outliers start: 72 outliers final: 25 residues processed: 310 average time/residue: 0.5785 time to fit residues: 203.6612 Evaluate side-chains 265 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 148 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 184 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 GLN B 888 GLN D 79 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.156627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098329 restraints weight = 31325.439| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.66 r_work: 0.2985 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20175 Z= 0.124 Angle : 0.580 10.297 27135 Z= 0.289 Chirality : 0.041 0.196 2925 Planarity : 0.003 0.047 3526 Dihedral : 5.066 64.688 2687 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.34 % Allowed : 20.24 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.17), residues: 2440 helix: 1.78 (0.14), residues: 1364 sheet: -1.05 (0.44), residues: 127 loop : -0.80 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.016 0.001 TYR E 153 PHE 0.017 0.001 PHE B 359 TRP 0.014 0.001 TRP B 829 HIS 0.008 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00272 (20174) covalent geometry : angle 0.58033 (27133) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.05200 ( 2) hydrogen bonds : bond 0.03758 ( 1100) hydrogen bonds : angle 4.35125 ( 3189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 262 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7873 (pttp) REVERT: B 825 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7796 (mmmm) REVERT: B 846 GLU cc_start: 0.8560 (mp0) cc_final: 0.8270 (pm20) REVERT: B 883 GLU cc_start: 0.8410 (tp30) cc_final: 0.8005 (tm-30) REVERT: B 886 ASP cc_start: 0.8024 (m-30) cc_final: 0.7748 (t0) REVERT: C 68 GLN cc_start: 0.8906 (tt0) cc_final: 0.8679 (tt0) REVERT: C 71 ASP cc_start: 0.9062 (t0) cc_final: 0.8812 (t0) REVERT: C 117 ASN cc_start: 0.8685 (t0) cc_final: 0.8315 (t0) REVERT: D 111 MET cc_start: 0.7008 (tmm) cc_final: 0.6460 (tmm) REVERT: D 112 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7331 (tp40) REVERT: D 115 SER cc_start: 0.8157 (p) cc_final: 0.7661 (p) REVERT: E 26 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: E 118 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8459 (mm110) REVERT: F 28 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8137 (tm-30) REVERT: F 44 ILE cc_start: 0.8308 (pp) cc_final: 0.7529 (mm) outliers start: 71 outliers final: 24 residues processed: 311 average time/residue: 0.5366 time to fit residues: 191.5689 Evaluate side-chains 268 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 0.0020 chunk 33 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 241 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 391 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN B 661 ASN B 686 ASN D 148 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102514 restraints weight = 31390.087| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.39 r_work: 0.3026 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20175 Z= 0.130 Angle : 0.582 14.375 27135 Z= 0.285 Chirality : 0.041 0.257 2925 Planarity : 0.003 0.049 3526 Dihedral : 5.044 66.536 2687 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.68 % Allowed : 21.69 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2440 helix: 1.84 (0.14), residues: 1366 sheet: -1.01 (0.45), residues: 127 loop : -0.81 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.015 0.001 TYR A 310 PHE 0.018 0.001 PHE B 359 TRP 0.018 0.001 TRP B 829 HIS 0.007 0.001 HIS D 148 Details of bonding type rmsd covalent geometry : bond 0.00291 (20174) covalent geometry : angle 0.58182 (27133) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.99124 ( 2) hydrogen bonds : bond 0.03568 ( 1100) hydrogen bonds : angle 4.25962 ( 3189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 265 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8448 (t0) cc_final: 0.8234 (t0) REVERT: A 72 LYS cc_start: 0.8213 (ptmm) cc_final: 0.7954 (pttp) REVERT: A 830 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6171 (mtm) REVERT: A 890 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7818 (tp-100) REVERT: B 719 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8211 (ttt90) REVERT: B 825 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7929 (mmmm) REVERT: B 846 GLU cc_start: 0.8418 (mp0) cc_final: 0.8077 (pm20) REVERT: B 883 GLU cc_start: 0.8477 (tp30) cc_final: 0.8090 (tm-30) REVERT: B 886 ASP cc_start: 0.8148 (m-30) cc_final: 0.7892 (t0) REVERT: C 68 GLN cc_start: 0.8956 (tt0) cc_final: 0.8726 (tt0) REVERT: C 71 ASP cc_start: 0.8893 (t0) cc_final: 0.8630 (t0) REVERT: C 117 ASN cc_start: 0.8675 (t0) cc_final: 0.8381 (t0) REVERT: D 48 ASP cc_start: 0.8826 (p0) cc_final: 0.8499 (p0) REVERT: D 111 MET cc_start: 0.7210 (tmm) cc_final: 0.6658 (tmm) REVERT: D 112 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7248 (tp40) REVERT: D 115 SER cc_start: 0.8242 (p) cc_final: 0.7838 (p) REVERT: E 26 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: E 70 MET cc_start: 0.6763 (pmm) cc_final: 0.6492 (pmm) REVERT: F 28 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 44 ILE cc_start: 0.8210 (pp) cc_final: 0.7420 (mm) REVERT: F 115 ILE cc_start: 0.3401 (OUTLIER) cc_final: 0.2773 (pt) outliers start: 57 outliers final: 22 residues processed: 306 average time/residue: 0.5344 time to fit residues: 187.3410 Evaluate side-chains 265 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 163 GLN A 391 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.155933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102267 restraints weight = 31179.722| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.85 r_work: 0.3037 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20175 Z= 0.200 Angle : 0.615 16.370 27135 Z= 0.303 Chirality : 0.042 0.154 2925 Planarity : 0.003 0.041 3526 Dihedral : 5.163 68.808 2687 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.06 % Allowed : 21.79 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2440 helix: 1.74 (0.14), residues: 1375 sheet: -1.06 (0.45), residues: 128 loop : -0.87 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.017 0.002 TYR A 310 PHE 0.028 0.001 PHE E 80 TRP 0.008 0.001 TRP B 438 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00471 (20174) covalent geometry : angle 0.61538 (27133) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.87555 ( 2) hydrogen bonds : bond 0.03741 ( 1100) hydrogen bonds : angle 4.32454 ( 3189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8477 (t0) cc_final: 0.8271 (t0) REVERT: A 72 LYS cc_start: 0.8243 (ptmm) cc_final: 0.7956 (pttp) REVERT: A 830 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6193 (mtp) REVERT: A 890 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7690 (tp-100) REVERT: A 932 MET cc_start: 0.0643 (tmt) cc_final: 0.0148 (tpp) REVERT: B 359 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 530 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 719 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8178 (ttt90) REVERT: B 825 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7951 (mmmm) REVERT: B 883 GLU cc_start: 0.8516 (tp30) cc_final: 0.8119 (tm-30) REVERT: B 886 ASP cc_start: 0.8152 (m-30) cc_final: 0.7903 (t0) REVERT: C 68 GLN cc_start: 0.8969 (tt0) cc_final: 0.8742 (tt0) REVERT: C 71 ASP cc_start: 0.8837 (t0) cc_final: 0.8584 (t0) REVERT: C 89 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8639 (tt) REVERT: C 117 ASN cc_start: 0.8668 (t0) cc_final: 0.8362 (t0) REVERT: D 111 MET cc_start: 0.7297 (tmm) cc_final: 0.6652 (tmm) REVERT: D 112 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7087 (tp-100) REVERT: D 115 SER cc_start: 0.8250 (p) cc_final: 0.7657 (p) REVERT: D 138 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7029 (m-40) REVERT: E 26 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: F 28 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8101 (tm-30) REVERT: F 44 ILE cc_start: 0.8152 (pp) cc_final: 0.7437 (mm) REVERT: F 115 ILE cc_start: 0.3098 (OUTLIER) cc_final: 0.2467 (pt) outliers start: 65 outliers final: 25 residues processed: 294 average time/residue: 0.5590 time to fit residues: 187.9375 Evaluate side-chains 273 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 152 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 2 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 51 optimal weight: 0.0040 chunk 97 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.157604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101767 restraints weight = 31195.454| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.20 r_work: 0.3020 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20175 Z= 0.134 Angle : 0.599 15.894 27135 Z= 0.291 Chirality : 0.041 0.176 2925 Planarity : 0.003 0.039 3526 Dihedral : 5.071 68.045 2685 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.64 % Allowed : 23.29 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2440 helix: 1.87 (0.14), residues: 1367 sheet: -1.06 (0.45), residues: 127 loop : -0.82 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.015 0.001 TYR A 310 PHE 0.019 0.001 PHE E 104 TRP 0.007 0.001 TRP B 438 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00304 (20174) covalent geometry : angle 0.59919 (27133) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.86852 ( 2) hydrogen bonds : bond 0.03480 ( 1100) hydrogen bonds : angle 4.21596 ( 3189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8531 (t0) cc_final: 0.8265 (t0) REVERT: A 55 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8148 (pp20) REVERT: A 72 LYS cc_start: 0.8221 (ptmm) cc_final: 0.7939 (pttp) REVERT: A 830 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6268 (mtp) REVERT: A 890 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7899 (tp-100) REVERT: B 73 GLU cc_start: 0.8566 (tp30) cc_final: 0.8339 (tp30) REVERT: B 359 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7565 (t80) REVERT: B 719 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8199 (ttt90) REVERT: B 825 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7904 (mmmm) REVERT: B 830 MET cc_start: 0.6975 (mmm) cc_final: 0.6773 (mmm) REVERT: B 846 GLU cc_start: 0.8530 (mp0) cc_final: 0.8161 (pm20) REVERT: B 883 GLU cc_start: 0.8484 (tp30) cc_final: 0.8160 (tp30) REVERT: B 886 ASP cc_start: 0.8079 (m-30) cc_final: 0.7732 (t0) REVERT: C 71 ASP cc_start: 0.8981 (t0) cc_final: 0.8697 (t0) REVERT: C 117 ASN cc_start: 0.8632 (t0) cc_final: 0.8310 (t0) REVERT: D 58 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7495 (mmp80) REVERT: D 111 MET cc_start: 0.7156 (tmm) cc_final: 0.6539 (tmm) REVERT: D 112 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7201 (tp-100) REVERT: D 115 SER cc_start: 0.8222 (p) cc_final: 0.7616 (p) REVERT: E 26 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: F 28 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8161 (tm-30) REVERT: F 44 ILE cc_start: 0.8171 (pp) cc_final: 0.7449 (mm) REVERT: F 115 ILE cc_start: 0.3073 (OUTLIER) cc_final: 0.2492 (pt) outliers start: 56 outliers final: 27 residues processed: 298 average time/residue: 0.5514 time to fit residues: 188.1984 Evaluate side-chains 278 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 391 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN D 138 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101500 restraints weight = 31278.983| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.71 r_work: 0.3010 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20175 Z= 0.173 Angle : 0.627 16.577 27135 Z= 0.306 Chirality : 0.042 0.210 2925 Planarity : 0.003 0.041 3526 Dihedral : 5.123 68.787 2685 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.21 % Allowed : 23.67 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2440 helix: 1.80 (0.14), residues: 1372 sheet: -1.10 (0.45), residues: 127 loop : -0.85 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 131 TYR 0.017 0.001 TYR E 153 PHE 0.020 0.001 PHE B 359 TRP 0.008 0.001 TRP B 438 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00405 (20174) covalent geometry : angle 0.62719 (27133) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.81170 ( 2) hydrogen bonds : bond 0.03606 ( 1100) hydrogen bonds : angle 4.26570 ( 3189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8607 (t0) cc_final: 0.8348 (t0) REVERT: A 72 LYS cc_start: 0.8259 (ptmm) cc_final: 0.7955 (pttp) REVERT: A 830 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6395 (mtp) REVERT: A 890 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7748 (tp-100) REVERT: B 73 GLU cc_start: 0.8483 (tp30) cc_final: 0.8207 (tp30) REVERT: B 719 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: B 825 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7963 (mmmm) REVERT: B 830 MET cc_start: 0.7016 (mmm) cc_final: 0.6795 (mmm) REVERT: B 846 GLU cc_start: 0.8542 (mp0) cc_final: 0.8212 (pm20) REVERT: B 877 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7914 (tpt) REVERT: B 883 GLU cc_start: 0.8509 (tp30) cc_final: 0.8123 (tm-30) REVERT: B 886 ASP cc_start: 0.8080 (m-30) cc_final: 0.7847 (t0) REVERT: C 71 ASP cc_start: 0.8909 (t0) cc_final: 0.8636 (t0) REVERT: C 117 ASN cc_start: 0.8635 (t0) cc_final: 0.8316 (t0) REVERT: D 58 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7587 (mmp80) REVERT: D 111 MET cc_start: 0.7262 (tmm) cc_final: 0.6598 (tmm) REVERT: D 112 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7158 (tp-100) REVERT: D 115 SER cc_start: 0.8248 (p) cc_final: 0.7638 (p) REVERT: E 26 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8372 (mp10) REVERT: E 57 MET cc_start: 0.4008 (ttt) cc_final: 0.3325 (ttp) REVERT: F 28 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 44 ILE cc_start: 0.8137 (pp) cc_final: 0.7462 (mm) REVERT: F 115 ILE cc_start: 0.2881 (OUTLIER) cc_final: 0.2271 (pt) outliers start: 47 outliers final: 30 residues processed: 285 average time/residue: 0.5524 time to fit residues: 180.3364 Evaluate side-chains 279 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 877 MET Chi-restraints excluded: chain B residue 921 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 152 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 82 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.102544 restraints weight = 31238.484| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3027 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 20175 Z= 0.135 Angle : 0.629 16.916 27135 Z= 0.304 Chirality : 0.041 0.208 2925 Planarity : 0.003 0.040 3526 Dihedral : 5.078 68.129 2685 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.21 % Allowed : 23.91 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.05 (0.17), residues: 2440 helix: 1.88 (0.14), residues: 1366 sheet: -1.08 (0.45), residues: 127 loop : -0.80 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.015 0.001 TYR A 310 PHE 0.019 0.001 PHE B 856 TRP 0.007 0.001 TRP B 438 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00313 (20174) covalent geometry : angle 0.62868 (27133) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.82287 ( 2) hydrogen bonds : bond 0.03497 ( 1100) hydrogen bonds : angle 4.21625 ( 3189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8244 (ptmm) cc_final: 0.7945 (pttp) REVERT: A 830 MET cc_start: 0.7152 (mmp) cc_final: 0.6368 (mtp) REVERT: A 890 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7799 (tp-100) REVERT: B 73 GLU cc_start: 0.8502 (tp30) cc_final: 0.8210 (tp30) REVERT: B 719 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8164 (ttt90) REVERT: B 825 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7994 (mmmm) REVERT: B 830 MET cc_start: 0.6942 (mmm) cc_final: 0.6704 (mmm) REVERT: B 846 GLU cc_start: 0.8499 (mp0) cc_final: 0.8179 (pm20) REVERT: B 883 GLU cc_start: 0.8476 (tp30) cc_final: 0.8178 (tp30) REVERT: B 886 ASP cc_start: 0.8128 (m-30) cc_final: 0.7809 (t0) REVERT: C 68 GLN cc_start: 0.9024 (tt0) cc_final: 0.8640 (tt0) REVERT: C 71 ASP cc_start: 0.8839 (t0) cc_final: 0.8619 (t0) REVERT: C 117 ASN cc_start: 0.8604 (t0) cc_final: 0.8309 (t0) REVERT: D 47 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8547 (mm-30) REVERT: D 58 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7670 (mmp80) REVERT: D 111 MET cc_start: 0.7290 (tmm) cc_final: 0.6630 (tmm) REVERT: D 112 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7152 (tp-100) REVERT: D 115 SER cc_start: 0.8265 (p) cc_final: 0.7670 (p) REVERT: E 26 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: E 57 MET cc_start: 0.3909 (ttt) cc_final: 0.3231 (ttp) REVERT: E 162 HIS cc_start: 0.8670 (m-70) cc_final: 0.8388 (m90) REVERT: F 28 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8122 (tm-30) REVERT: F 44 ILE cc_start: 0.8126 (pp) cc_final: 0.7431 (mm) REVERT: F 57 MET cc_start: 0.7689 (pmm) cc_final: 0.6694 (pp-130) REVERT: F 115 ILE cc_start: 0.2688 (OUTLIER) cc_final: 0.2062 (pt) outliers start: 47 outliers final: 31 residues processed: 292 average time/residue: 0.5770 time to fit residues: 192.9803 Evaluate side-chains 284 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 921 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 121 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 194 optimal weight: 0.0670 chunk 204 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 391 ASN A 720 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.157969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103153 restraints weight = 31037.674| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.51 r_work: 0.3047 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 20175 Z= 0.136 Angle : 0.634 17.926 27135 Z= 0.309 Chirality : 0.042 0.254 2925 Planarity : 0.003 0.042 3526 Dihedral : 5.071 68.142 2685 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.98 % Allowed : 24.52 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2440 helix: 1.88 (0.14), residues: 1366 sheet: -1.06 (0.45), residues: 127 loop : -0.81 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.018 0.001 TYR E 153 PHE 0.018 0.001 PHE B 359 TRP 0.008 0.001 TRP B 438 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00314 (20174) covalent geometry : angle 0.63401 (27133) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.82075 ( 2) hydrogen bonds : bond 0.03484 ( 1100) hydrogen bonds : angle 4.22181 ( 3189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8296 (ptmm) cc_final: 0.8023 (pttp) REVERT: A 830 MET cc_start: 0.7234 (mmp) cc_final: 0.6484 (mtp) REVERT: A 890 GLN cc_start: 0.8511 (mm-40) cc_final: 0.7811 (tp-100) REVERT: B 73 GLU cc_start: 0.8351 (tp30) cc_final: 0.8000 (tp30) REVERT: B 719 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8188 (ttt90) REVERT: B 825 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (mmmm) REVERT: B 830 MET cc_start: 0.6916 (mmm) cc_final: 0.6684 (mmm) REVERT: B 846 GLU cc_start: 0.8471 (mp0) cc_final: 0.8127 (pm20) REVERT: B 883 GLU cc_start: 0.8471 (tp30) cc_final: 0.8170 (tp30) REVERT: B 886 ASP cc_start: 0.8095 (m-30) cc_final: 0.7769 (t0) REVERT: C 68 GLN cc_start: 0.9023 (tt0) cc_final: 0.8633 (tt0) REVERT: C 71 ASP cc_start: 0.8826 (t0) cc_final: 0.8598 (t0) REVERT: D 47 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8583 (mm-30) REVERT: D 58 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7724 (mmp80) REVERT: D 111 MET cc_start: 0.7293 (tmm) cc_final: 0.6634 (tmm) REVERT: D 112 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7172 (tp-100) REVERT: D 115 SER cc_start: 0.8268 (p) cc_final: 0.7679 (p) REVERT: E 26 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: E 57 MET cc_start: 0.3957 (ttt) cc_final: 0.3234 (ttp) REVERT: E 162 HIS cc_start: 0.8669 (m-70) cc_final: 0.8413 (m90) REVERT: F 28 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 44 ILE cc_start: 0.8126 (pp) cc_final: 0.7447 (mm) REVERT: F 115 ILE cc_start: 0.2786 (OUTLIER) cc_final: 0.2156 (pt) outliers start: 42 outliers final: 31 residues processed: 286 average time/residue: 0.5755 time to fit residues: 187.3587 Evaluate side-chains 278 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 921 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 231 optimal weight: 0.7980 chunk 121 optimal weight: 0.0060 chunk 23 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 171 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103353 restraints weight = 31360.162| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.29 r_work: 0.3062 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20175 Z= 0.128 Angle : 0.661 18.160 27135 Z= 0.317 Chirality : 0.042 0.337 2925 Planarity : 0.003 0.053 3526 Dihedral : 5.014 67.907 2685 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.74 % Allowed : 24.80 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.17), residues: 2440 helix: 1.90 (0.14), residues: 1365 sheet: -1.00 (0.45), residues: 127 loop : -0.79 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.019 0.001 TYR B 386 PHE 0.022 0.001 PHE B 856 TRP 0.019 0.001 TRP B 829 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00295 (20174) covalent geometry : angle 0.66051 (27133) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.82308 ( 2) hydrogen bonds : bond 0.03415 ( 1100) hydrogen bonds : angle 4.19402 ( 3189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8260 (ptmm) cc_final: 0.8029 (pttp) REVERT: A 830 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6358 (mtm) REVERT: A 890 GLN cc_start: 0.8528 (mm-40) cc_final: 0.7816 (tp-100) REVERT: B 73 GLU cc_start: 0.8364 (tp30) cc_final: 0.8022 (tp30) REVERT: B 530 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7767 (mm) REVERT: B 719 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: B 830 MET cc_start: 0.6819 (mmm) cc_final: 0.6593 (mmm) REVERT: B 846 GLU cc_start: 0.8519 (mp0) cc_final: 0.8178 (pm20) REVERT: B 883 GLU cc_start: 0.8476 (tp30) cc_final: 0.8181 (tp30) REVERT: B 886 ASP cc_start: 0.8026 (m-30) cc_final: 0.7733 (t0) REVERT: C 68 GLN cc_start: 0.9031 (tt0) cc_final: 0.8686 (tt0) REVERT: C 71 ASP cc_start: 0.8850 (t0) cc_final: 0.8621 (t0) REVERT: D 47 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8603 (mm-30) REVERT: D 111 MET cc_start: 0.7288 (tmm) cc_final: 0.6652 (tmm) REVERT: D 112 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7257 (tp-100) REVERT: D 115 SER cc_start: 0.8251 (p) cc_final: 0.7663 (p) REVERT: E 26 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8361 (mp10) REVERT: E 57 MET cc_start: 0.3875 (ttt) cc_final: 0.3169 (ttp) REVERT: E 71 MET cc_start: 0.5414 (mmt) cc_final: 0.5087 (mpp) REVERT: E 162 HIS cc_start: 0.8714 (m-70) cc_final: 0.8403 (m90) REVERT: F 28 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 44 ILE cc_start: 0.8131 (pp) cc_final: 0.7447 (mm) REVERT: F 57 MET cc_start: 0.7648 (pmm) cc_final: 0.6631 (pp-130) REVERT: F 71 MET cc_start: 0.8032 (mmt) cc_final: 0.7774 (mmm) REVERT: F 115 ILE cc_start: 0.2547 (OUTLIER) cc_final: 0.1884 (pt) outliers start: 37 outliers final: 30 residues processed: 282 average time/residue: 0.5781 time to fit residues: 186.7455 Evaluate side-chains 283 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 719 ARG Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 921 GLU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 58 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 152 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 391 ASN ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098847 restraints weight = 31191.230| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.37 r_work: 0.2990 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20175 Z= 0.182 Angle : 0.677 18.960 27135 Z= 0.328 Chirality : 0.043 0.332 2925 Planarity : 0.004 0.051 3526 Dihedral : 5.103 68.415 2685 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.98 % Allowed : 25.04 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.17), residues: 2440 helix: 1.78 (0.14), residues: 1371 sheet: -0.95 (0.45), residues: 127 loop : -0.85 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 131 TYR 0.017 0.001 TYR E 153 PHE 0.043 0.001 PHE F 143 TRP 0.028 0.001 TRP B 829 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00433 (20174) covalent geometry : angle 0.67695 (27133) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.79398 ( 2) hydrogen bonds : bond 0.03651 ( 1100) hydrogen bonds : angle 4.27519 ( 3189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9283.77 seconds wall clock time: 158 minutes 35.78 seconds (9515.78 seconds total)